1616681586

CHEMISTRY RESEARCH AND APPLICATIONS
QUANTUM FRONTIERS OF ATOMS

AND MOLECULES
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QUANTUM FRONTIERS OF ATOMS

AND MOLECULES
MIHAI V. PUTZ
EDITOR
Nova Science Publishers, Inc.

New York
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LIBRARY OF CONGRESS CATALOGING-IN-PUBLICATION DATA
Quantum frontiers of atoms and molecules / editor, Mihai V. Putz.

p. cm.
Includes index.
ISBN 978-1-61324-867-6 (eBook)
1. Chemical bonds--Mathematical models. 2. Dirac equation. 3. Quantum
chemistry. I. Putz, Mihai V.
QD461.Q36 2009
541'.28--dc22
2010001746
Published by Nova Science Publishers, Inc. New York

CONTENTS
Foreword ix
Chapter 1 Fulfilling Diracs Promise on Quantum Chemical Bond 1
Mihai V. Putz
Chapter 2 Duality within the Structure of Complementarity: 21
Right Where It Has No Place to Be
Constantin Antonopoulos
Chapter 3 Complementarity Out of Context: Essay on the Rationality 41
of Bohrs Thought
Constantin Antonopoulos
Chapter 4 Molecular Integrals over Slater-Type Orbitals. From Pioneers to 61
Recent Developments
P.E. Hoggan, M.B. Ruiz and T. zdoan
Chapter 5 Tunneling Dynamics and Its Signatures in Coupled Systems 91
S. Ghosh and S.P. Bhattacharyya
Chapter 6 Theoretical Calculation of the Low Laying Electronic States 111
of the Molecular Ion CsH+ with Spin-Orbit Effects
M. Korek and H. Jawhari
Chapter 7 Theoretical Explanation of Light Amplifying by Polyethylene Foil 141
Vjekoslav Sajfert, Duan Popov, Stevo Jacimovski
and Bratislav Tosic
Chapter 8 Anharmonic Effects in Normal Mode Vibrations: 157
Their Role in Biological Systems
Attila Bende
Chapter 9 Emergent Properties in Bohmian Chemistry 191

Jan C.A. Boeyens
vi Contents
Chapter 10 The Algebraic Chemistry of Molecules and Reactions 217

Cynthia Kolb Whitney
Chapter 11 Quantum and Electrodynamic Versatility of Electronegativity 251
and Chemical Hardness
Mihai V. Putz
Chapter 12 Physics and Chemistry of Carbon in the Light of Shell-Nodal 277
Atomic Model
G.P. Shpenkov
Chapter 13 Molecular Modeling of the Peanut Lectin - Carbohydrate 325
Interaction by Means of the Hybrid QM/MM Method
Alexei N. Pankratov, Nikolay A. Bychkov and Olga M. Tsivileva
Chapter 14 Electron Density Distributions of Heterocycles: 343
A Shortcoming of the Resonance Model
Ricardo A. Mosquera, Marcos Mandado, Laura Estvez
and Nicols Otero
Chapter 15 Electromerism in Small Molecule Activation by Metal 367
Centers of Biological Relevance
Radu Silaghi-Dumitrescu
Chapter 16 Structural Modelling of Nano-Carbons and Composites 387
Mihai Popescu and Florinel Sava
Chapter 17 Nanostructure Designbetween Science and Art 425
Mircea V. Diudea
Chapter 18 Quantifying Structural Complexity of Graphs: 479
Information Measures in Mathematical Chemistry
Matthias Dehmer, Frank Emmert-Streib, Yury Robertovich Tsoy
and Kurt Varmuza
Chapter 19 Topological Indices of Nanostructures 499
Ali Reza Ashrafi
Chapter 20 On Uniform Representation of Proteins by Distance Matrix 521
M. Randi, M. Vrako, M. Novi and D. Plavi
Chapter 21 Timisoara Spectral Structure Activity Relationship (Spectral- 539
SAR) Algorithm: From Statistical and Algebraic Fundamentals to
Quantum Consequences
Mihai V. Putz and Ana-Maria Putz
Chapter 22 On Plots in QSAR/QSPR Methodologies 589
Emili Besal, Jesus Vicente de Julin Ortiz and Lionello Pogliani
Contents vii
Chapter 23 Application of the Fuzzy Logic Theory to QSPR-QSAR Studies 607

Pablo R. Duchowicz and Eduardo A. Castro
Chapter 24 Modeling the Toxicity of Alcohols. Topological Indices versus 629
Van Der Waals Molecular Descriptors
Dan Ciubotariu, Vicentiu Vlaia, Ciprian Ciubotariu,
Tudor Olariu and Mihai Medeleanu
Index 669
FOREWORD
ATOMS AND MOLECULES AS THE QUANTUM FRONTIERS OF LIFE

Elements of Nature: elements of Life: atoms and molecules. From the earlier time of
rational modeling of the Universe, the atomistic vision (Leucippus & Democritus) gave the
mechanistic vision upon which all objects are created by unitary elementary entities; they
eventually later found the autonomic conceptualization by Leibnizs monads the veritable
frontiers, two-sided coins, of Creation. On one side they realize the first step from the non-
organized vacuum towards the matter structure, while on the other hand preserve the
entangled connection and unity between all the created/observed (and beyond) world. From
the epistemological point of view, the Atom at the base frontier of micro-to-macro Universe
marks a drastic unification of the ancient beliefs and myths of the Elements of Nature: water,
earth, fire, air all of them being in one way or another fluidization, sublimation, exaltation
or aeration of atomic systems in various conjugations or composites; moreover, Platos
geometric elements attributing the octahedrons to air, cubes to earth, tetrahedrons to fire,
icosahedrons to water, while dodecahedrons build the constellation and paradise appears as
a further atomic combination, yet in a more organized paradigm. Atoms therefore the first
frontier of microcosm, the most pre-eminent physical system in which the fermions
(electrons) live in a boson environment (atoms as a whole) so simple in principle to
describe and speculate upon, so difficult to model and quantify. The reason is because of
being material and also immaterial, since it spans in principle the whole Universe by its wave-
function. Moreover, all living Nature behaves like its most simple benchmark: Hydrogen. We
put under the Hydrogenic wave-function: life and death follows its localized-delocalized
curvatures, all events encountered as the Hydrogen wave-function shape; acceleration of
particles and bodies, the maximum metastable-equilibrium the climax of life, followed by
the smooth descent toward the zero ground of being, leaving nevertheless space for believers
regarding the eventual unification of minus and plus infinites, such that all of Nature works in
cycles, with the satisfaction of energy conservation. This is Nature this is Physics; but
maybe it is not enough. Just when more than one electron is stabilized in an atomic system
the atomic world diversifies in such manner that the multiple can spring out of Monads, the
Elements become now the Periodic Elements, the Chemistry arises. As such the Chem listens
by the words of his father Noah in bringing new life in the Universe by dissemination, and
cross-fertilization of the earths seeds, as such the cheos gives the fluids of Life, and archeos
x Mihai V. Putz
the archetypes of living, the paradigms of Nature. Living with more than one electron in an
orbital, the appearance of duality, of spinning, thats Chemistry. As a name enough obscure,
partly mythical from the dark side of Egypt, partly theological from the sacral combination it
provides (El-Chemia: Alchemy) towards the molecular world. With this we arrive at the
bonding mystery; it is called in general the chemical bond, but stays as the frontier of the
bigger world to come: the Bios. The biological component of Nature may be approached
through the generalization of the chemical bonding idea, or the resonance between the ionic
and covalent bindings, to the ligand-receptor one. Such picture is fully feasible after rooting
in the hard and soft acids and bases theory in which terms any chemical reaction can in
principle be formulated. On the other hand, for the bio-, eco-, and pharmaco-logical involved
systems the chemical bond appears unstable respecting the isolated systems, due to the
environment damping; in other words, a toxicological action (meaning a chemical binding
with a toxic effect) is diminishing in time as a consequence of metabolic actions (intern
factors) and of the environment (extern factors). This way, it raises the challenge in
formulating a theory of the chemical bond variable in time at the biomolecular level,
specialized on the in vitro enzymic case, and then extended to the in vivo situations in order
to better cover the record of the (non)toxic or therapeutic actions in organisms and the
environment. Recent attention was jointly focused on eco-, bio-, as well as on pharmaco-
sciences. In this stage new pharmacophoric reactivity indices may be formulated with the help
of quantum molecular topology combined with the graph theory (due to its versatility to be
iteratively computed from atoms to molecules) producing a direct quantification of the toxic
or therapeutic effect for a given chemical. The Hydrogenic atoms, the many-electron atoms,
and the (bio-)molecules: the Physics, Chemistry, and Biology and the wholeness they
cover in a rheological manner with the help of the quanta, fields and particles, in reciprocal
transformation, combination, excitation the thin red line of the Universe. Lifes frontiers
the quantum-verse, the true nature of the uni-verse!
With the actual ever-expanding developments of the edge technology with direct impact
on life and environment, a lucid review of the main foreground conceptual realms of
electronic matter at the level of atoms and molecules is by this volume unfolded aiming to
offer a unitary perspective of the quantum principles as applied to many-electronic states,
either in isolate and interacting context, to chemical bond and bonding as well to the relation
between the physical-chemical structure and chemical-biological reactivity and activity
manifestations of nature.
The volume widely gives larger and deeper coverage of the electronic matters through the
physical, chemical and biological ordered systems, with their increasing complexity through
gradually presenting the matter structure from the physical to chemical to biological
manifestations in an inter-disciplinary cross-fertilization manner. With equilibrated contents
provided by important scientists worldwide with a valuable impact on quantum fundaments
and applications, the book presents and reviews the avant-garde contributions for the XXI
century. In fact, the present volume steps aside to serve for the unification of the physical-
chemical-biological manifestation of atoms in molecules and in nanostructures by means of
expanding the quantum frontiers by conjunction with either relativity or topological or
information or graph theories as well. The book successfully balances among the physical,
chemical and biological sides of the quantum theory and of its applications emphasizing both
conceptual and computational sides while experiment is addressed only for reference; in this
regard the book is more focused on why rather than how quantum effects are produced with
Foreword xi
the inner belief that this way the second issue is self-contained in the first one. The book is
addressed to a large audience as well as to advanced research wisely combining the
epistemological, heuristic and philosophic aspects of quantum manifestation of matter in
atoms, molecules and of their combination in complex nano- and bio- structures. On the other
hand, the book likes to show how far the quantum theory furnishes the background and the
framework in which the simple as well as most complex electronic structures may unfold and
evolve in an interacting environment.
Overall, searching the unity of the manifestation forms of the chemical bonding at
various levels of matter organization had become a very active interdisciplinary field in the
last years, being one of the main goals in the frame of the nanosciences. The quantum
paradigm of bonding unification through the formulation of a minimal set of concepts and
quantities having as much universal multi-electronic relevance as possible represents a real
challenge for the conceptualization and prescription of the viable applicative directions of the
nanosystems, from atoms to biomolecules. For that we are certain that the present edited
volume will have a special role for making further advancement in improving the scientific
knowledge in this priority domain of research.
And last, but not least, Editor and Authors like to sincerely thank all the NOVA team
involved in the present challenging editorial venture, and to NOVA Vice-president Nadya
Columbus especially, for kind assistance and patience throughout all stages of publication.
Mihai V. PUTZ
(Volume Editor)
Chemistry Department
West University of Timioara
Romania
In: Quantum Frontiers of Atoms and Molecules ISBN: 978-1-61668-158-6
Editor: Mihai V. Putz, pp. 1-19 2010 Nova Science Publishers, Inc.
Chapter 1
FULFILLING DIRACS PROMISE ON QUANTUM

CHEMICAL BOND
Mihai V. Putz*
Laboratory of Computational and Structural Physical Chemistry,
Chemistry Department, West University of Timioara,
Str. Pestalozzi No.16, Timisoara, RO-300115, Romania
Abstract
One of the most fundamental issues of quantum chemistry, the forming and electronic
description of bonding, is here unfolded at the level of Diracs theory, in conjunction with the
density functional concept of chemical action or, equivalently, with the beloved
electronegativity for practical applications of encountering atoms in molecules. The resulting
chemical bonding equation allows for the first time the geometrical identification of molecular
region along bonding in which the parallel and anti-parallel spin-electrons coexist in anti-
bonding and bonding states, respectively.
1. Introduction
After the Nobel Prize 1933 jointly awarded to the productive contribution on atomic
theory for Schrdinger and Diracs theories of electrons, there was created the impression that
at least the chemistry world of phenomena will be entirely explained [1-17]. This is not
minor, because of the huge importance the Chemistry of atoms and molecules plays in life
and in metabolism [18].
Yet, soon it became clearer that the chemical systems are not as simple as the physical
models intend to imply; for instance, no spherical molecule exists to transfer upon the
principles of special orthogonal groups; or even more complicated the chemical systems
consist of manybut numerableelectrons, therefore not amendable with the
thermodynamic physical limit ( N ); or more subtle, the chemical bond is supporting
*
E-mail addresses: mvputz@cbg.uvt.ro, mv_putz@yahoo.com. Tel: +40-256-592633; Fax. +40-256-592620,
2 Mihai V. Putz
both the parallel and anti-parallel spins in different states, inversely known as anti-bonding
and bonding states, emphasizing that the first instance is firstly involved in the chemical
reactivity through belonging to the so-called valence state [3-5].
Although the molecular orbital theory attempted to explain this intriguing behavior by the
anti-symmetry rule of a given states spin-electron wave function, i.e. the total Pauli anti-
symmetry wave function may be obtained either by convoluting symmetrical spin with anti-
symmetrical coordinate wave functionsfor anti-bonding or anti-symmetrical spin with
symmetrical coordinate wave functionfor bonding states, this remains only as a qualitative
description with no practical effect on geometrical description of anti-bonding parallel spins
coexisting along the bonding [11-13]. One can say that since electrons are waves they
virtually occupy all space of bonding with an anti-symmetrical coordinate wave that
eventually does not interfere with that symmetrical one coming from the bonding wave; very
true, but also this seems a qualitative argument [8].
Therefore, one should be next interested in describing the geometrical locus along the
chemical bond where the bonding and anti-bonding waves behave as within resonators (since
they are stationary in the formed molecule), and eventually explaining why they do not
interfere (i.e., they are orthogonal states belonging to separate Hilbert spaces); and all these
with the help of Diracs theory directly since the spin problem is aiming to be responded, and
not by employing the Schrdinger indirect argumentum of coordinate symmetry [9].
To this end, the present work likes to step forward in elucidating the mystery of the
chemical bond through combining the fundamental Dirac equation with spinorial solution,
generalized from the Schrdinger equation, while being combined with the recently advanced
chemical action description of bonding [19,20].
2. Dirac-Schrdinger Equivalence
There is a known fact that the basic Dirac equation unfolds as the temporal generalized
operatorial form [1,21-23]
i= t [ ] = H Dir [ ] (1)
in a very similar shape with the Schrdinger one, however with the Dirac Hamiltonian
specialization:
H Dir = H Dir
0
+ v( x) (2a)
with the free particle and applied potential components:
G G
H Dir
0
= i=c + mc 2 , (2b)
v( x) = V ( x) , (2c)
Fulfilling Diracs Promise on Quantum Chemical Bond 3
respectively, with m - the particle mass, c - the light velocity, = - the Planck constant, while
G
the introduced special operators , assume the Dirac 4D representation:
0 k
k = , k = 1,2,3 , (3a)
k 0
10
= (3b)
0 1
in terms of bi-dimensional Pauli and unitary matrices (operators)
1 0 0 1 0 i 1 0
0 = 1 = , 1 = , 2 = , 3 = (4)
0 1 1 0 i 0 0 1
and with the wave function featuring the so called spinorial (bi-dimensional) equivalent
formulation
=i Et
[ ] = e

=i E t
e , E > 0 anti bonding states
0
= i
0 e + = E t , E < 0 bonding states

=i E t
e
= i (5)
+ = E t
e
However, there also arises the question whether the general Dirac equation (1) may be
reduced or transformed so that to represent the eigen-equation for the electronic states for a
given quantum system. For this, through closely analyzing the form of Eq. (1) with all its
contribution, one may resume the free motion Dirac operator to the working form [8]

D = i=A 0 + i= 1 + i= 2 + i= 3 + C (6a)
t x1 x 2 x3
and employing it to the stationary operatorial equation:

4 Mihai V. Putz
e i (kxt )
0 = D [ ] = D 1 i (kxt ) = D (6b)
2 e
with the oscillatory phase written so that to be in accordance with the prescription of eq. (5)
for the Planck energy-frequency identification:
E = = (7)
In these conditions, one notes that for the time and coordinate derivatives yields:

[ ] = i , (8a)
t

[ ] = ik k (8b)
xk
which reduce the above stationary condition (6) to the form
(=A1 + =k 1) + C = 0
k k (9)

Choosing now appropriately (that stands for the optimization procedure) the matrices
0 0 0 2 m
A = , C = 0 0 (10)
1 0
the last form (9) further rearranges as
=k k k 2m1
= 0 (11a)
=1 =k k k
leaving with the system:
=k k k + 2m1 = 0
(11b)
=1 + =k k k = 0
Now, since solving the first equation of the system (11b) in one variable, say
=k k k 1 p 1
= = k k (12a)
2m 2m
and substituting into the second one, there is obtained:
E1 =
( pk k )( pk k ) =
p k2 k2
=
p2
1 (12b)
2m 2m 2m
where the above Planck relationship was supplemented by the companion de Broglie one for
the momentum,
=k k = p k (13)
while the Pauli matrices basic property
k2 = 1 (14)
applies, as may be immediately verified from their realization of eq. (4). Nevertheless, the eq.
(12a) represents in fact the eigen-equation for the free motion, supporting the latent
generalization to the bounded state, either in anti-bonding or bonding existence
E = , E = (15)
This is an interesting result because abolished many odd perception about Dirac equation
and its meaning; actually, there follows that:
Dirac equation is formally related with the temporal Schrdinger one, while
producing the same eigen-problems, thus describing in essence the same nature of
the electronic motion;
The spin information modeled by the bi-dimensional spinors is not necessarily a
relativistic effect (beside completing the 2+2=4 relativistic framework dimension of
the Dirac equation) but merely a quantum one since fulfilling the eigen-value
problems, each separately;
The two spinors of the Dirac equation may be associated with the bonding (for
negative energies) and anti-bonding (for positive energies) of a system, being thus
suited for physically modeling of the chemical bond, beside the common
interpretation of negative/positive spectrum of free positronic/electronic energies in
the Dirac Sea.
However, before effectively pursuit to the chemical bonding description based on Dirac
equation one needs some background of the recent non-orbitalic quantum modeling of the
chemical bond.
6 Mihai V. Putz
3. Quantum Chemical Bond

3.1. Binding Functions and the Chemical Bond
Employing the dimensional quantum-relativity relationship
< energy > < distance >~ Joule meter ~ = c (16)
recently, there were introduced the chemical binding functions [19]:
1, 0
f ( , C A ) = 1 C A = (17a)
,
1, 0
f ( , C A ) = exp( C A ) = (17b)
0,
called as the anti-bonding and bonding functions, for the reason grounded on their
asymptotical behavior, respectively; the introduced -factor accounts for assumed
dimensionless nature of functions (17), being adequately settled as:
1
= = 0.506773 10 3 J 1 m 1 (18)
=c
and where stands for the localization distance, while C A stays for the chemical action
[19,20]
G G G
C A = (x )V ( x )dx [ ] (19)
o
expressed in A (ngstrom) and eV (electron-volts), respectively. Note that in eq. (19) the
equivalence between chemical action and electronegativity [ ] , as electronic density
functionals, was assumed based on their similar nature in convoluting the applied potential
with the concerned electronic density [24], although electronegativity is currently unfolded
as a generalization of the chemical action, being dependent on it, showing a more complex
density functional expression at various localization levels [25, 26].
Nevertheless, the bonding functions (17) reciprocally combine within a paradigmatic AB
molecule, with a coordinate system centered in A, to provide the electronic pair-localization
region within the bond length RAB by means of the binding equations (see Figure 1) [19],
( ) ( )
(I) : f A I , A = f B RAB I , B , (20a)
( ) (
(II) : f B RAB II , B = f A II , A ) (20b)
as the interval II I or as the single point II = I for the hetero- and homo- bonding
systems, i.e. having different or identical isolated electronegativities A and B ,
respectively.
Figure 1. Geometrical loci of the sigma-bonding (-B in blue), anti-bonding (-B in red), no-
bonding (-B in orange), and pi-bonding (-B in green) for chemical binding from equal
electronegativity influences of two systems A and B throughout equations (20) with binding functions
(17) through constants and parametric settings as = = c = 1 , A = B = 1 , RAB = 1.
In each of above equations (20) the binding points I and II appear as the informational
crossing (transfer) between the anti-bonding and bonding functions of both A and B systems
driven by their electronegativities; however, they fix the all types of involved bonding regions
(see Figures 1 and 2) as follows [19]:
the sigma-bonding region (-B in Figures 1 and 2) is uniquely defined and has no
nodes or discontinuities; it is delimited by the area under bonding crossing
functions inside of the pairing interval bordered by the projection of the points I and
II along the bond; it corresponds to the consecrated bonding obtained by the
2
composed wave-function density A + B in the conventional molecular orbital
(MO) theory [4];
the anti-bonding region (-B in Figures 1 and 2) is represented by the two parts
spanning the space from the systems A and B until the sigma-bonding limit, being
defined by the area under bonding functions f A and f B but outside of the interval
8 Mihai V. Putz
fixed by the projection of points I and II on the bond length; it corresponds to the
2
anti-bonding state density A B with separated parallel electronic spins in MO
theory [4];
the no-bonding region (-B in Figures 1 and 2) is composed of two parts, one in
each binding side respecting sigma-bonding, being formed by the area delimited by
all the binding functions of (17) around the binding points I and II, outside of their
projected interval on the bond length, while not intersecting between them and with
the bond length;
the pi-bonding region (-B in Figures 1 and 2) spans the bond length entirely
without crossing it, thus having nodes on it, being resulted from the area defined by
all the binding functions of (17) around the binding points I and II, partially outside
and partially inside (with a common point inside the projected interval of the points I
and II on bond; therefore, this region is compatible with the consecrated pi-bond type
of the MO theory.
Figure 2. Geometrical loci of the bonding regions as in Figure 1 for chemical binding from different
electronegativity influences of two systems A and B throughout equations (20) with binding functions
(17) through constants and parametric settings as = = c = 1 , A = 2 B = 2 , RAB = 1 .
Note that the difference between the equal and different electronegativity influences on
bonding in Figures 1 and 2 is reflected in sigma-bonding shift towards the more
electronegative bonding component, while slightly enlarging the spanning interval of
projection of points I and II on bond in Figure 2; moreover, the bond of Figure 2 is
accompanied by a slightly decreasing of the sigma bonding apex value on binding probability,
being now about 0.5 respecting the recorded 0.6 value in Figure 1. This may lead with the
meaningful consequence in describing the covalency (in Figure 1) and ionicity (in Figure 2)
characters of chemical bonding, in terms of quantum tunneling of the sigma bonding region:
covalent binding is characterized by a symmetric higher and thinner well of

electrons, being those more localized on middle of bond;
ionic binding features a dissymmetric taller and thicker well of electrons with more
delocalized pairing electrons towards the more electronegative component.
The bonding regions may appear as the consequence of equilibrium between binding
functions (17) that caries the density functional information either as chemical action or as
electronegativity. As a consequence, all above identified binding regions are defined within
positive (0, 1) realm of binding functions (17) allowing the natural probabilistic interpretation
for their inside. Nevertheless, there remains to explore their influence on bonding within the
Dirac equation framework, and how the Dirac equation in generals influences the chemical
bonding phenomenology when the spin (or spinors) are involved. This will be addressed in
the sequel.
3.2. Chemical Bond by Dirac Equation
The above spinorial identification as bonding and anti-bonding, see eq. (5), may be now
combined with the introduced bonding and anti-bonding functions (17) so that to create the
actual working binding spinor:
i
1 =c exp = E t
[ ] = i (21)
exp

exp + E t
=c =
where the previous chemical action dependence was here reconsidered as the more
generalized (density functional) electronegativity.
Next, we impose the condition the spinor (21) fulfilling the Dirac equation (1); for this
we separately express the involved terms, while self-understanding the presence of the (bi-
dimensional) unitary and other Dirac operators on both spinorial upper and down components
so that the implicit total dimension of the wave-function to be completed to four-dimensional
space:
the time derivative Dirac term is directly computed as:
i i
i=1 =c = E exp = E t
i= t [ ] =
i i
i= E exp
= exp + E t
=c =
10 Mihai V. Putz
i
E 1 =c exp = E t
= (22)
i
E exp exp + E t
=c =
the space coordinate Dirac derivative needs the pre-requisite of simple derivative
k
k = k k k = (23a)

providing the yield:

i
i=c k k exp E t
i=c k k [ ] = =c =
i=c k k exp exp + i E t

=c =c =
i
i k exp E t
0 k
=
=
k 0 i
i exp exp + E t
k =c =
i
i k k exp =c exp + = E t
= (23b)
i
i k k exp E t
=
the free + potential term:
i
1 exp E t
(mc ) ( mc + V ( x)
+ V ( x) [ ] =
2
) 0

=c =

2
0 ( 2
)
mc + V ( x) exp exp + i E t
=c
=

( ) i
mc + V ( x ) 1 =c exp = E t
2
= (24)

(
mc 2 + V ( x ) exp )

i
exp + E t
=c =
With these, the Dirac equation (1) now provides the system of equations:

= E t = E t
i i i
= i k k e =c e = + 1(mc 2 + V ( x) )1
E t
1 E 1 e e , (25a)
=c =c

i
i i
1(mc + V ( x) )e e
E t E t E t
1 E e =c
e =
= i k k e = 2 =c =
(25b)

Next, through getting out from the second equation (25b) the term containing the
covariant product:

k k = 1(mc 2 + V ( x) E )e =c

i (26a)

it is then replaced in the first equation (25a) to obtain:

(mc 2
+ V ( x) E )1
=c
2
+ e =c =0
(26b)

whose solutions expresses the energy conservation
E = mc 2 + V ( x) (27)
and the Dirac adapted bonding equation

2
e =c
= 1 (28a)
=c
Yet, due to the negative sign of the left hand side of eq. (28) one may infer that it is just
one solution of a quadratic equation, say

4
e =c
1 2 (28b)
=c
providing the second accompanied solution

2
e =c
1 (28c)
=c
However, there is noted the formal difference between eqs. (28a) and (28c) not only
because of sign but also due to the approximate nature of the second, coming from the form
(28b) in short range of binding distance regime 0 . Nevertheless, the appearance of two
12 Mihai V. Putz
() forms of Dirac chemical bonding equation is in accordance with the manifestation of the
Dirac positive/negative manifestation of energies respecting the electronic/positronic motions
within the Dirac Seas, respectively. Still, for the chemical bond description the difference in
sign allows for further mixing of the bonding equations for a paradigmatic AB molecule
generating more bonding points so modeling in more detail the bonding with spins in bonding
and anti-bonding states.
Therefore, the actual working Dirac binding functions are:
The Dirac anti-bonding function remains the same as given within density kernel
approach by eq. (17a):

f Dir ( , ) = 1 (29)
=c
The Dirac bonding function is modified respecting the previous one given by eq.
(17b) while being two-folded:

( + ) ( , ) = exp 2
f Dir , (30a)
=c

( ) ( , ) = exp 2
f Dir (30b)
=c
Now, the bonding geometric loci are determined, for the molecule AB, by the system of
equations:
(I) : f A (I , A ) = f Dir
( + ) (RAB I , ) ,
B B
(31a)
(II) : f B (RAB II , B ) = f Dir

( + ) ( II , ) ,
A A
(31b)
(III) : f A (III , A ) = f Dir

( ) (III , ) ,
A A
(31c)
( )
(IV) : f B RAB IV , B = f Dir
( )
B
(
RAB IV , B ) (31d)
which is regarded as Dirac generalization of the previous one of eqs. (20) by means of the last
two equations which quantifies the interference effect of the anti-bonding and the negative
bonding functions belonging to the same atom in the to be transferred towards a virtual
bonding partner.
The representations of Figures 3-4 show how the Dirac binding functions and equations
(29)-(31) provides more insight in modeling of chemical bonding respecting the previous
density functional ones of Figures 1 and 2.
The differences comes from two basic facts: the bonding function (17b) takes through
Dirac equation two forms, i.e. it degenerates into one positive and other negative, see eqs.
(30a) and (30b), respectively, while having also the modified argumentum. Instead, the anti-
bonding equation (17b) is Dirac preserved either as in form and multiplicity.
Due to this fact, depending on the electronegativity differences between the bonding
partners the anti-bonding spin state may be located in various locations between the mixed
(positive) bonding-antibonding crossing points I and II, eqs. (30a) and (30b), and the self
(negative) bonding antibonding crossing points III and IV, eqs. (30b) and (30c).
Even more, for equal electronegativity three types of parallel spin (antibonding)
separation may arise as illustrated by the Figures 3a, 3b and 3d, i.e. as being delocalized
outside, precisely localized at the edge and delocalized inside of the sigma-bonding region,
respectively, while the Figure 3c illustrates the case when the bonding pairing is precisely
localized on bond.
Actually, following the bonding points delivered by the system (31) one has, for the equal
electronegativity cases of Figures 3a-3d, the following configurations respecting the
electronegativity equal values, respectively:
Figure 3a:
A = B = 1 : IV
N< <
I <
II N III (32a)

providing the anti-bonding (parallel) spins delocalized outside of the region with delocalized
anti-parallel pairing electrons;
Figure 3b:
A = B = 2 : IV =N <
I II =
N III (32b)

providing the precise localization of the anti-bonding (parallel) spins at the margins of the
region with delocalized anti-parallel pairing electrons;
Figure 3c:
A = B = 2.22 :
I < III

= <
IV
N II (32c)

providing the precise localization of the anti-parallel pairing electrons at the half of the bond
length, being outside of it the delocalization of the anti-bonding (parallel) spins;
Figure 3d:
A = B = 3: N
I <
III
<

<N
IV II (32d)

providing the limited delocalization of the anti-bonding (parallel) spins at the margins of
regions with delocalized anti-parallel pairing electrons.
14 Mihai V. Putz
Figure 3a. Geometrical loci of the bonding regions as in Figure 1 for chemical binding from equal
electronegativity influences of two systems A and B throughout equations (31) with Dirac binding
functions (29) and (30) through constants and parametric settings as = = c = 1 , A = B = 1 , RAB = 1 .
Figure 3b. Geometrical loci of the bonding regions as in Figure 1 for chemical binding from equal
functions (29) and (30) through constants and parametric settings as = = c = 1 , A = B = 2 ,
RAB = 1 .
Figure 3c. Geometrical loci of the bonding regions as in Figure 1 for chemical binding from equal
functions (29) and (30) through constants and parametric settings as = = c = 1 , A = B = 2.2 ,
RAB = 1 .
Figure 3d. Geometrical loci of the bonding regions as in Figure 1 for chemical binding from equal
functions (29) and (30) through constants and parametric settings as = = c = 1 , A = B = 3 , RAB = 1 .
16 Mihai V. Putz
Figure 4. Geometrical loci of the bonding regions as in Figure 2 for chemical binding from different
functions (29) and (30) through constants and parametric settings as = = c = 1 , A = 2 B = 2 ,
RAB = 1 .
Worth observing that the case of the equal electronegativities presents the so called
critical electronegativity fulfilling the equation (31c), for instance, at the half of the bond
length:
R A RAB
f A AB , = f Dir
( ) , (33)
2 2
which give the information of precisely localization of pairing of anti-parallel electronic

spins. As well, the precise localization of the anti-bonding parallel spins of eq. (32b), namely
at the critical distances
I = IV = 0.445571 [ RAB ] , (34a)
II = III = 0.554429 [ RAB ] (34b)
on the actual bond length scale, are candidate for universal application for the given (known)
equal electronegativity as stipulated by the case (32b), in adequate units.
However, for both cases of eqs. (33) and (34), one providing localization of pairing anti-
parallel spins at half RAB / 2 of bond length for critical electronegativity, and the other the
critical localization of the parallel spins of the anti-bonding states for equal electronegativities
equaling the twice of current units, respectively, furnishes important practical result when one
likes to control the magnetic properties of quantum material composed by two aggregates.
The Figure 4 is nothing than the extension of the Figure 3a in ionic manner as was the
case for Figure 2 different from Figure 1. Still, for the present case worth remarking that due
to the Dirac treatment, that is by the involvement of the negative bonding function of (30b)
type, the actual model for anti-bonding state, although delocalized in Figures 3a and 4 is still
finite respecting the infinite asymptotic space coverage in Figures 1 and 2.
The final remark regards the height of bonding probability that is more and more
contracted for the increase equal electronegativity cases in Figures 3a-3d, while for different
electronegativities the appreciable contraction of width of the sigma bonding region is
recorded, see Figures 2 and 4.
Overall, the inclusion of the binding functions of eqs. (17) into the Dirac spinor of eq.
(21) leaves with the so called Dirac binding functions (30) that enlarge through the binding
equations (31) the cases of bonding and anti-bonding spin states, while being able to identify
the specific situation when either parallel or anti-parallel spin states are precisely localized
along the bond lengths, with presumed higher importance in designing and controlling of
atoms-in-molecules spin based reactivity, and of nano-composites [27].
4. Conclusion
Although containing a great amount of quantum and relativistic information about the
electronic existence, origin, and motion, the Dirac equation is usually used to correct the
atomic and molecular energies, eventually through the density functional Dirac-Kohn-Sham
equation employed the Dirac-Coulomb Hamiltonian (called as the no-pair approximation)
[17]:
[cG pG + (mc 2 G
) G
] G G
+ V (r ) + Vxc ( (r ) ) j (r ) = j j (r ) (35)
with
G
G (r ' ) G Z Z Z
V (r ) = G G dr ' G A G + G A BG + ... (36a)
r r' A RA r A B RA RB
G
G E [ (r )]
Vxc ( (r ) ) = xc G (36b)
(r )
G occ
G G
(r ) = n j +j (r ) j (r ) (36c)
j
where n j stay for occupancy numbers and where the exchange-correlation energy may be
appropriately chose according with the desired approximation framework [28].
18 Mihai V. Putz
The present approach goes beyond the energetic description of bonding while evaluating
the geometrical (physical) phenomenology of bonding employing the Dirac equation for the
binding functions abstracted from the density kernel approximation [19]:
G G
A [ ( r )] B [ ( r )]
exp 1 (37)
=c = c

bonding function anti bonding function

of atom A of atom B
Remarkably, when functions (37) are considered as bonding and anti-bonding parts of the
Dirac spinor and plugged into the Dirac equation they provide, beside the energy conservation
as the control correct result, also the quantum relativistic (Dirac) binding equations (28) are
obtained; their appearance differs from earlier binding functions (17) only in bonding terms
(30) which are now two-folded degenerate, in accordance with positive-negative Dirac
energetic Seas [1,10,21]; yet, the difference exists also in the bonding argument of eqs. (28)
that is doubled respecting the previous non-relativistic one of (17b). These special features of
Dirac treatment of binding provide a diversity of situations, depending on reciprocal
electronegativity influences of adducts, however, including the situations of precisely
localization of the bonding pair and of the anti-bonding non-pairing electrons along the bond
length. This may lead to important practical application in chemical reactivity driving by spin,
in nano-structures composites, as well as in bio-materials, throughout controlling the binding
and electronic bonding electrons by electronegativity. Overall, there is also proof that the
electronegativity concept and its realization may serve as the main ingredient in bonding
modeling, being related with the most intimate quantum-relativistic structures of matter [29].
These ideas are very fruitful and should be further unfolded and applied in forthcoming works
aiming to model Chemical Bonding and Reactivity.
References
[1] Dirac, P.A.M. The Quantum theory of the electron. Proc. Roy. Soc. A 1928, 117,
610-624.
[2] Bethe, H.A.; Salpeter, E.E. Quantum Mechanics of One- and Two-Electron Atoms;
Springer-Verlag, Berlin, 1957.
[3] Slater, J.C. Quantum Theory of Atomic Structure, Vol. 2; McGraw-Hill, New York,
1960.
[4] McWeeney, R.C.; Sutcliffe, B.T. Methods of Molecular Quantum Mechanics,
Academic Press, New York, 1969.
[5] Wilson, S. Electron Correlation in Molecules; Clarendon Press, Oxford, 1984.
[6] Lindgren, I.; Morrison, J. Atomic Many-Body Theory; Springer-Verlag, Berlin, 1982.
[7] Malli, G.L. (Ed.) Relativistic Effects in Atoms, Molecules, and Solids; Plenum Press,
New York, 1983.
[8] Boeyens, J.C.A. New Theories for Chemistry, Elsevier, Amsterdam, 2005.
[9] Hoffman, E. O. (Ed.) Progress in Quantum Chemistry Research, Nova Science
Publisher, New York, 2007.
[10] Grant, I.P.; Quiney, H.M. Foundations of the relativistic theory of atomic and
molecular structure. Adv. At. Mol. Phys. 1988, 23, 37-86.
[11] Pyykk, P. Relativistic Effects in Structural Chemistry. Chem. Rev. 1988, 88, 563-
594.
[12] Ziegler, T.; Snijders, J.G.; Baerends, E.J. Relativistic effects on bonding. J. Chem.
Phys. 1981, 74, 1271-1284.
[13] Schwarz, W.H.E. Fundamentals of relativistic effects in chemistry, in Theoretical
Models of Chemical Bond. Part 2. The Concept of the Chemical Bond, Ed. Z.B.
Maksi. Springer, Berlin, 1990, p. 593-643.
[14] Buenker, R.J.; Chandra, P. Application of configuration interaction for the study of
relativistic effects in atoms and molecules. Pure Appl. Chem. 1988, 60, 167-173.
[15] Hess, B.A. Applicability of the non-pair equation with free-particle projection
operators to atomic and molecular structure calculations. Phys. Rev. A 1985, 32, 756-
763.
[16] Buenker, R.J.; Chandra, P.; Hess, B.A. Matrix representation of the relativistic
kinetic energy operator: two-component variational procedure for the treatment of
many-electron atoms and molecules. Chem. Phys. 1984, 84, 1-9.
[17] Liu, W.; Dolg, M. Benchmark calculations for lanthanide atoms: Calibration of ab
initio and density-functional methods. Phys. Rev. A 1998, 57, 1721-1728.
[18] Putz, M.V. (Ed.) Chemical Bond and Bonding, special issue of Int. J. Mol. Sci. 2007-
2009, http://www.mdpi.com/journal/ijms/special_issues/bond_bonding.
[19] Putz, M.V. Chemical action and chemical bonding, J. Mol. Struct. THEOCHEM
2009, 900, 64-70.
[20] Putz, M.V. Levels of a unified theory of chemical interaction, Int. J. Chem. Model.
2009, 1, 141-147.
[21] Schweber, S.S. An Introduction to Relativistic Quantum Field Theory; Harper and
Row, New York, 1964.
[22] Jauch, J.M.; Rohrlich, F. The Theory of Photons and Electrons, 2nd ed., Springer,
New York, 1976.
[23] Harriman, J.E. Theoretical Foundations of Electronic Spin Resonance; Academic
Press, New York, 1978.
[24] Putz, M.V. Contributions within Density Functional Theory with Applications in
Chemical Reactivity Theory and Electronegativity, Disertation. Com, Parkland,
Florida, 2003.
[25] Putz, M.V. Systematic Formulation for Electronegativity and Hardness and Their
Atomic Scales within Density Functional Softness Theory, Int. J. Quantum Chem.
2006, 106, 361-386.
[26] Putz, M.V. Absolute and Chemical Electronegativity and Hardness, Nova Science
[27] Putz, M.V. (Ed.) Advances in Quantum Chemical Bonding Structures, Transworld
Research Network, Kerala 2008.
[28] Putz, M.V. Density functionals of chemical bonding, Int. J. Mol. Sci. 2008, 9, 1050-
1095.
[29] Putz, M.V. Can Quantum-Mechanical Description of Chemical Bond Be Considered
Complete?, in Quantum Chemistry Research Trends, Mikas P. Kaisas (Ed.), Nova
Science Publishers Inc., New York, (2007), pp.3-5.
Chapter 2
DUALITY WITHIN THE STRUCTURE

OF COMPLEMENTARITY:
RIGHT WHERE IT HAS NO PLACE TO BE
Constantin Antonopoulos*
Department of Applied Mathematics and Physics
National Technological University of Athens,
28 Oktovriou (Patision) 42,10682 Athens, Greece
Abstract
Bohr defines as complementary a pair of concepts united in the classical mode of
description. But waves and particles are not united in this mode of description. They are
separated in it. And from now on it only gets worse: Waves and particles are mutually
exclusive even in Classical Mechanics. And Classical Mechanics does not contain the
quantum. In other words, the incompatibility between waves and particles is self-sufficient and
fact-independent and therefore such as cannot even be attributed to the quantum. But then
again Complementarity (CTY) must at all costs be attributed to the quantum. In consequence,
the sort of incompatibility afforded by Wave-Particle Duality (WPD) is the wrong sort for
CTY, which is dependent on the quantum. Once this is realized, CTY is in search of a new
foundation. This foundation is not really new at all and is offered in abundance in Bohrs
conception of the wholeness of the quantum of action. CTY is what happens to our structural
conceptual scheme, when it is applied to the atom. Once CTY is properly derived in this way,
Bohrs ideas are further utilized to effect a reduction of WPD to the all pervasive, underlying
Wholeness. It will then follow that WPD is a derivative instance in Bohrs doctrine and not
the primitive axiom that almost everyone assumes it to be.
1. Why a Reappraisal Is Necessary

The closing decade of the twentieth century and perhaps the one immediately preceding it
have witnessed a literal explosion of philosophers interest in Bohrs quantum philosophy,
*
E-mail address: antonopoulos9@msn.com
22 Constantin Antonopoulos
considered now as a purely philosophical subject in its own right, and pursued after
increasingly complex pathways of contemporary semantics and epistemology. Accounts
exemplary in finesse and subtlety, by far transcending the clumsy, older presentations of
semi-instructed physicists, appear all around us, capable for the first time of doing real justice
to the depth of Bohrs thought (Hooker states [p.174] that he has had no cause to change his
earlier views on Bohr, as presented in his all-time classic monograph, see Hooker, 1972. I
mention this because I will be quoting essential passages from this monograph and very little
from this present work; see Hooker, 1994, 155-194).
Yet despite the number, the extent, the competence and the sophistication of the works
recently written on Bohrs obscure genius and its products, the issue of the relation between
Duality and Complementarity (CTY hereafter), if any, seems to be left untouched on the
whole and pretty much where it stood back in the forties (with possibly one other exception;
see D. Murdochs work of 1987).
Since 1984 I have made it clear [in a paper first presented in front of a live audience,
comprising the results of my doctoral thesis, in a conference held in Athens, titled Forms of
Physical Determinism; the paper proposed a compact argument for deriving energy-time CTY
on the basis of discontinuity alone, and without the intervention of duality, see
Antonopoulos 1985, 95; See also E. Marquits reference to this work, Marquit 1988, 193] that
I consider Wave-Particle Duality (WPD hereafter) an inelegant, facile, confused and, what is
of essence, an incoherent method for deriving the relations of mutual exclusion demanded by
CTY. It was therefore a matter of particular personal interest for me to observe, whether the
above noted sophistication of recent Bohrian scholars has at last branded the continuing
survival of Duality in Bohrs system as the anachronism it is, or whether, competence, depth
and subtlety notwithstanding, has otherwise resigned itself to a venerable tradition. The
answer to this question was not particularly satisfying to me, so I presently intend to do
something about it.
The line of authors who have explicitly rejected Duality as a basis of CTY is sadly not a
long one and the fingers of ones one hand suffice to do the numbering. I have actually found
two of them: Max Born and Adolf Grnbaum. Max Born makes it clear that, one: he fully
endorses Bohrs CTY; two: that he rejects the idea of waves altogether, claiming that waves
are waves of probability. They determine the supply of particles, that is to say, their
distribution in space and time [Born, 1951, 157; the authors italics]. Hence, there are no
real waves for the particles to be complementary to. Yet he otherwise speaks most
approvingly of CTY [Born, 1969, 98]. To him the relationship of CTY must therefore pertain
to and obtain between pairs of concepts other than the wave and the particle. Which are
my sentiments exactly I nevertheless doubt whether the reasons for Borns dismissal of
Duality as a basis, or even an instance of CTY, share much in common with my own. In all
probability this is but another case of two people having reasoned to the same conclusion
from different premises. But with A. Grnbaum it is not so. Here a good deal is shared:
<<It should be noted that the properties which are being referred to as complementary
here are those named by the values of the conjugate parameters of Heisenbergs principle and
not such supposed properties as being wave-like or particle-like. The latter had better be
omitted from quantum mechanical discourse altogether: it is a misleading carry-over from the
classical interpretations [...] whose very break down is the ratio essendi of the new theory.
The terms wave-like and particle-like should not be used as surrogates for bona fide
complementary parameter values>> [Grnbaum, 1957, 717; italics in the original].
Duality within the Structure of Complementarity 23
This is much closer to the complementary scheme of things I have in mind. Yet the
position I am about to defend is far stronger than Grnbaums. In fact, it is quite extreme:
waves and particles are not just a left over from classical methods and habits, and hence
totally unsuitable for a concept as unclassical as that of CTY, though left over and all the rest
they certainly are. Waves and particles are a logical impossibility as a putative basis of CTY.
It is not without interest to see how, if only by stark contrast to the extreme thesis I am
going to defend, WPD fares in recent, hence presumably well informed (?) literature:
Complementarity appears to have been introduced by Bohr in response to the wave-
particle duality, which becomes the wave-particle complementarity in his framework
[Plotnitsky, 1994, 68].
To complete this untroubled, and slightly museum-piece picture of things with what this
author is really aiming at, there is then introduced the irrationality lurking in the concept of
WPD: The author (predictably) infers that wave-particle complementarity is thus defined in
anti-epistemological terms. [ibid.] and is, to the same extent, the scientific counterpart of
contemporary French obscurantism, involving Derrida, deconstructionism and a curtailed
form of Hegelian dialectics, from which French philosophy finds it hard to at last emancipate
itself, the author quoted very probably included.
Having acknowledged subtlety and finesse in the texts of contemporary Bohrians does
not necessarily include all Bohrians nor all texts. It does not include the passage just cited nor,
for that matter, the one to now be, although its author, Henry Folse, is undoubtedly a very
well informed and very attentive reader of Bohrs text on nearly all other topics and
occasions. But even to a scholar of so high a fidelity to the original, as Folse is, the idea that
WPD may not be what is really behind CTY, has never occurred; or, perhaps because of it.
For suggesting, as Grnbaum has, that CTY is something other than WPD, or that it is
inconsistent with it, as I have, is not high fidelity. It is heresy. In consequence, Folse writes
that:
by 1925, when matrix mechanics appeared, both wave and particle representations
seemed necessary to describe the full range of phenomena in which atomic systems
and radiation were to be observed [Folse, 1985, 83; authors italics].
or that
by 1925 Bohr came to believe that the key to the new framework which would
resolve the inconsistencies between the classical and the quantum ideas was to work
with both particle and wave pictures [86; authors italics].
or that
what was needed [for Bohr] was not a victory for the particle picture or the wave
picture [for] by 1925 he was convinced that neither was to be discarded in favor of
the other [Ibid.; slightly rephrased].
Ergo, wave-particle CTY, of which there are plenty more samples in the relevant section
of Folses (otherwise excellent) book, some preceding the ones I quoted, some succeeding
them and some in between, convincingly backed up by bulky historical evidence too direct to
question, such as remembrances of Bohr by Heisenberg at al., private correspondence, notes
taken in a hurry, indeed everything it takes to make Grnbaum and myself (and perhaps Max
Born a trifle) weep bitter tears at our heretic presumption.
So I guess it is high time we got some of our own back and cause, if not bitter tears as
such, then at least a modicum of worry to the crowded orthodoxy, relying on evidence drawn
not from letters, nor from recollections, nor from ill remembered phrases and flashes of
memory nor, finally, from Bohrs still confused ideas of 1925, but from the first official
statement of CTY as it is specified in the first published volume of Bohrs work: <<The term
complementarity, which is already coming into use, may be suited to remind us of the fact
that it is the combination of features which are united in the classical mode of description
but appear separated in the quantum theory>> [Bohr, 1934, 19].
Here then: since CTY is the combination of features united in the classical mode of
description, if CTY obtains between waves and particles, waves and particles are united in the
classical mode of description. This routine definition of CTY, known to all to be as
commonplace as the ABC of the doctrine, should give Plotnitsky and Folse something to
really think about; for it is not waves and particles which are united in the classical mode of
description and separated in the quantum. If anything, waves and particles are (quasi)united
in the quantum mode of description and separated in the classical [And even there the
(quasi)unity is only pretentious; complementarists do say that they are properties of one and
the same micro-entity but the unrelenting classical opposition between waves (large) and
particles (small) not only is retained full force in QM. It is actually utilized to derive CTY]. In
consequence, if there is one possibility which this important passage excludes, this is the
possibility of wave-particle CTY.
On the other hand, what this common, but at the same time unique, passage establishes as
the proper pairs of complementary concepts are none other than those which Grnbaum has
already specified above, viz. the two pairs of classical conjugate concepts, whose products
(not unexpectedly) yield a unit of physical action: Et and pq. The very ones which also enter
Heisenbergs Uncertainty Relations (UR hereafter), in many ways Bohrs CTY expressed
quantitatively. For it is these, it goes without saying, which are united in the classical mode of
description and separated in the quantum. Not waves and particles. In consequence, treating
WPD as the basis, or an instance, of CTY creates a definite and insurmountable hermeneutic
impossibility. Bohrs own words directly forbid it. If they are adhered to, WPD is the last
thing in the world that fits the description.
Folse is too alert a reader of Bohrs text (quite unlike Plotnitsky and his un-welcome
improvisations) to have missed a point of such importance. But he receives it rather
differently than I:
It is clear that in this original statement of Bohrs new viewpoint, the complementary
relationship holds between space-time coordination and the principle of causality, both of
which were combined in the classical framework. Only later does Bohr speak of
complementarity between wave picture and particle picture [Folse, 1985, 114.]. If later in
this connection is supposed to mean in his mature years it wont do. Maturity to the extent
of self-contradiction is no development or enrichment of the doctrine. Bohr may have
included wave-particle CTY later, if Folse so wishes. But it is just as true, if not indeed
much more so, that the CTY between the classical conjugate concepts he has never retracted
or abandoned and only sheer folly would lead him to do a thing like that. CTY has the exact
same age that Heisenbergs UR have, and in Heisenbergs UR the concepts which are
mutually exclusive are still today the action products Et and pq.
Hence, E with t and p with q are still as complementary as ever. Are also the wave and
the particle, which were later added to complete the doctrine, of a like nature? If so, then on
the basis of Bohrs own definition, CTY should now obtain between concepts which are both:
united and separated in the classical mode of description, since the classical concepts E,t and
p,q correspond to the former account, the wave and the particle to the latter. In consequence,
unless Folse is to explicitly reject classical concept CTY for the sake of wave-particle CTY,
an idea whose pronouncement alone seems suicidally absurd, since the latter is said to
support the former, we shall inevitably have to make room for both of them. In other words
allow for CTIES between both, concepts united and concepts separated in the classical
theory. Some definition of CTY this is. I dont know whether to call it a contradiction, an
ugly patchwork or just an empty formula which licenses everything.
Let there be no mistake about that. Bohrs own words, as explicitly voiced in the quoted,
inconvenient passage, make wave-particle CTY exegetically impossible. And this, until now,
only as far as exegesis goes. But there is more. For the exegetic impossibility implicitly
contains a logical one, thus far concealed by the focus of emphasis. So let us reveal it, if only
in moderation, for not all the story should be told at so early a stage. I have claimed that
wave-particle CTY fails to satisfy the standards of Bohrs definition, because waves and
particles are not united, as the definition requires, they are separated in classical mechanics.
Separated they certainly are. But then again, without any help from the quantum. For nothing
of this sort exists in classical mechanics. Nevertheless, wave and particle are as incompatible
as ever, even in classical mechanics.
Waves (large) and particles (small) are self-sufficiently incompatible. So why need the
quantum to separate them? The incompatibility between large and small is fact-
independent and therefore cannot even relate to the quantum. But then again, as Im sure
Folse would be the first to agree, CTY has to relate to the quantum. How then can it be based
on WPD, which by definition can not? Complementarists, who make a habit of easy,
sweeping solutions, will not find an easy way out of this one. Nor, strangely, will any body
else.
2. The Relevance of the Classical Framework

Probing deeper into the logical structure of Bohrs relevant passage we can discern not
only which actual concepts should qualify as members of CTY; we can, through Bohrs
thrifty but pregnant words, also discern why. Why, that is, Bohr thinks that such concepts can
still complement one another in QM, despite their separation therein. They can, indeed they
must, because they are united in the classical mode of description. Hence, the prototype sets
as candidates for the relation of CTY such concepts only, which are firstly shown, united in
the classical mode of description. (But waves and particles are not united in this mode of
description. Still, people say that they are complementary.)
The demand that concepts complementary in QM must first be shown to be united in
Cl.M (classical mechanics) is not perchance a weak, dispensable analogy, to be dealt with or
waived aside on the physical aphorism, that QM has already undone Cl.M, so whats the
point of calling them complementary in the first place. For the demand to treat them as
complementary in QM, iff united in Cl.M, is not itself a physical argument at all. It is a
transcendental one. The pressures to call them complementary are not factual. They are
conceptual. The interference of the quantum may well undermine the physics of the situation,
which is in any case contingent and therefore transitory. But the conceptual aspects are not as
easily removable because of this and Bohr was the last person ready to remove them [Bohr
emphatically denies that the classical concepts can be replaced by different concepts in QM;
whence, of course, their resulting CTY. See for greater details my essay, Antonopoulos, 1987,
passim].
To put the point more forcefully, Et and pq are not complementary in QM just because
they are united in Cl.M. Far more than merely establishing the unity of Et and pq Cl.M. is
itself established on the presupposition of such unity; for the unity spoken of antedates
scientific systemization and is the rock bottom, transcendental foundation of its very
possibility. Whence the Kantian dimension of the point [Kants Transcendental Aesthetic,
treating space and time, and Transcendental Analytic, treating causality, combine to furnish
the transcendental substratum, whose joint fulfillment alone will confer upon a provisional
entity the status of an event. Compare this with Favreholdts description of Bohrian
epistemology: (All of this) fits well with Bohrs insistence that space, time and causality are
necessary forms of sensibility in human knowledge, see Favreholdt, 1994, 81; for Bohrs
transcendentalism, see also Honner, 1994, 142].
This, then, is the reason why momentum and position must be considered
complementary: Because they constitute equally necessary components of one and the same
phenomenon of motion; as Folse elegantly puts it, Motion is change of position in time
[Op.cit., 57], hence, the idea of motion without simultaneous reference to both of these
constituents, p and q, borders on conceptual impossibility. Whence, of course, the very roots
of the representational, intuitive, epistemological and even logical problems related with QM
and CTY, which demand their separation. However, in spite of their physical separation in
QM, position and momentum still remain inerasable conceptual correlatives, for their
correlation was other than physical to begin with. Hence, when split apart by the quantum of
action, they should still be considered complementary, because, even so, the two of them
belong to one another, if motion of any kind is to ever result. And in belonging to one
another, they therefore complement one another. (NB: Mutual complementation is also
necessary to CTY!)
Here now is why energy and time should be considered as complementary. They are
because the following principle, elementary in its simplicity, still continues to obtain in spite
of everything:
P.1: An object can only occupy a particular energy state at some time, or over a time, if
at all; which, in turn, has very little to do with QM or even Cl.M, for that matter. For it is
itself but a special case of a more general and fundamental principle, which underlies it:
P: An object occupies a state at some time, if at all (energy states included).
I hold this to be an important conceptual truth for its alternatives lead to absurdity. To
show this, I will restate P in the following, Kantian form; P': What happens, happens within
time, therefore at a time (or over a time). That is to say, cannot happen outside time (or
outside the flow of time). To then suppose it can, may be magic or miracle but it certainly
isnt physics. And, in any case, cannot be referring to what we normally call an event.
Since, therefore, P, P.1 and P' leave little room for coherent alternatives, energy states as
much as anything else must needs be associable with a time [Take, for instance, the following
assertion by D.M.Mackay: Energy must always be associated with a tract of time, see
Mackay, 1958, 112; italics the authors; what is so special about this assertion is that it comes
in the text just after the author has derived the energy-time uncertainty! Even that result is not
powerful enough to erase the transcendental correlatedness of the two concepts]. And hence,
even if energy and time are no longer directly associable at the physical level, due to the
quantum, they nevertheless retain their formerly established conceptual link and so their very
correlatedness. For the very arguments establishing such link are not themselves empirical
and contingent. They are transcendental. And this kind of link lingers on even in the face of
adverse empirical conditions, revealing its true origin. The time of its occurrence belongs to
an event and, conversely, the very notion of timing something can in turn only refer to an
event. Hence, the two complement one another and should be regarded as complementary in
all the cases, where the physical conditions obtaining prevent their hitherto joint application;
which brings us directly to Bohrs second string of definitions:
<<The word complementarity denotes the relation of mutual exclusion characteristic of
the quantum theory with regard to the application of the various classical concepts and ideas
[Bohr, 1934, 19] [...], which in a different connection are equally necessary for the
elucidation of the phenomena>> [Op. cit, 10]. In other words, such and only such pairs of
concepts qualify as complementary, which, in the presence of any one member of the pair that
is empirically realized, the absent member is still as necessary for a wholesome, cogent
representation of reality, as the present member is; which is only sound, plain sense. One
must never forget that, as can be verified from Bohrs own words, mutual exclusion is only a
necessary condition for CTY. Not a sufficient one. The other necessary condition trivially
being, I would suppose, the capacity of the alternatingly excluded member of the pair to
complement its complementary.
The epistemological insanity lurking within QM is that it precisely seeks to drive a wedge
and set apart such pairs of concepts, which make good sense only when taken together. This
is the nature of the conceptual pressures exerted upon us by the fundamental structure of the
classical framework, retrodictively demanding its toll even in the face of the quantum. Can I
put the point in plain, human, unpretentious terms? A concept A is complementary with a
concept B, iff it would have been preferable for human knowledge to have obtained A
together with B, rather than without it. Normally, this is what CTY is all about.
Now let us try and apply all these rather commonplace facts about CTY to the case of
waves and particles and see what follows. Waves are large (extended) and particles are small
(local). And assigning them both simultaneously to one and the same thing would result to a
silly contradiction. Is it then preferable for human knowledge to be able to obtain the wave
together with the particle, rather than without it? For this is what their alleged CTY would
boil down to.
What is the fundamental epistemological problem raised by QM and its complementary
account? It is, for example, that it renders a classical position incompatible with a classical
momentum, perennially frustrating Einstein, who has branded the theory incomplete because
of this very reason [Einstein, Podolsky, Rosen, 1935, 777-780]. Was Einstein complaining
about quantum incompleteness because QM forbids the co-existence (or the co-verifiability)
of waves and particles? Was that what Einsteins demand for completeness was about?
Here are some further, impressive similarities(?) between classical concept CTY and
wave-particle CTY, similarities which, Im sure, all concerned have noticed long before I
have. To start with, energy and time or position and momentum are attributes which can be
jointly assigned to a macro-system. Wave and particle are not attributes which can be jointly
assigned to a macro-system, except at the pain of blatant contradiction. Who can deny such
similarity?
Accordingly, for energy and time or position and momentum the descriptive problem
raised by CTY, or by QM as such, is that they cannot be observed together, when all
concerned feel they should. So, one must conclude, the problem would be removed if they
were observed together. But the descriptive problem raised by wave-particle CTY is not that
these two cannot be observed together. They cannot but, so far, no one has called this a
problem. The problems here would start, if wave and particle could be observed together,
though, thankfully, they cannot. For some pairs of concepts, it would seem, their CTY is a
deep frustration. But for some others, their CTY is pure salvation! Something here has gone
terribly wrong, terribly not just due to the magnitude of the mistake but, indeed, due mainly to
how easy it was to avoid it.
In view of these remarks I trust no one will invoke experiments to save the day and argue
that, since it is experiments which force upon us the two natures, we have no choice but to
comply. At this point experiments are irrelevant nor have I built my case on them.
Experiments can at best establish the existence of waves and particles. Not their
complementarity. CTY is a conceptual doctrine and the citing of brute experimental facts,
however persistent or inexplicable, is but a lame excuse for calling them complementary, thus
making a virtue of necessity. The deplorable logic of experiments are like that, so what we
can do? does not per se necessitate the application of CTY. How about doing nothing? In my
view, to argue in this way is to just take hold of a problem and, through its sheer longevity
and inexplicability, decide abruptly to turn it into its own solution, because it is a problem.
Duality experiments do not establish the complementarity of waves and particles. They
just establish their observation. And he is surely a poor reader of Bohr, who conflates these
two. If they also establish a contradiction in the world at least behind the scenes [See also
Folse, 1985, 83-4], then, at best, this is what CTY is supposed to handle. Not therefore what
CTY is supposed to be. Indeed, for CTY to be able to handle the contradiction, it must itself
be distinct from the contradiction. Otherwise, and were the contradiction also a CTY, the
problems plaguing the contradiction would eo ipso become the problems now plaguing CTY;
which is exactly what they have become, only spreading more and more butter on the bread
of Bohrs adversaries. And then, rather than solving the problem of WPD, CTY would itself
become a part of this problem. That alone is excellent reason for wanting to separate between
CTY and WPD. Hence, WPD experiments do not establish wave-particle CTY. Then what
does?
There are some who find it consoling to suppose that wave belongs to particle
because, they say, some of the concepts which even I have admitted as authentically
belonging to one another, viz. p with q and E with t, are themselves connected, some with the
wave and some with the particle [This confused contention is based on a tragically erroneous
reading of de Broglies p=h/, mistaking p, or mv, as the particle property, and so (correctly)
taking as the remaining, i.e. the wave property; but p is no longer the particle property in
this relation. p is the magnitude which is here determined by the wave, by simply assigning to
a unique value; then the fraction h/ can also receive a definite value; but a unique value to
entails the use of the wave picture, if to be assigned, indeed the picture of a harmonic wave,
which makes recourse to the particle impossible a priori, at least if complementarists
themselves are to be believed. So, if p is the particle property, p has to define in absence of
the particle, whose property it is! For a lengthier demonstration of the point see
Antonopoulos, 2004]. So if, they say, p belongs with q, so must wave belong with
particle, which is respectively connected to them. I honestly hope that no serious arguer
will attempt this circle against me. To assume that waves belong together with particles
simply because p and q also do, is to take for granted the very thing I have already called into
question. For I have been arguing that this is precisely what the relation between wave and
particle does not do and cannot do; namely, come even close to comparing with the relation
between p and q or that between E and t in the first place. To therefore suggest against me
that the wave is complementary to the particle, because these two correspond with p and q
or E and t, which latter are complementary, is to freely assume that they do so correspond and
this is the last thing I am presently inclined to allow.
In a nut shell; wave and particle are contradictory concepts, exactly as contradictory as
yes is with no. But energy with time and position with momentum are not contradictory
concepts. So the whole nonsense of associating waves and particles with energies and times
or positions and momenta is as sound and rational a practice as urging us to treat as
contradictory, concepts which we have ourselves admitted that are not contradictory. Other
than that, Plotnitsky sees no problem in calling waves complementary with particles, and then
proceeds full speed to the understanding of CTY in anti-epistemological terms. Were CTY
as incoherent as all that, it would definitely be anti-epistemological and, besides, every single
one of the things, which its opponents have claimed it, is for nearly seventy years now. Sadly,
this practice is adopted also by Folse, who latter should at least know better [In the Editorial
to the 1994 collection, see Folse, Faye, eds., 1994; Folse, if he is indeed the co-author of the
piece (I suppose he must be), speaks as if it is still evident to him that CTYWPD. There is,
however, a slight revision: The connection between wave-particle dualism and the
complementarity of the dynamic and kinematic properties remains a problematic issue for the
analysis of Bohrs philosophy and for the interpretation of QM, see Editorial, 1994, xvi. I
would say it does! But I think I may have an answer to it, see Section 5]. Well, if this is
orthodoxy, Id choose heresy any day. An exasperation shared by all heretics, Im sure.
3. On the Two Kinds of Incompatibility

If something is behind the mutual exclusion of the classical conjugate concepts, Et and
pq, and this cannot be WPD, then what can it be? Bohr is pretty clear about what it is. All we
need to do is listen:
Complementarity is a term suited to embrace the features of individuality of quantum

phenomena. [Bohr, 1958, 39]
The fundamental postulate of the indivisibility of the quantum of action [...] forces us to
adopt a mode of description designated as complementary [Bohr, 1934, 10].
Quantum theory is characterized by the emphasis on the feature of wholeness connected with
the quantum of action. [Bohr, 1963, 53]
Bohr stresses here that what is behind CTY of the classical conjugate concepts is not
some duality or other but, indeed, and very directly so, the indivisibility of the elementary
quantum; that is to say, its wholeness. Further exegetic efforts disclose remarkable
persistence on this point:
The essence of quantum theory may be expressed in the quantum postulate, which attributes
to any atomic process an essential discontinuity or, rather, individuality. This postulate implies
a renunciation of the causal, space-time description of atomic phenomena [Bohr, 1934, 43].
Once again it is the individuality of the processes, or their discontinuity, which is behind
the failure to coordinate the causal and the spatiotemporal description. CTY has appeared in
these passages several times already and still the word duality is spectacularly absent from
the text. And there is more. Bohr is well known to have attempted to generalize CTY over the
(philosophical) domains of Action, Mind and Life, where he claims that CTIES comparable
to those of QM can be detected. It is interesting to see why he thinks so in these other three
domains, where quantum wholeness is not present:
In general philosophical perspective [...] in other fields of knowledge, we are confronted with
situations reminding us of the situation in quantum physics. Thus, the integrity of living
organisms and the characteristics of conscious individuals present features of wholeness, the
account of which implies a typically (!) complementary mode of description. [Bohr, 1963, 7]
So, after all, a comparable wholeness is present in these other three domains, analogously
inviting application of the doctrine. Wholeness, it should be stressed, which implies a
typically complementary mode of description. How much more typically holistic does this
mode of description have to be, to at last detach itself from Duality? I think that after seventy
five years of CTY complementarists must simply accept the facts as they are and stop foisting
on Bohr the dualities of QM, or those of the Copenhagen Interpretation (a caricature of
Bohrs real doctrines, if there ever was one), or those of their own experiences with WPD, in
case they are also physicists. The man speaks differently. The man himself never said
complementarity is a description based on duality, as P.K.Feyerabend said in his name
some fort five years ago [1958, 94] and as Plotnitsky or Folse plus very many others still say
today. It is only natural to assume that, if Bohr thought CTY was based on Duality, this is
what he would have said right from the start, just as Feyerabend has, rather than unendingly
repeat that it is based on indivisibility and wholeness instead.
But I still have an ace up my sleeve, to determine once and for all whether it is the
indivisibility of the quantum that is behind CTY, or whether it is its duality which really is.
Either way, concerning the quantum of action one thing is certain. It is the quantum which is
behind CTY and nothing but the quantum, independently of what other properties it is
deemed to possess. I trust no complementarist will deny me that. This, besides, is what the
quantum uncertainties, Et, pqh, also say. For h0 both uncertainties would vanish.
Suppose then that it is essentially WPD which is behind the mutual exclusion of the four
conjugated parameters, i.e. the two pairs of classical concepts.
However, the wave and the particle are mutually exclusive even in classical mechanics.
And classical mechanics does not contain the quantum. How then can CTY, which according
to all quoted Bohrian passages is dependent on the quantum, be the synonym of a pair of
concepts, wave and particle, which are mutually exclusive without the presence of the
quantum? For wave and particle exclude one another even in classical mechanics and
therefore do so independently of the quantum. Some CTY this is! When I have emphatically
announced in the opening section of this essay that it is logically impossible for WPD to be
the basis of CTY I was not exaggerating. It is indeed no less than logically impossible to so
be.
The sole way that this inevitable conclusion can be avoided is to then argue that WPD is
the quantum. Whereupon CTY, by being dependent on the quantum, would eo ipso be
dependent on WPD. Accounts and interpretations of this sort are anything but hard to come
by and, it should be mentioned, are generally considered as the cultivated or the
sophisticated version of the ordinary and vulgar version of Duality. Needless to say, they are
nothing of the kind. They are as incoherent and confused as any other, less sophisticated and
far more vulgar presentation of wave-particle CTY available.
Suppose we examine this contention closer: Originally, wave and particle are two things;
in fact, two incompatible things; the quantum of action just one. How then are we to
understand the claim that WPD and the quantum are one? Is this supposed to mean that the
wave and the particle cease to be two incompatible things, becoming one, or that the quantum
ceases to be one, becoming two incompatible things? Isnt all this asking of us to swallow
unresistingly more and more logical curiosities as we go along, rather than less and less, as it
would be if the answers given us were only clear, convincing and reasonable?
Identifications have their own strict rules. What we have here as candidates for
identification are a pair of mutually exclusive concepts, on the one hand, and a (so far) unique
concept, on the other, in whose frame the former two are alleged to be joined; but treating a
pair of concepts as mutually exclusive presupposes treating them as not being able to be
joined in the frame of a third concept, if it presupposes anything. Else there is no point in
calling them mutually exclusive in the first place. In consequence, any identification of the
sort presently proposed is impossible to implement without severe loss of identity of either of
the participants. Either the two hitherto incompatible concepts will lose their identity, and
cease being mutually exclusive (to no benefit of wave-particle CTY!), or else they will retain
their identity, warranting mutual exclusion, and then, if WPD is the quantum, for the quantum
to partake in the identity, the quantum will have to be mutually exclusive to ... itself. Which
conclusion is more incoherent and absurd than even the vulgar versions of wave-particle CTY
it seeks to replace. If complementarists are to be taken seriously they must give up such
symptoms of exasperating double talk and start talking some sense.
WPD cannot constitute the foundation of CTY because it yields the wrong sort of mutual
exclusion. But then, if there is such a thing as the wrong sort, there must also be the right sort
as well. In other words, there must be two kinds of mutual exclusion, that is to say, two kinds
of incompatibility, only one of which is suitable for CTY. This brings us to the title heading
of this section.
Consider, then, the propositions A>B and A=B. These are certainly incompatible.
Consider next the proposition your money or your life! as pronounced by the proverbial
bandit. Are these two cases of incompatibility anything at all like one another? They are not.
They are diametric opposites.
The former, logical incompatibility is a consequence of definitions and is therefore
necessary (as Leibniz would say). The latter, factual incompatibility is a mere consequence of
obtaining facts and is therefore contingent (as Leibniz would say). Contingent, that is to say,
upon a fact (e.g. the quantum) [A preliminary formulation of this distinction I have given in
Antonopoulos, 1988, 323; Its complete and comprehensive formulation can be found in
Antonopoulos, 1994, 187-9, its application to the EPR-Bohr debate in Antonopoulos, 1996,
1998 and its application to the problem of nonlocality in Antonopoulos, 1997a, 1999 and,
partly, 2005]. This we may entitle the prohibitive fact [Antonopoulos, 1994, 188] (e.g.
again the quantum). Hence, on the whole, there is fact-dependent and there is fact-
independent incompatibility. And Wave-Particle Duality is of the latter sort. Not of the
former. This, I believe, suffices to make all the mess perfectly clear as it suffices, I hope, to
make clear, why it is a mess. WPD, in expressing a logical incompatibility, which its own
defenders go out of their way in establishing (!), is therefore fact-independent and, as such,
cannot even relate to the quantum. At least not coherently, though otherwise it certainly can.
And is therefore unsuitable not just for CTY but for QM itself on the whole.
Most people assume that WPD is the mystery of QM, the sole quantum mystery there is,
the rest of them, if any, presumably reducible to its narrower or at worst its wider frame.
Three physicists, for instance, one of whom, R.Feynman, is quite well known and popular,
introduce the reader to their discussion of Duality (i.e. the double slit experiment) in the
following way:
We choose to examine a phenomenon which is impossible, absolutely impossible, to
explain in any classical way, and which has in it the heart of quantum mechanics. In reality, it
contains the only mystery. In telling you how it works we will have told you about the basic
peculiarities of all quantum mechanics [Feynman, Leighton & Sands, 1965, 1-1; italics the
authors].
That it is a mystery, I can see as much as the next man. That it is a quantum mystery, I
cannot. Since WPD incorporates a logical and therefore a fact-independent type of
incompatibility, hence a type of incompatibility that is given a priori, I simply see no way in
sight of how to even relate it with the quantum, which is a fact, and only given a posteriori;
and so with QM.
4. Wholeness and the Proper Logic for Complementarity

Having regarded the distinction between logical and factual incompatibility of paramount
importance for the proper understanding of QM and CTY and, most definitely, of the true
place of Duality in either of the two former, I have been systematically scanning the quantum
literature for traces of its presence in other authors. The following two accounts, which really
come close, are the best that I have been able to come up with:
Bohr believes that while it has seemed to us at the macro-level of classical physics that
the conditions were in general satisfied for the joint applicability of all classical concepts, we
have discovered this century that this is not accurate and that the conditions required for the
applicability of some classical concepts are actually incompatible with those required for the
applicability of other classical concepts. This is the burden of the doctrine (B4).
[=Complementarity] This conclusion is necessitated by the discovery of the quantum of
action and only because of its existence. It is not therefore a purely conceptual discovery that
could have been made a priori through a more critical analysis of classical concepts. It is a
discovery of the factual absence of the conditions required for the joint applicability of
certain classical concepts [Hooker, 1972, 137; italics the authors].
The distinction between the two types of incompatibility previously spoken of is certainly
presupposed in this passage. For where there is a factual absence (in italics) forbidding joint
applicability, there must also be a logical one, to which the former is implicitly contrasted.
But Hooker did not pursue the issue further. In fact, he gave it up altogether later on and,
indeed, repudiated it! [Hooker wrote to me: These remarks... lead me to be cautious about
your insistence that wave-particle duality must be abolished in Bohrs philosophy as well as
in quantum theory itself, Hooker, letter dated 15 August 1983, upon receiving a draft of my
doctoral thesis. Of course, my rejection was based on the distinction under consideration. In
subsequent communication he even questions the overall validity of the distinction. In his
letter of 18th December 1989 he tells me that regarding formal as opposed to factual
aspects of the problem at hand naturalists like me (him) cannot make a sharp distinction
between the two kinds of truth. Well, up there he has! Lets only hope first thoughts are best
thoughts].
The second passage faintly reflecting the same logical differences between CTY and
Duality, which I have been insisting upon, belongs to G.Holton: Position and momentum are
not mutually exclusive notions since both are needed to specify the state of the system. But
they are complementary in the restricted sense that they cannot both at the same time be
ascertained with arbitrary precision [...] In contrast (!), the wave-particle aspects of matter are
complementary and mutually exclusive [Holton, 1970, 1050; italics the authors].
Position and momentum are not mutually exclusive notions, that is to say, they are not
really incompatible, and so it takes a fact to make them so in a restricted sense. By
contrast, wave and particle are complementary and mutually exclusive. That is to say,
logically incompatible right from day one and, therefore, independently of the quantum
(which detail escapes Holtons attention). Hence, so far as the distinction between
incompatibilities goes, this passage is practically identical with my point. But here all affinity
stops. Holton sees no obstacle in speaking of restricted as opposed to unrestricted forms of
CTY and accommodates them both under the same broad conceptual roof. But if it makes no
difference, whether two concepts are restrictedly or unrestrictedly incompatible for being
commonly called complementary, it makes no difference either, whether two concepts are
restrictedly or unrestrictedly incompatible in the first place. So the difference is denied right
within the very reasoning which detects it. This is why, besides, this potentially shrewd
remark remains entirely idle in the work referred to [Antonopoulos, 1988].
Having designed the appropriate logical instrument for CTY, the sole available for
permitting it to relate to the quantum, I shall now proceed to its application to indicate at least
structurally what I take the logic of CTY to be. However, I will do so in purely abstract and
formal terms, perhaps too abstract and too formal at that, but such as can surely make CTY
accessible to any fellow philosophers, namely, the people I am presently addressing. Yet
staying close to at least the spirit of Bohrs words and that of QT I will still make
indivisibility the centre of my arguments. Abstraction of the sort I have in mind will involve a
slight modification of terminology. In physical terms I have spoken of CTY as presupposing a
fact-dependent type of incompatibility. Since I will now discuss purely abstract (numerical)
entities I will add the following, already implied provision. Fact-dependent incompatibility is
conditional incompatibility. Conditional, that is, on the very fact it is dependent upon. Since
all fact-dependent incompatibility is eo ipso conditional, the modification is minimal and
valid.
Consider therefore a simple equation of the form A+B=x, where all three variables, A B
and x, are to be receiving values exclusively from the field of natural numbers, i.e. positive
integers without zero. (Some say because zero is not a number. I would say because zero is
not a positive number.) Then for every value ascription to x such that x>1, it is always
possible for both the other two variables of the equation, A and B, to receive equally precise
and definite values themselves. E.g. for the ascription x=7, one can correlatively assign A=2
and B=5 in satisfaction of the equation, or any other mutually constrained values he chooses,
values the availability of which increases in direct proportion to the value assigned to x; and
decreases in comparable manner.
So then consider what happens for the limiting ascription, x=1. Now it will no longer be
possible for the other two variables, A and B, to both receive a precise and definite value.
There is now but a single value available, 1, and this latter cannot be distributed among the
two variables, A and B. It will therefore be assigned as a whole either to A or to B but not to
both. (Observe how naturally talk of wholes enters this description.) If it is assigned as a
whole to A, and this is the only way it can be assigned, then we get: A=1, B=indefinite since
zero is not a possible natural ascription. And if it is assigned as a whole to B, and this is the
only way it can be assigned, we get: B=1, A=indefinite for the same reason. Due to the
indivisibility of 1 in this particular number field, the two variables simultaneously referred to
it are thereby driven to mutual exclusion. This, I submit is (the logic of) Complementarity.
The incompatibility of simultaneous and definite value assignments for A and B is
conditional on the value assignment to x. For any value ascription x>1 A and B are
compatible. For x=1 they are not. We have not assumed an incompatibility between the
variables A and B themselves. Their incompatibility is extrinsic to their nature, not intrinsic to
it as is the case with Duality. For any value assignment x>1 it disappears as much as it will, if
we change the entire number field from that of the naturals to that of the fractional numbers,
now permitting simultaneous value assignments even in the case that x=1.(This would
correspond to a return to the classical ontology.)
Mutual exclusion is in this case ascription-dependent, fully corresponding to the fact-
dependent incompatibility required by the indivisibility of the elementary quantum, of which
1 as a natural, is presently the formal representation; that is to say, ascription-dependent and
not a priori. And, it goes without saying, it is this very possibility which allows us to link the
resulting variable incompatibility with the indivisibility of the elementary entity, to which
they are simultaneously referred and applied. The whole logic of the scheme is: Two into one
wont go. (This is a logical truth.)
Incidentally, and since there has been a fleeting reference to Einsteins demand for
quantum completeness, which is something essential to the cogency of CTY, the structure of
the foregoing model makes it perfectly clear that the disjunctive (and definite) value
ascriptions available are the best possible ones allowed by the nature of the mathematical
phenomenon at hand and, respectively, by the nature of the comparably indivisible quantum.
The fact that either value ascription is available, prior to actually ascribing any, will not go to
show that they are both assignable simultaneously.
5. The Reduction of Duality

The structure of the numerical model on the basis of which I have designed the logic
appropriate for CTY, not only for staying true to the actual words of Bohr, naming
indivisibility as the raison dtre of CTY (an exegetic requirement), but also for warranting
the possibility of even relating CTY with indivisibility, (a logical requirement), is a structure
utterly opposed to anything we can extract from WPD. A priori incompatibility cannot relate
to the world, and therefore cannot relate to whatever exists in the world, which is predicated
as indivisible; in other words, the quantum. This alone is reason enough to dismiss WPD as a
possible basis for CTY or a possible basis for anything. Having demonstrated this
unsuitability and having set the record straight on the basis of Bohrs so poorly understood
doctrines, I would consider my obligations fulfilled and my investigation concluded.
So far as Im concerned they are. But so far as Bohr is they arent. For Bohr has an
explanation for WPD, deriving it as the consequence of deeper laying realities, that is to say,
of Indivisibility. This, come to think of it, is anything but surprising and certainly anything
but incongruous. So I will stretch the limits of this enquiry somewhat further as an ultimate
test of the unity and the consistency of his thought. The aim of this last section is therefore to
indicate the relevance of Indivisibility (or Wholeness) to the emergence of WPD. I will
commence with my own version and proceed with Bohrs. Here then, in a nutshell, is my
version:
AXIOM: If an indivisible thing is successfully predicated, the predication will

embrace the entire thing. (This is an analytic truth.)
THEOREM: An indivisible thing can only manifest undivided aspects of itself.
It would then follow that alternative predications of an indivisible thing, in being

impossible to contain in their rightful place each, will embrace the indivisible thing in its
entirety, its wholeness, and hence conflict with one another in ways which would never
obtain, if this thing was subdivisible and therefore such as to allow its predications to be kept
separate, and thus distinct and combinable. Wholeness will not permit its partial
predications, which for an ordinary object could certainly be distinct and therefore
consistently attributable.
Hence, any pair of alternative, successful predications, A and B, of an indivisible entity
will successively apply to its entirety, now representing the entity as all-A, and therefore as
no-B, or as all-B, and therefore as no-A, which two, given the appropriate context, will most
certainly conflict. The appropriate context is, in this case, the Part-Whole relation, which is,
essentially, what the Axiom and Theorem, above formulated, are all about. If no parts of an
indivisible thing can ever be obtained, the would-have-been part (for any other, sub-
divisible entity) will now emerge as the whole thing instead. And then the two (holistic)
predications will have to conflict, for the would-have-been part, peacefully coexistent with
another of its kind, will now extend to the entire thing, blocking the other part out; and
conversely.
The question may arise, whether it is at all legitimate to introduce parts in the case of
indivisible things, even if permanently behind the scenes, and derive the conflict on their
implicit presence, which is precisely what Ive done. Indivisible things should have no parts,
one might point out. This is not so. It is true that something simple has to be indivisible, e.g.
the unit of my complementary model. But the converse is not likewise true; something
indivisible does not have to be simple. It may be possessed of parts, the difference being that
theyd have to be inseparable parts. Nor are we in want of concrete examples. The good old
proposition is such an indivisible, though structural whole. The properties of truth and
falsehood emerge with the entire proposition as such. They do not accompany any of the
propositional terms, when separately regarded, not even in analogy. The proposition is a
whole which, as metaphysical tradition has so correctly grasped, is greater than the sum of its
parts. So also in my argument each resulting part is greater than itself, becoming the whole.
If that is denied, no predication of an indivisible entity will ever be successful and then wed
simply have no problem in the first place.
A quick regress to several of the Bohrian passages I have quoted, and to many which I
have not, directly reveal that in his general epistemology Bohr conceives of classical
mechanics as the methodology of subdividing, analyzing and dissecting its objects. Of
course, if the objects turn out to be indivisible, rather than being themselves dissected, they
will dissect us, that is to say, the structural conceptual scheme which we habitually apply to
our objects. And will divide it in two, rendering it complementary. (My rudimentary atomic
model shows exactly how this is brought about.) Were the question to ever arise, and it has,
whether Bohr adopts any Kantian-like category of the understanding as an a priori formula
for future experience, that would surely have to be the Category of Divisibility. We can only
make sense of divisible, analyzable, dissectible phenomena. We are habitual analyzers [This
is, incidentally, Henrgy Bergsons view of the understanding as well, incapable of grasping
the duration, i.e. the wholeness of organisms and our own uninterrupted flow of
consciousness. I have already quoted one Bohrian passage to this end but there are countless
to choose from, see Antonopoulos, 1997c, where all are gathered]. Hence, when confronted
with indivisible phenomena we cannot but persist in our customary ways (a favorite
Bohrian motto) of analysis and subdivision, ways that now are bound to be frustrated.
One consequence of this practice is, of course, CTY. Our structural, i.e. composite
conceptual scheme will not be accommodated by a structureless, simple reality, symbolized
by 1 in my model. The scheme can only apply to it complementarily (Two into one wont
go); the other consequence of this practice is what else? the wave - particle duality.
Indivisible entities, when differently dissected will either retreat and become inaccessible or
else emerge by manifesting undivided aspects of themselves, which, given the conditions of
dissection currently obtaining, namely, our specific macro-inspired experiments, are the sole
permitted to be realized in the setting. To overcome dissection and stay true to their nature
atomic phenomena must make up for the severed part of their identity by replacing it, as it
were, by whatever other properties the dissecting environment allows them to manifest. So in
a dissecting A-environment they will emerge as if all-A and in a B-dissecting environment as
if all-B, which are evidently inconsistent.
Depending on the dissection or predication chosen, the indivisible thing will respond
accordingly, if it will respond at all. And will emerge transformed, manifesting properties
which it can be independently shown to not autonomously possess. The contradictions
resulting from atomic phenomena, when too closely looked at (dissected) are not original.
They are nothing but the combined result of their indivisibility and our own attempts at
subdividing them. The contradiction is not inherent in the world itself. The contradiction is of
our own making, when due to our persistent macro-habits we do to an object something
contrary to its own nature. This is what Wave-Particle Duality is all about for Bohr, if it is
anything, and, it should be stressed by the by, there is really nothing subjectivist in this
situation. The thing is indivisible, so it behaves indivisibly, so it reacts indivisibly, so it
interacts indivisibly, so it is observed indivisibly. When others see the human subject in all
this, I see nothing but an entity always staying true to its independently asserted nature (So
none of the usual, subjectivist fairy tales please! See also the next Chapter).
Bohrs way of reducing WPD to the underlying quantum wholeness is similar to mine
and is distinguished from it only in the respect of introducing indivisible interactions, when I
have found it more convenient to speak of directly indivisible entities instead. I cannot say
whether this deviation contains elements of substance in it or is just an idiosyncratic
peculiarity. Be that as it may, Bohr proceeds in his reduction by the following steps:
The finite magnitude of the quantum of action prevents altogether a sharp distinction
between the phenomenon and the agency by which it is observed [Bohr, 1934, 11].
Object-device inseparability is, as is well known, the opening stage of Bohrian
wholeness, directly connected to the indivisibility of the quantum itself. [Also Hooker, 1972,
195] Once this is laid down, the next step consists in dragging to surface the potential
consequences that such inseparability is expected to produce, when we are warned of the
impossibility of any sharp separation between the behavior of atomic objects and the
interaction with measuring instruments [Bohr, 1958, 39].
From this premise Bohr proceeds to obtain immediately below that under these
circumstances an essential element of ambiguity is involved in ascribing conventional
physical attributes to atomic objects, as is at once evident in the dilemma regarding the
corpuscular and wave properties of electrons and photons, where we have to do with
contrasting pictures, each referring to an essential aspect of empirical evidence [ibid.].
All three passages now jointly entail that such contrasting pictures emerge during
experiments because of the impossibility of separating between atomic object and measuring
instrument for the duration of the experiment. That is to say, Duality exists because
Wholeness exists first. Any denial of the proposed connection between the two, intending to
posit WPD as fundamental and irreducible in Bohrs system of interdependent axioms, must
now take its case with these revealing and restrictive passages. And also take its case with
those that follow:
<<The universal quantum of action expresses a feature of wholeness that prevents the
distinction between observation of the phenomena and independent behavior of the objects
[Bohr, 1958, 59] immediately leading to difficulties in talking about properties independent
of the conditions of observation and, in the end, to material particles producing
interference effects>> [Ibid.]. The whole conception from beginning to end is epitomized in
the following, comprehensive way:
(a) Phenomena like individual, atomic processes, due to their very nature, are essentially
determined by the interaction, between the objects in question and the measuring
instruments. [Hence]
(b) No result of an experiment concerning [such] a phenomenon can be interpreted as
giving information about independent properties of the objects but is inherently
connected with a definite situation in the description of which the measuring
instruments interacting with the objects also enter essentially. [So]
(c) This fact gives the straightforward (!) explanation of the apparent contradictions
which appear when results about atomic objects are tentatively combined into a self-
contained picture of the object [Bohr, 1958, 25-6].
What Bohr is saying, therefore, though it is clear enough to be plain to all, is roughly this:
If during an indivisible interaction atomic object and measuring instrument form an
inseparable whole, in the sense of becoming indistinguishable, then they are one thing. But if
object and instrument become one thing in a given measurement and another thing in a
different measurement, then one and the same thing will appear as different to itself as the
two measurements are to one another. This corresponds with my own alternative predications,
extending to the entirety of the atomic object whereupon, by being uneven to one another,
will compel the indivisible object, capable only of displaying undivided aspects of itself, to
appear uneven to itself. Bohr implies the exact same thing:
In the study of atomic phenomena we are presented with the situation where the
repetition of an experiment with the same arrangement may lead to different recordings, and
experiments with different arrangements may give results which at first sight seem
contradictory [Bohr, 1958, 18].
Hence, in view of all the preceding, namely, my analysis and that of Bohrs, it is simply
impossible for Duality to be anything else save a created situation. It nowhere follows from
any of the previous considerations that Duality is a foundation of the doctrine. In this vein I
would also call the readers attention to the following point. The reduction of WPD to
indivisibility was here not the inductive procedure which many suppose it to be, beginning
from collected and contradictory experimental results, and inferring therefrom that the
devices of observation must have something to do with the contradictions. This is the eternal
(and pernicious) route which takes us from Duality to wholeness between observational
results and the devices by means of which they were acquired; which reasoning essentially
continues to posit WPD as the sole physical basis behind quantum effects.
The reduction of Duality to wholeness was here furnished as a deductive process,
commencing from wholeness and advancing to the emergence of the contradictory
predications of it, where wholeness itself was taken as an independently ascertainable
property of the indivisible object, entailing the contradictions when treated in disregard of
its true nature. Whether or not we will obtain inconsistent predications thereafter depends
solely on the Theorem, that an atomic thing will only manifest undivided aspects of itself.
Psychologically, we had to see it first to become aware of it. But the logical order is strictly
one way in either derivation, mine or Bohrs. Wholeness precedes and Duality follows, which
is what a proper reduction consists of.
This, I submit, is all there is behind Bohrs account of wave-particle duality and this is its
true status in his doctrines; namely, but a second order consequence of a presupposed
wholeness and of our own attempts at subdividing it. It is therefore a derivative notion and
not a primitive axiom at all, as it has been so frequently asserted all the way to the very
present. It is, so to speak, a side product of indivisibility, not an ontological property
inherently subsisting in the things themselves, and as a side product it should be regarded
both in Bohrs philosophy and QM as such. In this light Duality is divested of any special
privilege in delivering all the other, subordinate propositions of the doctrine, least of all of
Complementarity.
There is but one such protagonist in Bohrs doctrines and its name is not wave-particle
duality at all. It has a far simpler, one-word name: Wholeness.
References
[1] Antonopoulos, C. Discontinuous Alterations of State and the Question of
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between Discontinuity and Duality. Microphysical Reality and Quantum Formalism,
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2, 1989.
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Objective Metaphysics of Complementarity. Idealistic Studies, 27, 2, 1997.
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1, 1999.
[10] Antonopoulos, C. Reciprocity, Complementarity and Minimal Action. Annales de la
Fondation Louis de Broglie, 29, 3, 2004.
[11] Antonopoulos C. Investigating Incompatibility: How to Reconcile Complementarity
with EPR. Annales de la Fondation Louis de Broglie, 30, 1, 2005.
[12] Bohr, N. Atomic Theory and the Description of Nature. Cambridge University Press,
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[14] Bohr, N. Essays 1958-62 on Atomic Physics and Human Knowledge. R.Clay & Co,
Suffolk 1963.
[15] Born, M. The Restless Universe. Dover Publications, New York 1951.
[16] Born, M. Physics in My Generation. Springer&Verlag, New York 1969.
[17] Einstein, A., Podoslky, B., Rosen, N. Can Quantum Mechanical Description of
Physical Reality Be Consired Complete?. Physical Review, 45, May 1935.
[18] Favreholdt, D. Niels Bohr and Realism. Niels Bohr and Contemporary Philosophy,
Faye, J. & Folse, H. eds., Kluwer, Dordrecht 1994.
[19] Feynman, R., Leighton, R., Sands, M. The Feynman Lectures on Physics. Addison-
Wesley, California 1965.
[20] Feyerabend, P.K. Complementarity. Proceedings of the Aristotelian Society,
supplementary vol. xxxii, 1958.
[21] Folse, H. The Philosophy of Niels Bohr. North Holland, Amsterdam 1985.
[22] Folse, H. Bohrs Framework of Complementarity and the Realism Debate. Niels Bohr
and Contemporary Philosophy, Faye, J., Folse, H., eds. Kluwer, Dordrecht, 1994.
[23] Grnbaum, A. Complementarity in Quantum Physics and its Philosophical
Generalization. The Journal of Philosophy, lvi 23, 1957.
[24] Holton, G. The Roots of Complementarity. Daedalus, 99, 1970.
[25] Honner, J. Description and Deconstruction: Niels Bohr and Modern Philosophy. Niels
Bohr and Contemporary Philosophy, 1994.
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Paradoxes, University of Pittsburgh Press, 1972.
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supplementary vol., xxxii, 1958.
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[31] Plotnitsky, A. Complementarity. London 1994.
Chapter 3
COMPLEMENTARITY OUT OF CONTEXT:

ESSAY ON THE RATIONALITY OF BOHRS THOUGHT
Constantin Antonopoulos*
Department of Applied Mathematics and Physics
National Technological University of Athens,
28 Oktovriou (Patision) 42,10682 Athens, Greece
Abstract
It has been suggested by several people that Bohrs Complementarity (CTY) is a form of
context-dependence. In defense of the realism and objectivism of Bohrs doctrine, I provide
the following refutations: A. Position and momentum are not the same word in different
contexts. They are different words in the same context, = a single instance of motion. Hence,
are complementary in a single context rather than so across two. This refutes a contextualist
reading of CTY. B. CTY does not resemble Kuhnian paradigms, unless it is identified with
Duality. But the incompatibility between waves and particles is self-sufficient, hence such that
makes the quantum redundant. Hence CTY, which is dependent on the quantum, is unlike
Duality; hence unlike paradigms. C. The foundation of CTY is shown to be Indivisibility, that
is to say, Atomism. An atomic singularity, thus conceived, splits in two and renders
complementary a pair of classical concepts, E with t and p with q, on the basis of the analytic
truth that two into one wont go, except of course complementarily. For this kind of
singularity Bohr is shown to speak as a realist. He says it in principleresists an
analysis, implying that we try and fail. The failure however is due to the thing, not to the
analysis. Bohr is therefore a metaphysical realist and, as an atomist, a metaphysical realist
twice over.
1. Complementarity Contextualized
The view that Bohr is a nonrealist, due mainly to the ideas of older physicists
inadequately instructed in matters philosophical, has recently dropped out of fashion. It was a
deserving fate but there are still some pockets of fierce resistance left in this country [see
*
E-mail address: antonopoulos9@msn.com
Note 1] and abroad. The roles have slightly changed, however. Bohr is no longer labeled as
an out and out idealist. He is now depicted as a contextualist, hence still a nonrealist. One
version of the point is delivered by his grandson, Christian:
In order to prepare for my comparison between Complementarism and Anti-Realism let
me attempt an Anti-Realists approach to these problems: According to Post-Tractatus
Wittgenstein, problems (philosophical problems, it is) in principle arise because of the rules
of language usage being violated. In the case of mans free will the problem is that it
dependent (roughly) on whether we look into our selves or study other beingsseems
consistent with experience to assume both that we do have, and that we dont have a free will;
with the two contentions being of course mutually inconsistent. And the cure for this
apparent inconsistency is the understanding that we though using the same word, scil. will,
still are not using it with the same meaning, because we have changed the context. [...] Now
lets see how the same problems are attacked with Bohrs complementarity analysis. A case
for complementarity arises, if I understand Bohr correctly, when our use of two (or more)
words, vocables, terms, etc., involves us in inconsistencies and ambiguities, because these
words, though intimately related in ordinary usage, as a consequence of the different
conditions for their use actually belong in different contexts. [Chr. Bohr, correspondence,
received 18 April 97. All italics mine. Other than that, the authors text is quoted unchanged.]
This, therefore, is an identification of CTY with context-dependence spreading, as it
seems, throughout the entire conceptual matrix. But it is anything but a solitary proposal; not
by any means. For that matter, it stands in the company of a good deal of influential names in
the issue at hand, past and present, such as those of N.R. Hanson, P.K. Feyerabend, Th.Kuhn
(as interpreted by others, however; cf. C.Glymour), Gonzalo Munevar (editor of the Kluwer
volume dedicated to Feyerabend [see Note 2]), and last (in my list, at least) C.Glymour
himself [see Note 3]. Nor would I ever venture to launch an attack against contextual CTY
drawing merely from the limited confines of my personal correspondence with Chr. Bohr,
however close to the man himself he might otherwise have been, without cross referring it
with available literature.
From the list of complementarian contextualists above offered I would only wish to
exempt a single name as a potential target of my criticisms that of N.R.Hanson. I have always
interpreted Hanson far more realistically than most and probably far more than Hanson
himself intended. I have, in fact, received Hansons transitoryand expendable quantum
quasi-contextualism as but a more elaborate, semantic version of underlying realities, which
to me have always signaled a deep going macro-micro domain dualism; this is a view which I
myself espouse and which Bohr also had. Hansons Patterns of Discovery may abound with
(seemingly) contextualist talk, but one that is not particularly difficult to de-contextualize:
Classical mechanics as a whole is said to be but a special case of quantum mechanics. They
are apparently clusters of statements in the same language. Statements and languages
however do not work in this way [Hanson, 1961, 151]. Finite and transfinite arithmetic,
Euclidean and non-Euclidean geometries, the language of time and the language of space,
the language of mind and the language of body, these show themselves to be different and
discontinuous on just this principle: What can be meaningfully said in one case may express
nothing intelligible in the other [Op.cit., 152].
I myself entertain not the slightest doubt, as neither does he, that the rift between
quantum and macro phenomena is only evaded by the mathematical scheme, in other words
by the quantitative cover up, convenienced by the numerical convergence of classical and
Complementarity Out of Context 43
quantum laws in the case of large numbers, a technique, on the whole, especially designed to
patch up the irreducible qualitative discrepancies between the two classes of events. But my
own reaction is, in due accordance, that the asymptotic nature of the two languages results
from the nature of the phenomena themselves and is to that extent only derivative. It is the
phenomena that manifest the primordial discrepancy; not the languages, which but follow.
The fact that physicists are professionally inclined to nourish dreams of integration and
unification of the micro with the macro within some grand comprehensive scheme or other is
no evidence of the essential, besides the numerical, continuity between the two realms.
Hooker describes this (classical) presupposition, coming natural to Einsteinians, with the
following words: All complex objects consist of definite structures of the fundamental
elements which are their constituents [Hooker, 1972, 70.]. Where, Hooker notes, it is the
word definite which carries the primary ontological weight. But this untroubled assumption
can be shown to falter even within a mathematical frame, provided it is suitably devised.
Here, then, is the frame in question, manifesting by analogywithin the confines of a single
rudimentary model all the requisite properties, starting from atomicity upwards and all the
way to CTY, the quantum uncertainties (UR hereafter), Bohrian holism as such and the
micro-macro dualism previously referred to plus, as a bonus, the completeness of the
quantum mechanical description of micro phenomena, a consequence of course of the
repeatedly noted micro-macro dualism.
Consider an elementary equation of the form A+B=x, where all variables, A, B and x are
to receive values exclusively from the field of naturals (for obvious reasons), that is to say, of
positive integers, not including zero. (Some say because zero is not a number. I would say
because zero is not a positive number.) Once the previous condition is posited, then what
follows is that for any value ascription to x, ranging from 2 to infinity, we shall at all times be
capable of assigning definite and simultaneous bound values to variables A and B. But for the
unique value ascription, x=1, this is no longer possible. For x=1 and therefore for A+B=1, we
can either ascribe the entire, non-distributive value, 1, to A, whereupon A=1 and
B=indeterminate or, conversely, ascribe it to B, whereupon, B=1 and A=indeterminate. (Zero
is not a permissible value ascription.)
This, I will argue in the appropriate places, is Bohrs doctrine of wholeness. In my
numerical model the wholeness is that of 1 as the smallest natural in existence; the atom at the
basis of the natural sequence. This wholeness takes us almost immediately to the mutual
exclusion imported within the components of the schema |A+B|, because the schema itself is
structural, whereas 1 in this field is simple and devoid of structure and cannot be divided in
consistency with the premises of the argument. We shall later on see Bohr referring to
phenomena comparable to 1 as a natural, when aiming at defending the completeness of the
complementary description, by stressing that they in principle resist such an analysis;
which is a realist, and a dualist, thesis, for if atomic phenomena resist analysis, as macro
objects do not, both classes of phenomena turn out to behave exactly as independently
predicated; which is much closer to hard core realism, than to any other option, because
reality behaves as independently predicated.
But the rift between macro and micro, in the frame of the model the dualism between x=1
or x>1, is none the less irreducible, and in this case even mathematically irreducible, though
to no noticeable hindrance to a realist account of the situation. If S can be used to express an
intelligible statement in one context, says Hanson, but not in another, it would be natural to
conclude that the languages involved in these different contexts were different and
discontinuous [Hanson, 1961, 151]. What is unnatural, however, is to conclude that therefore
the linguistic phenomenon is thereby elemental and primitive, with no traceable ontological
roots to anchor it upon. Mutual exclusion of value ascriptions in this model results from
alternating conceptions of reality: x>1 or x= 1, the macro (=sub-divisible) and the atomic,
respectively. And atomicity is a predicate of reality, not of complementary languages. Bohr
is pretty clear about this: The fundamental postulate of the indivisibility of the quantum of
action forces us to adopt a mode of description designated as complementary in the sense that
any given application of classical concepts precludes the simultaneous use of other classical
concepts which in a different connection are equally necessary for the elucidation of the
phenomena [Bohr, 1934, 10].
And, I take it, the quantum of action is a property of the world. Not the property of a
language, whatever that might come to mean in this weird connection and however such a
language might have then been adopted. Bohr himself has no particular qualms, concerning
how this language is adopted. It is forced upon us by the restrictions of reality, that is to say,
indivisibility, affecting the current operation of our descriptions.
My own numerical model of CTY reflects just this sort of dependence. The mutual
exclusion between the related variables, A and B, in the context of my model results from the
predication of atomicity to 1 and this predication is independent of the schema |A+B| per se,
which latter is the language. There is nowhere discernible within the confines of the
schema, that it must needs receive values from the field of naturals and at exclusion of other
possibilities. It could just as well receive values from the fractionals, depending on what
universe of discourse we are after representing, and then no mutual exclusion of simultaneous
and definite value ascriptions would ever come up.
The provision that the values be drawn from the naturals is extrinsic to the schema. And
is therefore the foundation for its subsequent complementary reaction, when the limiting case
x=1 commands it. ...=1 is not a vocable in any coherent sense here, as Bohr the grandson
has suggested to me. [C. Bohr, April 97.]. It is the schema A+B that is if anything has to be.
And ...=1 is what forces us, to use Bohrs own words, to adopt a mode of account
designated as complementary. A and B in themselves considered are nothing of the sort. Just
try x=2, 3, 4 or any other natural up to infinity. A and B will never enter a relation of mutual
exclusion, because A and B are not mutually exclusive to one another and independently of
selected assignments. They are rendered so for the specific and unique- ascription x=1. But
otherwise are cosatisfiable. |A+B| can handle all the cases except the simple. The quantum is
not just a miniature of the macro. To this extent, therefore, Hanson is right: How can
intelligible empirical assertions become unintelligible just because quantum numbers get
smaller? Conversely, how can unintelligible clusters of symbols become meaningful just
because quantum numbers get larger? [Op.cit. 152].
Well, how can A+B>1 yield coherent answers but A+B=1 not? They do because they
refer to incompatibly predicated aspects of reality; aspects which, as I am at pains to stress,
are both there. The atomic and the macro. It is not that the meaning of the variables, A or B,
has changed or even that the meaning of the entire schema |A+B| as a whole has, now being
intelligible now unintelligible. It is that the conditions of its application to reality have
changed, those being now atomic, now divisible; hence, now jointly, now disjunctively
permitting definite value ascriptions. |A+B| responds to their alternation without changing its
meaning. It just responds to them by rearranging its conditions of internal relatability; which
is what CTY is all about.
Were we to suppose any different, mutual exclusion itself would be jeopardized or falsely
attributed; to postulate a change of meaning in the schema |A+B| as we alternate between x=1
and x>1 value assignments is exactly the same as postulating that, if books A and B cannot fit
together within a drawer of a size smaller than their sum of surfaces, they have eo ipso
changed their shape! And this is patently absurd. Not just because this supposition is
evidently false, as it clearly is. But because it is even compatible with the supposition that, in
having changed their shapes thus, the books could now very possibly fit in the said drawer.
And this is surely contradictory to the assumption. The books are no different. The drawer is.
Similarly, the self identity of the schema |A+B| stays rigid across whatever number field we
might consider, natural or fractional.
|A+B| can receive values either from the field of naturals or the field of fractionals. Yet
its internal identity stays rigid across its transfer from one field to the other. The only
transformation apparent, comes with the limiting ascription x=1 in the field of the naturals.
And this ascription introduces a dichotomy not between the two number fields, as it were, but
one within the self same number field instead, that of the naturals alone. Which latter, I would
suppose, should feature here as a single context. Perhaps complementarian contextualists
could explain to us how, in this case, |A+B| manifests properties of mutual exclusion in a
single context, that of the naturals for x=1, and no such thing when |A+B| travels across one
number field to another, for any natural ascription x>1. Concepts which behave
complementarily in a single context for the ascription x=1, still behave identically across two
distinct contexts, the naturals as opposed to the fractionals, for any natural value ascription
greater than 1. Hence, mutual exclusion is due to a factor other than change of context. But
not other than the ascription x=1 of a context.
I submit therefore that Hansons view above quoted is dualistic and realistic. The un-
intelligibility, as quantum numbers get smaller, results from not having any more numbers at
our disposal. Reality itself is running out on us. Until, for x=1, the tank is empty. And the
intelligibility is restored, as quantum numbers get larger, because now we have as many of
them as we care to count up to. The monads [=1] have no windows, Leibniz warns us
[Monadology, prop.7] But the rest of things open theirs to us. What Hanson understandably
refers to as fluctuations of intelligibility are essentially fluctuations of available reality.
Whatever happens to our concepts thereafter is purely conditional on just how much reality
there is. This is a contextual account of Bohrs correspondence principle and, by extension,
of his CTY, that I can quite comfortably live with. Other such, I certainly cannot; Time then
to rebut them.
2. Complementarity: A Stumbling Block on the Way to Context

C. Bohr began his contextualist narrative of CTY by briefly mentioning the word will
as potentially emerging in distinct, hence uncommunicating, contexts, pointing to
Wittgenstein as the ultimate source for this suspicion [see Note 4]. I will briefly indicate my
initial reply, for isolating whatever elements will be requisite for the quantum integration of
the point. First, let me remind to all concerned, the exact position of context-dependence: The
meaning of the same word differs in different contexts. Now then; either freecaused or
mindbody are pairs of words semantically connected or else words not semantically
connected. Suppose first they are not connected. Then they are simply two different words,
signifying two different concepts. Then they will trivially not have the same meaning, since
they are different words to begin with. And this rules out all contextual treatment ex
hypothesi. So suppose they are semantically connected instead, as they clearly seem to be.
But then this semantic connection of theirs can be none other than their very opposition.
For if free is just taken to mean not caused, and mental to mean not bodily, and
vice versa, i.e. the only provision at our disposal for semantically connecting the two pairs of
words (otherwise we fall back to the previous horn: different words), then, unless Im horribly
mistaken, such pairs of terms have now been turned into straightforward contradictories. And
contradictory descriptions must have a unique reference, if to be at all contradictory. If you
say this car is moving and I say this car is at rest but point at different cars, we are
certainly not disagreeing. Again there is no profit of sorts for the contextualist here. In fact,
my former impasse still persists. Either these pairs of concepts are unconnected, whereupon
their difference in meaning is semantically trivial and not susceptible to a contextualist
analysis, or else they are connected, but are then contradictories and hence such, as
designating and belonging to a unique context, antithetically predicated; The context being, a
single act.
Now to quantum CTY; the contextualist motto is still what it always has been (or is it?);
Different meanings (in different contexts) of the same word. But the quantum or, for that
matter, the classical terms position and momentum are certainly not the same word. They
are two different words. Why should we ever expect a meaning variance between words
which are different in any case, and which C.Glymour somewhat (self) forgetfully conflates?
Meaning holism has the consequence that if beliefs about a collection of sentences
change, so do the meanings of the terms of the sentences. This phenomenon is sometimes
called meaning variance [Glymour, 1992, 124, the authors italics]. Then, extending this to p
and q, which should normally be elements of a single collection, he concludes: Just as no
world of experience combines different conceptual schemes, no reality we can experience,
even indirectly through our experiments, combines precise position and precise momentum.
[Glymour, 1992, 128, my italics].
Just as...? Just as what? When we speak of meaning variance, what exactly is it, which
the variance is a variance of? A different word? A different word does not yield variance of
meaning, in the sense here demanded. It just yields a difference of meaning because it is a
different word; period. And so far as I can see momentum and position are different words of
a collection. Not the same word in two collections. For although, perhaps, different
conceptual schemes are not combinable, on whose authority are momentum and position
elements of different conceptual schemes? Are they not, then, constituents of a single
phenomenon of motion? Classically, the velocity, U, is given by U= ds/dt, where ds in the
limiting case is position, derived by means of velocity and, indeed, conversely, since velocity
is itself a derivative of position. To compare these two with different conceptual schemes is,
in a word, nonsensical. As constituents of a single phenomenon of motion, they evidently
belong to the same context. Motion is change of position in time, as H.Folse puts it
concisely [Folse, 1985, 57]. This, if it is evidence of anything, is evidence that they belong,
by definition, to one and the same context. And if the mutual determinations of position and
momentum get in each others way at all in QM, this is because they belong to the same
context in the first place. For were they unrelated instead, their determinations would be
independent of one another and hence attained in combinable separation (see below), in utter
contrast to Glymours different conceptual schemes.
This situation, though it does lead directly to their CTY, rather than leading to their
claimed context dependence at the same time, obeys instead laws of logic and semantics
which are the very negation of Glymours analogy. Let us consider mass and position
instead. Mass is a concept definable in contexts differing, or even unrelated, to contexts
appropriate for defining position. The two of them are, for that matter, as distinct,
unconnected and divergent as we care to imagine. The question of where an object is, is the
last question relevantly entering issues of specifying its contained quantity of matter (or
inertia). The two of them belong, one is entitled to declare, to totally alien contexts.
Then, perhaps, C.Glymour would care to enlighten us just how it happens that, wide
disparateness of context notwithstanding, position and mass are still not complementary
quantities in QM! And how, instead, position and momentum, which are clearly constituents
of a single phenomenon of motion, and are therefore closely bound to one another within the
confines of a single context instead, do happen to so be. Well, to me the answer is simple.
CTY has nothing to do with context dependence and, I venture to propose, a lot to do with
context independence. A question, then, for some people at Pittsburgh University: How can
two contextually unrelated concepts be compatible, and definable with arbitrary precision,
while two contextually connected ones, and both immersed within a single context, motion,
be complementary?
If I have done my quantum homework, as some contextualists no doubt also should, it is
actually because position and mass are thus unrelated, that they are thereby jointly, rather
than disjunctively, definable within the frame of the theory. Because, in other words, their
mutual determinations are effectively isolatable, never interfering in any form with one
another. Hence, position and mass are both known and they are both known simply because
they have nothing at all in common. Their contextual diversity is not their CTY. It is their
compatibility. On the contrary, position and momentum cannot both be known because,
unluckily, they have a lot in common. Their contextual identity is their CTY. Its not
therefore as if CTY is a tacit form of context-dependence or, even, vice versa. If anything, to
call a pair of concepts complementary, in Bohrs sense, is to call these concepts context
insensitive. Which is a point going beyond the confines of the present approach, and
generalizable over all relevant cases. The very notion of CTY rules out contextdependence.
Complementarian contextualists have got the truths all backwards; again.
3. The Duality Route to Context

Gonzalo Munevar and P.K.Feyrabend have developed between themselves a parallel
version of subjecting complementary relationships to contextdependence. This, Munevar
explains, was on Feyerabends incitation. [Munevar, 1995,6.] Well, surely that wont make
things better for either of them! Here the scheme of things, unlike the cautious formulation
earlier preferred by Chr. Bohr, assumes all the features of grandiose ambition, reaching to
giddy heights when, together with complementary conceptual schemes of different cultures,
we are announced of complementary conceptual schemes between humans and bats!
[Munevar, 1995, 6-8.] The term CTY here mainly serves the purpose of stressing the
equality in epistemic status of the disjunctive world accounts. Possibly, even, the equal
epistemic status between human and bat cognition: <<The views of the world produced by
different frames may thus be complementary in a sense akin to Bohrs. It is possible, then, to
produce information in one frame that is not logically, conceptually, theoretically, or

mathematically equivalent to any produced in another, even if it is presumably about the same
aspect of reality>> [Munevar, 1995, 6; italics the authors.].
This, I would imagine, is a big step away from momentum-position or energy-time CTY.
We no longer have to do with CTIES established between concepts collectively belonging to
a certain conceptual scheme and rift apart by indivisibility, or do with indivisibility itself for
that matter. Rather than dealing with disjunctiveness between concepts constitutive of a
conceptual scheme, such as the products Et and pq formerly of classical mechanics, we are
now dealing with one conceptual scheme disjunctive to another. Whence, of course, the
irresistible temptation on the authors part to involve Kuhnian Paradigms in the discussion,
not an uncommon supposition in the matter at hand, as we shall soon see, though at least one
wished that he wouldnt have to drag bat cognition together with them just to drive the
point home [Munevar, 1995, 6].
The analogy supporting all this, or in any case what Munevar takes an analogy to be, is to
be located, he claims, to quantum experiments disclosing corpuscular and/or undulatory
properties of micro-systems: As Bohr pointed out, one experimental arrangement that
enables us to see the electron behave as a wave complements, but also rules out, another
arrangement that enables us to see the electron behave as a particle. The wave and the
particle descriptions are thus complementary there is no sense in which they are equivalent.
The same may obtain between descriptions produced in different frames [Munevar, 1995, 6;
the italicized words directly connect CTY with context].
So there is really no escape, is there? After ninety years of complementary theorizing and
still Bohrian scholars, methodic or perfunctory, aficionado or free lance, subtle or populist,
exhaust what little imagination they can muster, to take us back to the CTY of waves and
particles. Contextualists regard themselves as avant guarde progressivists in life, art, politics,
and philosophy as well as in science. But on this matter they just never learn; from
Feyerabends early formulation of the thesis, CTY is a description based on duality
[Feyerabend, 1958, 94], repeated a few years later (...duality as well as the idea of CTY
based upon it. [Feyerabend, 1962, 223]), we proceed to more recent times with an
occasional, but not too decisive, and always back stepping, improvement: <<It is clear that in
his original statement of Bohrs new viewpoint, the complementary relationship holds
between space-time coordination and the claim of causality, both of which were combined
in the classical framework. Only later doesBohr speak of CTY between wave and particle
pictures>> [Folse, 1985, 114].
Well, close enough. But back steps are, it seems, the rule in the pathway to CTY. Thus,
even more recently we are once again assured that CTY is introduced by Bohr in response to
the wave-particle duality, which becomes wave-particle complementarity in his framework
[Plotnitsky, 1994, 68]. The message transmitted has now become all the more ominous for the
handful of objectivist complementarists still in life (counting Folse and myself) and the even
fewer rationalist ones (just counting myself, presumably). According to this author wave-
particle CTY is, thus, defined in anti-epistemological terms [ibid.] and hence serves almost
as the scientific Trojan horse that throws the gates wide to contemporary French
obscurantism, Derrida, deconstructionism and a curtailed version of Hegelian dialectics, from
which last French philosophy simply finds it impossible to emancipate itself, the author
included, it would seem.
Bohr, surely, has on occasion spoken of wave-particle CTY, though mostly as a rather
degenerate instance of the concept and, chiefly, as a derivative situation in QM, rather than as
the primitive axiom which these authors take it to be. But, and thats what matters, he has also
spoken very differently: The term Complementarity, which is already coming into use,
may be suited to remind us of the fact that it is the combination of features which are united
in the classical mode of description but appear separated in the quantum theory [Bohr, 1934,
19].
But it is not waves and particles which are united in the classical mode of description and
separated in the quantum. It is the conjugated classical concepts, whose products, Et and pq,
yield a unit of action. To say nothing of the fact that, on the very words of most
complementarists of the persuasion in question, wave and particle are just about united in
the quantum mode, besides being separated in the classical and, I would add, everywhere else
as well. Once again contextualists have got the truth backwards.
There has been, I strongly suspect, too much casual reading of Bohrs text and too much
poor logic involved. Let me then demonstrate, and I mean demonstrate, not just indicate,
suggest or argue, why wave-particle duality literally cannot be an instance, let alone the basis
for CTY. The first step I will take hand in hand with Hookers account: Bohr believes that
while it has seemed to us at the macro level of classical physics that the conditions were in
general satisfied for the joint [see Note 5] applicability of all classical concepts, we have
discovered this century that this is not accurate and that the conditions required for the
applicability of some classical concepts are actually incompatible with those required for
the applicability of other classical concepts. This is the burden of the doctrine (B4) [Doctrine
(B4)=CTY]. This conclusion is necessitated by the discovery of the quantum of action and
only because of its existence. [...] It is a discovery of the factual absence of the conditions
required for the joint applicability of certain classical concepts [Hooker, 1972, 137; dark
letters for the authors italics].
In a word, CTY and its quantitative expression by the two UR is conditional on the
quantum. (As if it could ever be otherwise.) Precisely as the mutual exclusion of the two
variables of my own complementary model, A and B, is conditional on whether the value
ascription is x=1 or x>2 &c. And this entails a conditional form of incompatibility;
Conditional, in this case, on the quantum of action itself.
But the incompatibility of waves and particles is not conditional on anything. Waves
(large) and particles (small) are incompatible by definition and hence incompatible in the
ways of logic. That is to say, necessarily incompatible. This is why, besides, it is called a
duality in the first place. And in being necessarily rather than conditionally
incompatible, waves and particles are also incompatible in classical mechanics. And classical
mechanics does not contain the quantum. Stated in the simplest of terms, waves and particles
are mutually exclusive without any help from the quantum.
Were CTY to be grounded on the incompatibility afforded us by the wave and the
particle, CTY would equally have no need of the quantum. This sort of incompatibility is self
contained and obtains independently of the quantum. So then would a CTY based upon it, in
direct contradiction with the premises of the argument. Waveparticle duality, rather than
being the basis of CTY and/or the UR, is in actual fact a situation yielding exactly the sort of
incompatibility which renders the quantum redundant. And this is patently absurd. Duality, I
submit, yields the wrong sort of incompatibility. Let me rephrase this. The wrong sort, if there
ever was one. Duality is an unmanageable idea and the sooner one gets rid of it altogether, the
better for CTY. In more recent years this is beginning to tentatively dawn upon
commentators, at long last: The connection between wave-particle dualism and the
complementarity of the dynamic and the kinematic properties remains a problematic issue for
the analysis of Bohrs philosophy and for the interpretation of QM [Faye & Folse,
Editoditorial, 1994, xvi].
So then does, to put it mildly, the ambitious plan of associating CTY with context
dependence. If Duality was retained, together with its correlative subjectivism (see Munevars
account earlier cited) the task would have looked more promising. If, that is, we incorrigibly
stick to the old ways, always known to die hard, and continue to identify CTY with the
technique, applicable to all domains of experience, where the phenomena depend on the
conditions on which they appear [Petersen, 1968, 242] this would (albeit still erratically)
suggest a plausible similarity with Kuhnian Paradigms, capable, if their author is to be
believed, of making us see things because we have been operating within this Paradigm,
while other researchers, operating within the confines of a different Paradigm, would literally
see different things, because secluded in that other Paradigm [Kuhn, 1970, 110ff.]. Either
way, the complementary or the paradigmatic, the phenomena experienced would intrinsically
depend on the conditions of their observation, either as wave and particle properties,
depending on the experimental design chosen but arising from a unique referent, or as non-
communicating, incommensurable and Paradigm-dependent visions of a per se inaccessible
referent (as in Munevars account). If there is a temptation at all, to the task of tracing down
parallelisms between CTY and context-dependence, this is it: namely, Duality. This is the
sole (good) reason behind the intended comparison. Thus: <<What properties the world
exhibits depends on what we ask of it. Niels Bohr called this phenomenon
complementarity. [...] Changing the experiments we conduct is like changing conceptual
schemes or paradigms: we experience a different world>> [Glymour, 1992, 127-28].
This is really most regrettable, when affirmed by so many. That what the world exhibits
may have something to do with what we ask of it, is, so far as I can see, at best a necessary
condition for the answers we receive. Not a sufficient one. Were it not so, why pray, do we
get Complementarity of the classical concepts in the first place, right when we were all so
complacently confident beforehand that, asking in the way we had, we would get their
compatibility instead? My own answer [1987] is quite simple: We do, because the world
refuses to comply with our preferred conceptual instructions and goes its own way. And if
thats not evidence for realism, then I recommend to the authors above to rethink their
thoughts on this as carefully as I promise to do mine.
But none of this is really necessary. Once Duality is stripped bare of its pretenses, namely
that it matches the logical structure of CTY, when it cannot even coherently relate to the
quantum, then I suspect that not even contextualists will be all that eager to assimilate such
incoherence in their scheme of things. But when it comes to contextualists, one should never
be too sure.
4. Incommensurability: Last Resortand Last Exit

Feyrabend claims that: The combination of duality with the second set of empirical
premises introduced (the Einstein-de Broglie relations) shows that the duality [see Note 6]
between the wave and the particle properties of matter may also be interpreted as a duality
between two sets of variables, e.g. position and momentum [Feyerabend, 1962, 225].
Well, if this is so, I suppose I just have to repeat for positions and momentum what just a
few pages ago I said for waves and particles. The incompatibility between waves and
particles is self-sufficient and has no need of the quantum. In consequence, if the
incompatibility between position and momentum mirrors the former, as Feyerabend asserts, it
will likewise have no need of the quantum. Some interpretation of pqh this is; one that
derives pqh without the quantum; Now to further disasters.
Consider the following argument: (a) Position and momentum are either incompatible by
virtue of Logic, or, (b), not incompatible by virtue of Logic. Suppose first that (a). Then, if
position and momentum are incompatible by virtue of Logic, just as Duality also is, they must
be incompatible across the board. But then they must be incompatible even in classical
mechanics. And then QM and Cl.M. would not be incommensurable at all, for they would
both manifest the same type of incompatibility between position and momentum, now
holding across theories. (As Zeno was the first to contend!)
Suppose then that (b). Position and momentum are not incompatible by virtue of Logic.
Then they must be incompatible due to specific conditions, obtaining in QM but not also in
Cl.M. But then their incompatibility in QM is due to reasons other than their meaning.
Consequently, position and momentum have not changed their meanings in QM. Therefore
QM and Cl.M are not incommensurable theories, despite their evident contrast in all else.
Thus, both exhaustive alternatives refute contextdependence.
But they do not refute Complementarity. In fact, they confirm it down to its last letter.
The combination of features which are united in the classical mode of description but appear
separated in the quantum theory, is what we have witnessed Bohr demand in [1934, 19] for
the establishment of a complementary relationship. And if the classical concepts are merely
factually [see Note 7] incompatible in QM due, of course to the premise that h>0, which
could have gone the other way but compatible otherwise, hence compatible also in CM, then
the classical concepts behave exactly as Bohrs definition of CTY prescribes in both the
theories considered. But they behave contrary to what context- dependence prescribes for
both theories considered, for when separated in QM by a premise extrinsic to their root core
meaning, they eo ipso enter a relation of incompatibility without a change of their meanings,
even though now, qua incompatible (NB: factually), they operate in a different physical
theory. Hence, though QM and CM are certainly different physical theories due to this, they
are anything but incommensurable.
Hence, there is no such thing as context-dependence, entailing the incommensurability
between CM and QM, and if there is none such in their case, there is none such anywhere at
all, the quantum revolution being the strongest case ever for conceptual revolution. I have
begun intent on freeing CTY from the unappealing clutches of context-dependence. What this
has resulted down to, however, is a refutation of context-dependence per se. In my impasse to
Feyerabend and contextualism, above, the alternatives logical or factual incompatibility is
exhaustive. There is no middle type of incompatibility. And the concepts themselves, which
are thereby involved, simply manage to preserve their semantic core, whether we treat them
as logically or as factually incompatible instead. For if the former, CM and QM are thereby
united. And there would then be no incommensurability; And if the latter, then only
extrinsically incompatible, whereupon CM and QM would be different theories, as they
clearly are via the said incompatibility, but still different without incommensurability.
Either-or therefore, contextualism is rebutted per se. Consider this a bonus of the point,
rather than a side effect.
5. The Concept of Action Quantization

In view of the mistakes and confusions thus far listed, it is crucial to get our primary as-
sumptions right, before we ever embark on the issue of what CTY actually is. So it is
essential to start building from rock bottom upwards. Olivier Darrigol writes: <<Einsteins
form of the quantum condition fitted well with de Broglies idea that action played the role of
a phase. Langevin called the action variables the cyclic periods of the action integral. This
denomination implied that Langevin regarded action as a periodic function>> [Darrigol,
1993, 330].
The meaning of this most illuminating account is that in QM the least possible exem-
plification of a dynamical quantity, E or p, can only be recorded over a period; a wave period.
If this period is expressed in terms of the frequency, , we obtain E=h and so Et=h. If it is
expressed in terms of the wavelength, , we obtain p=h/ and so p=h, as two alternative
expressions of minimal action, h.
The idea, stated in more precise terms discloses that the basic quantum relation, E=h or
E, signifies that E, exactly like , can no longer be defined at an instant dt0, as was
classically assumed, but only over a period t>0, whose boundary instants {t1,t2} are here
given by the frequency of this period, . Correspondingly, p also cannot be determined at a
point location, dq0, but only over a distance, whose boundary points {q1q2}are given by
the wavelength of this period, .
It is because E cannot be defined at an instant dt0, but can only be mapped over a
period, that the resulting product of action Et is not arbitrarily reducible to a diminishing
value, Et0, but can only be determined over a limiting period t>0, that it is rendered a
quantum of action, h, instead. Clearly, in the case that E could be recorded at an instant,
taking that instant as narrow as we might wish, leading to a t0, the product Et would be a
vanishing quantity and no quantum of action would result.
But since a t={t1,t2}>0 as opposed to a t0 is a time latitude, and q={q1q2}>0 a place
latitude as opposed to a q0, it immediately follows that the dynamical quantities E and p
cannot be defined within an arbitrarily narrow space-time interval, as was classically
assumed, but only over such limiting space-time latitudes, in other words only within
accuracies not smaller than periods, instead of instants, and not smaller than distances, instead
of points. Hence, E can only be defined over a t and p only over a q. The quantum
uncertainties already announce themselves in the mere unpacking of the concept of quantized
action. So let us proceed to derive them. [See also Appendix.]
Eth: If there is such a thing as a shortest time permissible, i.e. a time limit, imposed
on the conditions warranting the very manifestation of E, this being a time limit of
dimensions t={t1t2}or , then any subsequent narrowing of this interval, of the order, say,
t'={t1t2}/2 can only mean that the overall energy determination will only be reciprocally
affected and, therefore, reciprocally inaccurate. For if we require at least a time length of
dimensions t, if we are to determine the energy with an accuracy E=n, where n is
sufficiently small to stand for a high E approximation, then, all other conditions being
identical, at half the time formerly allowed, i.e. within t/2, we can only expect to end up
with an uncertainty E=2n if the action product itself, of which E and t are the components, is
to always remain constant, i.e. h. And so on, reciprocally, for any other diminution.
In other words, if energy can never be defined within an instant t0, and hence is on-ly
to be defined over the boundaries {t1,t2}=t, as is dictated by the assumption that the action
unit which is the product of components E and t is to remain constant (or minimal) at all
times, then the optimal definitions of these two action components, E and t, cannot
themselves be any better than the said limiting product, Et. And therefore that the joint errors
in the definitions of these two action components, E and t, can at best be equal, or if not, then
greater than this limiting product Et. Hence, in symbols, EtEt. But Et=h. So Eth.
pqh: By strict analogy with energy before, if momentum can only be defined over a
distance and therefore not at a point location q0 (whence also Zenos paradox), hence
only over a distance of dimensions q={q1q2}(=), it equally follows that any attempt at its
definition within spatial boundaries narrower than those specified, will be as inaccurate, as
the distance itself employed for its definition is taken shorter. Same as before, if we need at
least a distance of dimensions {q1q2}==q, if we are to determine the momentum within an
accuracy p=n, where n is sufficiently small to stand for a high momentum approximation,
then, all other conditions being identical, at half the distance formerly allowed, i.e. at
{q1q2}/2, we can only expect to end up with an uncertainty p=2n, if the action product
itself, of which p and q are the components, is to always remain constant, i.e. h.
So, in general, if momentum cannot be defined at a space point, but is only to be defined
over the spatial boundaries {q1q2}=q, as is dictated by the assumption that the product p is
to remain constant (or minimal) at all times, then the optimal definitions of these action
components, p and q, cannot themselves be any better than the limiting product p. And then,
consequently, the joint inaccuracies in the definitions of p and q can at best be equal, or if not
then greater, than this limiting product p; hence, in symbols, pqp. But p=h; so
pqh.
And thus the CTY between energy and time and the corresponding CTY between
position and momentum have been derived, simply and, I believe, elegantly, from the mere
analysis of the quantization of action alone. The definition of quantized action included, it has
all taken me but a page. And CTY (or the UR), in this deduction, were shown to be strictly
dependent on the quantum; which is the primary requirement.
Let us then embed this result, i.e. the UR thus derived, in the deeper spirit of CTY. The
structure of quantized action its limiting value- demands a delicate balance to be maintained
overall, which, once upset by leaning too heavily on either side of the balancing scale
(defining either complementary quantity involved too accurately) can only result to leaning
too lightly on the other side (total loss of its complementary), because the quantum they
jointly comprise (Et or p) has itself to stay rigid either way. A sharp instant of duration
t0 at a sharp point q0, though themselves ideally accurate, will eo ipso make the
definitions of E and p, respectively, impossible, if energies are to be defined only over
periods, momenta only over distances. And, conversely, when energies and momentum are to
be defined only over periods and distances, respectively, then their determinations will have
been attained within margins way too wide and hence way too inaccurate, when compared
as above- with instants of duration t0 and points of dimensions q0; all this because of
the inward reciprocity [see Note 8] possessed by the indivisible action block. Expand it at one
end, it will eo ipso contract at the other, in directly reciprocal manner, to keep itself a
constant, undiminishing quantity. This, then, is indivisibility. And this is how such
indivisibility forces us to adopt a mode of description designated as complementary.
Well, then. Has there been any duality assumed? None has. For what I have said, and
what Darrigol has said before me, was not that a particle is associated with a wave period,
but that action so is. Hence, reading Duality into this argument is quite simply a misnomer.
What this argument discloses is that the quantities E and p must stretch out over periods or
distances, if to at all materialize and be determined. And not that particles must so stretch. To
read particles into the quantities themselves, E and p, is not what the two quantum relations
entail but what the two quantum relations preclude.
The restriction that energy is to be defined over a period rather than at an instant, says
nothing at all about particles. It just says how long it takes to (minimally) define energy. That
the energy thus defined is that of a particle is but a gross non sequitur and the last thing that
the relation E=h, i.e. the relation that E, will ever license. Energy is connected with the
frequency, is what the relation itself prescribes, hence by definition not with a particle. And
the restriction that momenta be defined over a distance, now related in spatial terms with the
said period, rather than at a point, is the very thing which makes reference to a particle
literally impossible, for particles can only have a locally concentrated momentum, not one
spreading over a distance.
Particles, therefore, emerge in these relations from literally nowhere. They are simply
imported by an act of fiat, whereas so far as the two quantum relations are concerned,
particles only originate in the great outside and it is from there alone, that they are introduced
in the action scheme. To persist associating the dynamical quantities E and p with the
presence of a particle (a phrase usually attributed to de Broglie) is but the product of a
classical remnant within relations whose presence alone should be sufficient warning against
this very practice. The thought behind it all is, if there is energy and momentum, there must
be a particle around, a loan from classical preconceptions, if there ever was one. Not even
the face of a particle is inscribed in these relations. It is action, not particles, which is
periodic, and hence wavelike. And action as such is not even material, in the sense that
particles are. For it is a process; not a thing.
Once Duality is shut off from the picture, either on the side of waves or on that of
particles, the only backdoor to contextualizing CTY in the ways indicated by Munevar,
Feyerabend or Glymour, is shut together with it. Were Duality a coherent way of stating the
quantum situation, then the relativism that has become part and parcel of this notion would
provide the basis for a fusion between CTY and context-dependence, itself a method of
regarding meaning and fact (cf. Paradigms) relative to a context, i.e. what Duality is also
supposed to do in its usual descriptions. But Duality, as I trust I have established, does very
many others things as well, none of them too good for the theory (as several have already
surmised). Duality is a quantum myth and a lethal one at that. Hence, context-dependence has
really nothing to go by for their planned assimilation, except, that is, that context-dependence
may be a myth too, and a lethal one at that, whence the obstacles to their unity are thereby
removed.
Now to another matter; an inherent part of wave-particle duality reasoning is the one we
have extracted from Petersens (alleged) definition of CTY, as a method of handling such
phenomena, as those which depend on their own observation. Which is a very definite form
of relativism (and one, I will not deny, that Bohr has frequently encouraged, when addressing
audiences or cultures which he had a mind, or a diplomacy, to flatter); but what relativism
and what observations? In my own primordial- derivation of the two UR, and their
correlated CTY, there were no measurements assumed at all. Only strictly purified quantum
axioms and their immediate logical entailments, i.e. the two UR derived as theorems.
I have done nothing but unpack the contents of the concept of quantization. I have not
said a word about measurements or observations or any such irrelevancies. But CTY has
been derived, simply and directly, from such a concept alone and despite my not once having
introduced or even so much as hinted at observations. What I have derived, valid or not, I
have derived prior to observations; which is precisely what it takes in the first place, if the
resulting theorems, the two UR, are to be subsequently confirmed by experiment, if at all.
CTY, therefore, has no need of any measurements to come forth, as it had none in my
|A+B|=1 model, where mutual exclusion was warranted a priori.
To proceed to measurements directly, as so many physicists are professionally prone to
do, implying in practice that there can be no uncertainties, or no CTY, unless a measurement
is first performed, as if the purely ontological counterparts of these notions are literally absent
when no measurement is in process to then spring forth from zero only upon measurement,
not only makes the practice of experimenting utterly incomprehensible. What are the
measurements about? Themselves? But, in addition, and due precisely to such obscure
experimental self-reference, this tendency makes talk of contextdependence and Paradigms
almost inevitable. If measured uncertainties only measure measured uncertainties (!), rather
than limitations built into reality itself, then surely there is nothing behind them, except a
shapeless, amorphous void and not the atom (i.e. the foundation). My reply is really quite
simple. I have assumed no measurements. Hence whatever CTY was deduced in the process,
was deduced from an ontological premise and that alone.
In addition, in my account of CTY and the UR, the quantized products Et and pq (or p)
are not the same words featuring in different contexts. They are different words featuring in
the same context, namely, the one, unique wave period, and thereby the one, unique unit of
action they jointly comprise. This is why they are complementary. And this refutes context
dependence not just as a possible reading of Complementarity but as a possible reading of
anything. Does the period t, over which E is defined to yield Et, belong to a context other than
E? Does the distance , over which momentum is defined to yield p, belong to a context
other than p? Do, that is, concepts operating in a certain context, serve in defining concepts
that operate in a different context and still define them? This is the sole way contextualism
could ever handle the present situation and it is a way that leads it to but a blatant
contradiction. But that is nothing new.
6. Tying Loose Ends

There are, I believe, not too many of them in the argument. But there are points
unmentioned or points only hinted at, such as dualism, atomism, foundations, and, ultimately,
realism, which need to be brought to focus.
An atomist is a metaphysicist, twice over. Once, because he is a realist, and this is a
metaphysical position, twice because he is an atomist and atoms (since Leibniz) are said to be
anything but physical. Kants 2d Antinomy between the Composite and the Simple reflects
the same thing [402 ff]. Atomists, in addition, are foundationalists. Ancient atomism began as
a response to Zenos paradoxes, which led infinite divisibility of processes to a literal dead
end. I shall name but one such paradox, that of the stadium runner (though the arrow paradox
is saturated with complementary connotations), to drive the point home. The runner, in order
to cross the stadium must take the step which is the most crucial step of all that follow; the
first ever. But there is no first step to take, if distances are infinitely divisible [see Note 9].
The first step would be right where hes standing; to realize this clearly, suppose you ask
someone to start counting from the beginning. He will go one, two, three, four ... and so
on. No problem. Now ask him to start counting, again from the beginning, but count
fractional numbers instead. He cannot. There just is no place, from where to start. It is a
logically impossible task to count fractional numbers from the beginning. He will remain as
speechless as Zenos runner is said to have remained motionless. There is nowhere to start
from and, respectively, nowhere to go.
Atomism seems the sole escape from this riddle. Atomism is a way to start and therefore
atomism is a form of foundationalism. It is however, once atoms are closer examined, a form
of dualism as well. Atoms, to circumvent perpetual divisibility, turn out to consistently lack a
structure, for structure is a (near) synonym of inward separability; and so of divisibility. And
what lacks a structure cannot become the part of a thing possessed of one. Hence, strictly
speaking, atoms cannot be the parts of anything. One would think that this undermines the
very essence of their introduction, namely, that of offering a foundation. I am of the opposite
inclination myself. If atoms were within the structures, which they are supposed to support,
then they would themselves become part of the structure in need of the support. And it would
be then that the foundation would be shaken, not now.
Hence an atomist can hardly avoid being a dualist. And can therefore hardly avoid
running across Hansons paradox. As (quantum) numbers get smaller, unintelligibility will
result, not perchance because we have changed languages, which in a way we have, but
because we are running out of reality. And it is this that changes the language, rendering it
complementary, whereas it was unified previously, and will again become so, as (quantum)
numbers start growing larger. As my numerical model of CTY endeavors to disclose, and as
the directly quantal derivation of CTY per se affirms, the atom is just too narrow to make
room for all our macro attributes in any one attempt at fitting them to it. But it will make
room for them disjunctively, which is what CTY is all about. Two into one wont go this is
an analytic truth and, despite our efforts, the indivisible will only manifest undivided aspects
of itself; that is to say, complementary ones. If we lean too hard towards the way of the
prospective attributes E and p, the other two remaining, prospective attributes, t and q, will
vanish from the picture, and conversely, because the quantum is indivisible and can respond
affirmatively to either pair of them only in distinct succession, if at all. Language does what
Hanson notices only because it conforms to the restrictions.
Is this nonrealism? On whose irresponsible definition? If the atomic resists
accommodating all our macro attributes at any one time, disjunctively manifesting only
undivided aspects of itself [see Note 10], in what exact fashion, pray, does it behave
differently than its specified nature? And what other inference would be consistent with the
premises of the argument, viz. that of indivisibility? In accordance: In quantum mechanics
we are not dealing with an arbitrary renunciation of a more detailed analysis, but with the
recognition that such an analysis is in principle excluded [Bohr, 1958, 62]. This is because:
Any consistent use of the concept of the quantum of action refers to phenomena resisting
such an analysis [Bohr, 1963, 94].
How on earth, then, when an object resists its analysis, can this have anything to do with
context-dependence or subject-dependence, if it came to that? It can only have to do with the
object. Phenomena resisting analysis, our analysis, and frustrating our attempts at subdividing
them because they are unanalyzable (NB: in principle), is the closest approximation to hard
core realism ever. The quantum resists its analysis as any true atom should in strictest
accordance with its own, independent nature. The language of CTY simply preserves and
mirrors this effect by inwardly splitting up in classical halves because the quantum it seeks to
describe in corresponding halves itself just wont. Namely, exactly what my numerical model
in the naturals succeeds in preserving. For A+B=1, it will be the variables, not the Unit, that
will undergo the splitting.
The resulting descriptions, which are complementary in a language (that of classical
physics) rather than two languages complementary to one another, as some find it convenient
or consoling to suppose, have everything to do with the independent predication of the world
as atomistic and non-distributive and nothing at all to do with contextdependence, or its
ideological aims [see Note 11].
Bohr is, quite simply, a modern day atomist; and so a dualist, a foundationalist and a
metaphysical realist. Relativism and context-dependence have little or nothing to do with any
of that. Human rights apart, they have little to do with an anything.
Appendix
I have presented the derivations of section 5 twice already, in Author, Refs. 3 and 4;
Now, I will present an additional proof, nor presented before, which reconfirms them:
Assume first that E=h. Then assume that we know the energy, E, within the margins of an
error E. Then, tautologically, E=h and, since =1/t, =h1/t. Then, since cannot
concern h, we obtain =h(1/t). Now, it already becomes clear even at this early stage of
the argument that (1/t) is an error in the time, derived tautologically from the initial premise,
E=h, leading (tautologically) to E=h.
In my initial derivation, t>0 = t, since, in accordance with it, the very fact that E cannot
be defined in an instant, t0, but only over an interval t>0, is the raison detre of an
uncertainty in time. Now it is known that, in accordance with Error Theory, the expression
(1/t) is equal with t/t2. Therefore, by substituting for t/t2 in E=h(1/t), we obtain:
E=ht/t2. Since, however, in my initial derivation, t>0=t, the denominator of the fraction
becomes (t)2. Hence, E=ht/(t)2. This, in turn, yields E=h1/t and this, finally,
Et=h. The point of importance is this: Unless it is assumed in this line of reasoning that
t>0=t, which is the exact same assumption in my initial derivation, Et=h will never
follow from E=h, itself derived tautologically from E=h, thus contradicting the theory.
In short, if E=h implicitly entails E=h, then E=h can only be turned into
Et=h and indeed how can it not be? iff t>0=t, in other words, iff the t of the primary
relation, E=h, is interpreted as a limiting time latitude for the definition of the energy,
exactly as postulated in my first deduction. This second proof of Et=h, not only reconfirms
the first but, in addition, it furnishes in the process a by and large self-contained deduction of
Et=h, fully crosschecking with the first.
Notes
1. Mainly by Dr. V. Karakostas. See his Nature of Physical Reality in the Light of
Quantum NonSeparability [Oviedo, Spain, 713 August 2003] or his
Nonseparability, Potentiality and the Context-Dependence of Quantum Objects.
Dialectica, 2005 (to be published).
2. Beyond Reason: Essays on the Philosophy of Paul Feyerabend. Gonzalo Munevar
ed., Kluwer, Dordrecht, 1991.
3. Plus, that is, eight other people signing the text. John Earman and Wesley Salmon are
two of them. (See 2d paragraph from the end, Section 3.)
4. The general idea is that when language-games change, then there is change in
concepts, and with the concepts the meanings of words change [Wittgenstein, 1977,
66.].
5. The very expression joint applicability of the classical concepts, eo ipso excludes
waves and particles as its possible recipients, which are trivially not jointly
applicable in classical mechanics. Only the variables of the products Et and pq are.
6. The correct thing to say, of course, is that the two quantum relations, when submitted
to a Fourier treatment, will alternatively represent the system as either an extended,
plane wave or as a localizable wave packet. The former allows the determinations of
E and p, since a unique wavetrain is employed, the latter, the determinations of t and
q, since a superposition of many waves is employed. And thus the classical concepts,
E and p, on the one side, t and q, on the other, will through this process assume an
incompatibility analogous to that between one and many. The sole duality,
therefore, derivable from this reasoning is that between waves and wave packets.
That is to say, of waves alone, though in antithetic wave profile configurations.
Particles are absent even here.
7. This is what Hooker has earlier referred to as the factual absence for classical
compatibility. For a thorough analysis of logical vs factual incompatibility see my
essays [2, 1994, pp.187-9 and 4, 223-5, 2005].
8. I can hardly overemphasize the importance of this word, soon to be abandoned by
Bohr for the sake of the dominant term, CTY, [1934, 19], although the former
shows exactly how complementary counter happenings at either end of the
indivisible cluster result from uneven balance. The two notions, I should think, go
hand in hand.
9. More strikingly, Zeno shows that no body can ever start its journey: it can never
take the first step, since there is no first step to take [Barnes, 1982, 262]. This, of
course, is Kants problem in the Second Antinomy, that between Composite and
Simple and the frustration thereby of constructing the former by repetitive
accumulations of the latter. It is anticipated, in a uniquely important degree, by
Zenos paradox of extension: How can a line of finite length be divided into
infinitely many parts of finite length? And how can a line which is made up of
lengthless parts add up to a line which has length? [Harrison, 1996, 273].
10. Dimly, Duality is discerned in the distant horizon. What can only manifest
undivided aspects of itself, will reasonably manifest such aspects as may conflict
with one another, when what should otherwise be only a part of the entity, must
now extend over its whole profile instead; and may thus conflict with its alternative,
indivisibly manifested profile. Duality is not a primitive assumption in this
syllogism. It is only a side product of Indivisibility.
11. The aim is, of course, an equalitarian ideology, offered in abundance through
humanitarian incommensurability. Incommensurable scientific beliefs let alone
moral, social, political or aesthetic ones, are impossible to bring to conflict, therefore
impossible to select from. They are all just as good (or just as bad, if it came to that).
For the essentially ideological character of context-dependence see [Katz, 1978, 364]
and, it goes without saying, A. Sokals pseudo-paper [Longino, 1977, 119]. But
Feyrabend himself has beaten them all to it, openly confessing that his scientific
relativism is preferable because more humane [1971, 33; and 1978 passim].
Scientific truth must be silenced, if it conflicts with politics.
References
[1] Antonopoulos C. Innate Ideas, Categories and Objectivity. Philosophia Naturalis, 26,
2, 1987.
[2] Antonopoulos C. Indivisibility and Duality; A Contrast. Physics Essays, 7, 2, 1994.
[3] Antonopoulos C. Investigating Incompatibility: How to Reconcile Complementarity
With EPR. Annales de la Fondation Louis de Broglie, 30, 1, 2005.
[4] Antonopoulos C. Making the Quantum of Relevance. Journal for General Philosophy
of Science, 36, 2, 2005.
[5] Barnes, J. The Presocratic Philosophers. Routledge and Kegan Paul, London, 1982.
[6] Bohr, N. Atomic Theory and the Description of Nature. Cambridge University Press,
1934.
[7] Bohr, N. Atomic Physics and Human Knowledge. New York, 1958.
[8] Bohr, N. Essays 1958-62 on Atomic Physics and Human Knowledge. Suffolk, 1963.
[9] Darrigol, O. Strangeness and Soundness in de Broglies Early Works. Physis, 30,
1993.
[10] Feyerabend, P.K. Complementarity. Proceedings of the Aristotelian Society,
supplementary volume, xxxii, 1958.
[11] Feyerabend, P.K. Problems in Microphysics.Frontiers of Science and Philosophy,
R.Colodny, ed., University of Pittsburgh Press, 1962.
[12] Feyrabend, P.K. How to Be a Good Empiricist. The Philosophy of Science, P.H.
Nidditch ed., Oxford University Press, 1971.
[13] Feyerabend, P.K. Science in a Free Society, NLB 1978.
[14] Faye, J., Folse, H. eds. Niels Bohr and Contemporary Philosophy. Dordrecht 1994.
[15] Folse, H. The Philosophy of Niels Bohr. Amsterdam, 1985.
[16] Hanson, N.R. Patterns of Discovery. Cambridge University Press 1961.
[17] Harrison, C. The Three Arrows of Zeno. Synthese, 107, 1996.
[18] Hooker, C.A. The Nature of Quantum Mechanical Reality. Paradigms and Paradoxes,
The University of Pittsburgh Press, 1972.
[19] Kant, Imm. The Critique of Pure Reason. Transl. N.K.Smith, Macmillan, 1973.
[20] Karakostas, V. The Nature of Physical Reality in the Light of Quantum
Nonseparability. Oviedo, Spain, 713 August 2003.
[21] Karakostas V. Nonseparability, Potentiality and the Context-Dependence of Quantum

Objects. Dialectica, 2005 (to be published).
[22] Katz, J. Semantics and Conceptual Change. The Philosophical Review, 88, 1979.
[23] Kuhn, Th. The Structure of Scientific Revolutions. The University of Chicago Press,
1970.
[24] Leibniz, W. Monadology. The European Philosophers from Descartes to Nietzsche.
M.C.Beardsley ed., New York, 1960.
[25] Longino, H.E. Alan Sokals Transgressing Boundaries. International Studies in the
Philosophy of Science, 11, 2, 1997.
[26] Mackay, D.M. Complementarity. Proceedings of the Aristotelian Society, suppl.
volume xxxii, 1958.
[27] Munevar, G. Bohr and Evolutionary Relativism. Explorations in Knowledge, xii, 2,
1995.
[28] Munevar, G., Ed., Beyond Reason: Essays on the Philosophy of Paul Feyerabend.
Dordrecht, 1991.
[29] Petersen, A. On the Philosophical Significance of the Correspondence Argument.
Boston Studies in the Philosophy of Science, Volume 1966-68.
[30] Rosenfeld, L. Foundations of Quantum Theory and Complementarity. Nature, 190,
1961.
[31] Plotnitsky, A. Complementarity. London 1994.
[32] Salmon Marilee H., Earman, J., Glymour C., Lennox J., Machamer P., McGuire, J.E.,
Norton J.D., Salmon Wesley C., Schaffner, K.N. Introduction to the Philosophy of
Science, Prentice Hall, New Jersey 1992.
[33] Wittgenstein, L. On Certainty, transl. by G.E.Anscombe, B.Blackwell, Oxford 1977.
In: Electrostatics: Theory and Applications ISBN 978-1-61668-549-2
Editor: Camille L. Bertrand, pp. 61-89
c 2010 Nova Science Publishers, Inc.
Chapter 4
M OLECULAR I NTEGRALS OVER S LATER -T YPE

O RBITALS . F ROM P IONEERS TO R ECENT
D EVELOPMENTS
Philip E. Hoggan1,, Mara Belen Ruiz2, and Telhat Ozdogan3
1 LASMEA, UMR 6602 CNRS, University Blaise Pascal,
24 avenue des Landais, BP 80026,

63171 AUBIERE Cedex, France
2 Department of Theoretical Chemistry of the Friedrich-Alexander-University
Erlangen-Nurnberg, Egerlandstrae 3, D-91058 Erlangen, Germany

3 Department of Physics, Faculty of Arts and Sciences, Rize University,
53100 Rize, Turkey
Abstract
It can readily be demonstrated that atomic and molecular orbitals must decay exponen-
tially at long-range. They should also possess cusps when two particles approach each
other. Therefore, Slater orbitals are the natural basis functions in quantum molecular
calculations. Their use was hindered over the last four decades by integration prob-
lems. Consequently, Slater orbitals were replaced by Gaussian expansions in molec-
ular calculations (in spite of their more rapid decay and absent cusps). From the 90s
until today considerable effort has been made by several groups to develop efficient al-
gorithms which have fructified in new computer programs for polyatomic molecules.
The key ideas of the different methods of integration: one-center expansion, Gauss
transform, Fourier transform, use of Sturmians and elliptical co-ordinate methods are
reviewed here, together with their advantages and disadvantages, and the latest devel-
opments within the field.
A recent approximation separating the variables of the Coulomb operator will be
described, as well as its usefulness in molecular calculations.
Recently, due to the developments of the computer technology and the accuracy
of the experiments, there is a renewed interest in the use of Slater orbitals as basis
functions for Configuration Interaction (CI) and Hylleraas-CI atomic and molecular
calculations, and in density functional and density matrix theories.
E-mail addresses: Philip.Hoggan@univ-bpclermont.fr
E-mail addresses: Maria.Belen.Ruiz@chemie.uni-erlangen.de
62 P.E. Hoggan, M.B. Ruiz and T. Ozdogan
Keywords: Slater orbitals, computer programs, Kato conditions, accurate molecular wave-
functions
1. Introduction
Slater-type orbitals (STO) [1] are the natural basis functions in quantum molecular cal-
culations. Nevertheless, their use has been rather restricted, mostly due to mathematical
integration difficulties. Even today there are no simple general algorithms to solve all the
integrals appearing in a Hartree-Fock (HF) or Configuration Interaction (CI) molecular cal-
culation, where integrals involving up to four atomic centers may appear. In spite of these
difficulties the research on Slater orbitals has always continued. The reason is the require-
ment for large basis sets of Gaussian orbitals (GTO) and large wave function expansions to
perform more accurate calculations of energy and properties of ever larger interesting sys-
tems. As a consequence those calculations need enormous computational times. In 1981,
in a Congress in Tallahassee about Slater type orbitals, Milan Randic described the situa-
tion: Gaussian functions are not the first choice in theoretical chemistry. They are used
(...) primarily because molecular integrals can be evaluated, not because they posses desir-
able properties. Today this may be a valid reason for their use, but tomorrow they may be
thought of as bastard surrogates, which served their purpose in the transition period, have
no longer viable merits and will fall into oblivion [2]. The use of an expansion of GTOs
instead of an STO was then a pragmatic solution and originally intended for solving the
problems in the calculation of the first molecules on early mainframe computers. The GTO
expansion together with the popular distribution of computer programs like GAUSSIAN
have encouraged the use of GTOs for accurate calculations of large systems. The limits are
receding with respect size of the systems and dimension of the wave function, i.e. HF cal-
culations of clusters of hundreds of atoms, CI calculations including hundreds of thousands
of Slater determinants. In spite of the rapid development of the computer technology and
the availability of supercomputers, the computational times are unreasonably long, so that
the computational chemist is restricted i.e. to perform numerous test calculations. This mo-
tivates the search for basis functions, where fewer would give a good CI, in particular. The
possibility of using Slater orbitals, where a minimal basis would consist in one function per
atom would provide a forward impulse to theoretical and computational chemistry. Since
the difficulties are of a purely mathematical nature, e.g. definite integrations, it would be
worthwhile pursuing investigations of Slater orbitals.
The purpose of this paper is to explain the key ideas about Slater orbitals for readers out-
side the field. It is beyond our scope to review the whole work of the all authors in this field,
what would deserve a longer treatment. The history of Slater orbitals and the first computer
programs using them is exposed and the currently used computer programs are listed. The
STO and GTO are defined and compared. The methods used in the literature are explained
recalling in the key ideas in which these methods are based. The last developments within
the field are reported.
Molecular Integrals over Slater-Type Orbitals 63
2. Early History of the Slater Orbitals

The history of STOs is the history of theoretical chemistry. In 1928 Slater [1] simplified
the hydrogen-like orbitals (which are eigenfunctions of the Hamiltonian for a one-electron
atom) obtaining the orbitals which bear his name. Curiously Slater called these orbitals at
that time Hartree orbitals. Slater orbitals are a simplification of the hydrogen-like orbitals,
which are eigenfunctions of the atomic one-electron Schrodinger equation.
Brief time-line of events in molecular work over Slater type orbitals to date:
1928 Slater and London.
1929 Hylleraas: He atom.
1933 James and Coodlidge: Hylleraas calculations on H2 .
1949 Roothaan LCAO paper.
1950 Boys: first Gaussian expansion of STO published.
1951 Two-center Coulomb Integrals. Roothaan formulae.
1954 Boys and Shavitt Automated calculations.
1958 Tauber: Work on analytic two-center Exchange integrals: Poisson equation.
1962 Scrocco: first publishes STO work, (in Italian) but with a programme. This
follows early molecular work in 1951-53. [3, 4].
1963 Clementi produces tables of optimised single zeta basis sets for atoms. Shavitt
B-Functions described.
1970 The Journal of Chemical Physics published work on STO codes by E. Scrocco
and R. Stevens. Gaussian 70 prepared for QCPE by J. Pople and R. Ditchfield.
1973 E. J. Baerends: numerical integration over STO used for ADF DFT code.
1978 Filter and Steinborn: Fourier transform work. B-functions and plane-wave ex-
pansion of Coulomb operator.
1981 ETO conference in Tallahassee. Weatherford and Jones.
1994 First STOP (Slater Type Orbital Package, QCPE 667 1996) code. Bouferguene
and Hoggan.
2001 First SMILES (Slater Molecular Integrals for Large Electronic Systems) code.
Fernandez Rico, Lopez et al.
2008 Gill: Coulomb resolution.

Very soon with Slater at MIT, researchers broached the problem of evaluating the two-
electron integrals in this basis. During the 1950s the Chicago group led by Mulliken took
on the task of evaluating all the molecular integrals. Roothaan treated the Coulomb and
Hybrid two-center integrals [5,6], Rudenberg the exchange integrals [7]1 . Among the many
authors who were working around the world on the solution of the necessary integrals one
may mention Masao Kotani in Japan [8], who wrote the famous tables of integrals which
bear his name and that were widely used. Coulson in Oxford (England) proposed a method
to evaluate the three- and four-center integrals [9], Lowdin in Uppsala [10], and young
American scientist called Harris [11] were involved. Work in the early 50s mostly focused
on integrals over STO.
The interest was to make the first theoretical calculations of some molecules starting
with the diatomic systems H2 , N2 . For three-center molecules the problem of integration
was encountered (orbital translation). Mulliken and Roothaan called this The bottleneck
of Quantum Chemistry [12], Mulliken mentioning it in his Nobel Lecture in 1966, on the
molecular orbital method.
Boys in Cambridge published his landmark paper [13] containing the evaluation of
three- and four-center integrals using Gaussian functions, for which he derived the so-called
product theorem: the product of two Gaussian functions located on different centers is a
new Gaussian function located on a new center. Thus four-center electron distributions
could be reduced to single-center distributions and evaluation was analytically facilitated.
Boys regarded his work as an existence theorem. It was to change the course of molecular
computations. Note that the product theorem for Slater orbitals leads to complicated infinite
sums, making evaluation awkward compared with the simple closed forms for Gaussians.
In 1954 Boys, Shavitt et al [14] expanded Slater orbitals into Gaussians to perform
quantum mechanical calculations. In 1963 Clementi presented the so-called basis set using
Slater orbitals [15]. Later Pople would base his programs on Boys pragmatism.
3. History of the STO Computer Programs

The first (and surely the last) manual calculation of a molecule, the N2 molecule, was
done by Scherr in 1956. It was necessary the work of 2 (sometimes it appears 3 ) men for 2
years. Afterwards this calculation was reproduced by the first digital computer calculation
[16, 17], taking 35 minutes.
In 1962 Shull initiated the Quantum Chemistry Program Exchange (QCPE) at Indiana
University.
The first automatic computer program was POLYATOM [18] which used nevertheless
GTOs with SCF-LCAO. The program was developed at MIT in 1963 when Slater was there.
In 1963 the program IBMOL [19] was developed by Clementi and others when he visited
the Chicago group.
In 1968 a STO code was developed by Scrocco and Tomasi from Pisa. Preliminary
work by Scrocco is reported in Italian as early as 1962 [4].
1 The two-center two-electron integrals are classified according to the centers a, b. Writing them according
the charge distributions [(1)|(2)] the Coulomb integrals are [aa|bb], the hybrids [aa|ab] and the exchange
integrals [ab|ab]. The most difficult are the exchange integrals because the charge distribution of every electron
is located over two centers.
This program was also used by Berthier in France. The program ALCHEMY in 1968
was originally developed using Slater orbitals by Clementi and the staff of the IBM labora-
tory in San Jose [20], afterwards, the new ALCHEMY 2 by Bagus and others used GTOs.
The program DERIC [21] by Hagstrom in 1972 perform STO calculations of two-center
molecules.
In the 80s, the advent of GAUSSIAN [22] saw development in the STO field hibernate
somewhat. By the 90s several groups around the world developed new STO computer
programs which are now distributed. The program STOP, by Bouferguene and Hoggan [23]
was published first in 1996. It is based on the single center strategy and was first presented
in 1994 at the 8th ICQC in Prague. New versions appeared, the latest (parallel) in 2009.
Then in 1998 a program was written using B-functions by Steinborn, Weniger, Homeier
et al, in Regensburg [24]. The program SMILES by Fernandez Rico, Lopez, Ema, and
Ramrez in Madrid appeared in 1998 and new versions have appeared, the latest in 2004 for
the HF and CI calculations of molecules [25].
The program CADPAC [26] in Cambridge uses techniques like density fitting, involv-
ing auxiliary Slater type orbital basis sets to perform Hartree-Fock and Density Functional
Theory (DFT) calculations with a reduced number of indices in requisite integrals. They
aimed to obtain better Nuclear Magnetic Resonance (NMR) chemical shifts on the basis
involving nuclear cusps.
In the density functional theory field in 2001 the program ADF (Amsterdam Density
Functional) [27] begun in 1973 by Baerends et al uses Slater orbitals for their calculations.
This much-used package offers a very extensive series of atomic basis sets for input, in-
cluding most elements. It is a numerical grid strategy and this review will not detail it.
The program ATMOL of Bunge et al performs large highly accurate CI calculations on
atoms using Slater orbitals [28].
In the first century of the third millennium much interest is concentrated in generating
more efficient calculation algorithms, use of non-integer Slater orbitals, numerical solution
of integrals when using B-functions and in the electron correlation when using Hylleraas
wave functions.
4. Slater Orbitals & Gaussian Orbitals

It is well known that hydrogen-like orbitals are the solution of the Schodinger equation
for a one-electron atom. For helium and atoms with more electrons the Schodinger equation
has no analytical solution due to the potential term 1/ri j which correlates the (otherwise)
independent electrons. It is assumed that for systems with N 2 this form of the exponential
er will be the asymptote of the formal solution. The hydrogen-like orbitals have nodes,
i.e. the 2s orbital is of the form (1 br) er , and higher quantum number orbitals are
similar but STOs are node-less. A related problem appears for Gaussians.
In 1928 Slater [1] regarded the hydrogen-like orbitals as polynomials in r which make
the calculations messy and proposed the use of single powers of r i.e. linear combinations
of hydrogen-like terms.
A picture which helps to visualize the differences between Slater and Gaussian orbitals
is the representation of the 1s orbital function of both types, see Figure 1.
Figure 1. Comparison of the shape of a STO and GTO functions.
STOs represent well the electron density near the nucleus (cusp) and far from the nu-
cleus (correct asymptotic decay). STOs thus resemble the true orbitals. Conversely, the
GTOs have erroneous shape near and far from the nucleus (no cusp). One can observe that
far from the nucleus the GTOs tend to zero much faster than STOs.
To reproduce a 1s STO using 3 GTOs (the so-called minimal GTO basis) an orbital is
obtained with the shape of a Gauss curve, no cusp, see Figure 2. To reproduce a single STO
many GTOs are necessary, but the electron cusp at the nucleus is missing. This is one of
the reasons of the slow convergence of the wave function solutions to the exact (HF or CI)
result. In general, if the basis function is not a formal solution of the Schrodinger equation
its convergence is slower. That means that more Slater determinants are required to obtain
the same result. Thus Slater orbitals show faster convergence when increasing their number.
Another advantage of Slater orbitals is the size of the basis, one orbital per electron is
of reasonable quality and multiple-zeta basis sets converge fast to the Hartree-Fock limit.
therefore, the number of integrals to be evaluated is dramatically smaller. CI is spectacularly
more efficient. Finally, conceptually the Slater orbitals give a more intuitive description of
the atomic orbitals and of the molecular orbitals (MO) formed with them.
The disadvantages of Slater orbitals have been already mentioned: the three- and four-
center two-electron integrals are the bottleneck. There is no general analytical solution
for them, which would be the most effective and fastest way of calculation. Instead there
are a number of approximate methods of calculation, involving infinite series, or truncated
approximations to the Coulomb operator itself. They will be treated in the next Sections.
The radial Slater functions do not represent the bonding region adequately, it being then
necessary to add higher angular momentum functions.
It is nevertheless possible to use linear combinations restoring radial nodes. This ap-
proach is advocated particularly for ADF, where the hydrogen-like basis is obtained by
fixing the coefficients for combining Slater functions.
Another disadvantage is that some of the two-center integrals since the times of
Roothaan and Rudenberg have been solved for a co-axial conformation of the atomic coor-
dinate systems (the z-axes point to each other) that is not the molecular frame. Therefore
rotations and reflections are necessary. These problems have been solved, but it requires
Figure 2. Construction of a STO with 3 GTOs.
additional calculations [29].

Nowadays, Slater orbitals are used in atomic calculations, especially in highly accurate
calculations of atoms using Hylleraas wave functions (with explicit ri j dependence, and
also in diatomics. They are used in DFT and in Density matrix theories. Traditionally they
have been used in semi-empirical calculations where of course the three- and four-center
integrals were neglected.
The Gaussian orbitals are generally used in standard quantum mechanical calculations.
As explained they are not shaped like analytical orbitals, with no cusp at the nucleus, for that
reason they are not good for the calculation of properties where the density at the nucleus
has to be well described. Also the radial dependence is not well represented and the number
of integrals increases with the dimension of the basis dramatically.
The major advantage of GTOs is the existence of a product theorem. Over many years,
workers have improved the calculation of the necessary integrals, having achieved a con-
siderable speed-up. For example the Coulomb operator with a Laplace transform enables
to calculate three- and four-center integrals like two center integrals.
Concluding, the main defect of GTO expansions is the absent cusp which slows the
convergence and the large number of integrals to be computed.
5. Types of Exponentially Decaying Orbital, Based on Eigen-

functions for One-Electron Atoms
In general one calls Slater-type orbitals those with an exponential radial factor of the
form rn er , for n a positive integer (or 0). The atom-centered Slater orbitals are defined
as:
nlm (r) = rn1 erYlm (, ), (1)

where n, l, m are the quantum numbers. Ylm (, ) are the spherical harmonics defined using
the Condon-Shortley phase:
1/2
2l + 1 (l m)!
Ylm (, ) = (1) m
Plm (cos )eim , (2)
4 (l + m)!
Plm (cos ) are the associated Legendre functions. The spherical harmonics are eigenfunc-
tions of the angular momentum operator L2 and its z-projection Lz .
The complex spherical harmonics are used mainly in atoms and in developing theo-
ries because it is easier to work out general formulae and derivations with them. The real
spherical harmonics are linear combinations of the complex ones. These are used mainly in
molecules.
Note that they are written using polar coordinates. They can be also straightforwardly
converted into Cartesian Slater orbitals by the exchange:
x = r sin cos , (3)

y = r sin sin , (4)
z = r cos , (5)
obtaining in general:
nlm (r) = xnx yny znz rn1 er . (6)

Cartesian Slater type orbitals are very seldom used compared with Cartesian Gaussians,
that are an almost systematic choice.
When the principal quantum number n in Eq. (1) is a non-integer we have the NISTOs
(Non Integer Slater Orbitals). The main difficulty when working with these orbitals is
during the derivations a binomial has to be used with an non-integer power what leads to an
infinite expansion. These orbitals are widely investigated in the present [30]. The additional
flexibility of using non-integer quantum numbers brings a lowering in the energy results.
There is the possibility to transform also the polar coordinates to elliptical coordinates.
Traditionally the Elliptical Slater orbitals have been used as basis functions for two-center
molecules [31]- [33]. These orbitals are known to lead to lower energy results, see Ref. [34].
Using = 1 = ra + rb and = 1 = ra rb :
nlm (r) = n l (2 1)m/2 (1 2 )m/2 e eim , (7)

where , , are the elliptical coordinates.
Now we go to orbitals which are linear combinations of Slater orbitals: B-functions
[35], hydrogen-like, Sturmians [36].
The B-functions are Bessel functions. The orbitals have some helpful properties like a
compact Fourier transform. Written in the form
n
(2n j 1)!
Bnlm (r) = 22n+l1 (n + l)!(n j)!( j 1)! (r)l+ j1 erYlm (, ), (8)
j=1
one can see that they are a linear combination of Slater orbitals. The angular parts are the
spherical harmonics.
The hydrogen-like orbitals which are solutions of the Schrodinger equation for the hy-
drogen atom have a radial part which is a Laguerre polynomial. The polynomial and the
exponent coefficient depend on the atomic number Z and the principal quantum number n:

2Zr l Zr m
nlm (r) = Nnl Lnl1
2l+2
r e n Yl (, ). (9)
n
Due to that fact, the hydrogen-like orbitals do not form a complete set (for finite n), they
need orbitals of the continuum to be complete. This would be important for the convergence
of the solutions.
Shull and Lowdin [37] realized that this was due to the dependence of Z with n that
dilates the orbitals and they proposed the following orbitals where these were substituted
by adjustable parameters, i.e. usual orbital exponents:
nlm (r) = Nnl Lnl1

2l+2
(2r) rl erYlm (, ), (10)
so these orbitals form a complete set. These orbitals were subsequently called Coulomb
Sturmians because they fulfill the so-called Sturm-Liouville theorem for eigenfunctions of
such differential equations, with central Coulomb attraction.
In the Section 7 methods of the literature we will see how these kinds of orbitals have
been used.
6. Types of Integral over Slater Orbitals

Due to the form of the Hamiltonian and of its expectation value we find the following
kinds of integrals. First the integrals which appear when using Hartree-Fock and CI wave
functions, in general ab initio methods. The integrals are classified according the number
of electrons and centers which are linked. We present them in order of difficulty.
6.1. One-Electron Integrals

These are the one- and two-center overlap integrals ha|bi, kinetic energy integrals ha|bi
and two-center nuclear attraction ones ha|1/rb |bi.
Other case of one-electron integral is the three-center nuclear attraction, originated from
the nuclear attraction operators in the Hamiltonian: ha|1/rc |bi.
6.2. Two-Electron Integrals

They can be up to four-centers because of the determinant giving the wave-function and
thus the four orbitals which form the integral. According to the number of centers:
The two-center integrals have been traditionally the most investigated, they have the
following nomenclature: The Coulomb integrals where the charge distribution of every
electron is located at a center: [aa|bb]. Hybrid integrals, one charge distribution is located
at one center and the other over two centers [aa|ab] and their equivalents [bb|ab]. The
exchange integral is more difficult, it leads in case of different exponents to an infinite
sum. Every electron is located in two centers: [ab|ab]. To solve these integrals a change to
elliptical co-ordinates is useful. The Coulomb operator in elliptical co-ordinates contains
associated Legendre functions of the first and second kind, for which integration is very
difficult. In the case of slightly different exponents there are some singularities.
In actual calculations, the Coulomb and Hybrid integrals are calculated exactly, nume-
rous methods exist. The exchange integrals are calculated with great accuracy.
The three-center integrals are of several types [aa|bc], [ab|ac]. For different exponents
there is no general solution.
The four-electron integrals are of the type [ab|cd].
6.3. Three- and Four-Electron Integrals

They appear in the Hylleraas-CI method [38] when using one inter-electronic distance
ri j per configuration. For the two-center case they have been solved generally by Budzinski
[39]. Three- and higher number of centers have not been solved yet.
These can be many-center integrals, as every electron from right and left in the ex-
pectation value operator may be in a different center. These integrals are of the type,
i.e. the easier [aa|r12 r13 |ab|bb], to the most difficult [ab|r12 r13 |ab|ab]. Four-electron ones
[aa|r12 r13 /r14 |bb|ab|bb], and so on.
For three- and higher number of centers one would find three- and four electron integrals
with as many centers as the molecule has up to 8. These integrals are still not solved. In-
terest nowadays focusses on the solution of two and three center molecules using explicitly
correlated methods.
7. Methods in the Literature

In this section the main methods of evaluation of the three- and four-center integrals
over Slater orbitals from the literature will be explained. The methods are approximate be-
cause they consist in transformations, expansions or include numerical integrations. There-
fore they are not as effective as analytical integration would be. Nevertheless, by these
methods the evaluation of these integrals is possible and the programs are even as competi-
tive as those using Gaussians.
7.1. Single-Center Expansion

The single-center expansion method requires expanding the Slater orbitals located at
different centers at only one of them and then as for atoms to perform the integrations.
The translation method consists in selecting an atom as origin then the translation of other
orbitals from their atom to the origin. Therefore both methods are essentially the same. To
expand one function centered in A at another point B the following expansion:
Z
Ai = Ai B j d B j . (11)
j=1
This formula is due to Smeyers [40]. In brackets, the requisite coefficients. The different
methods of single-center expansion differ in the way to calculate these coefficients.
This method was first proposed by Barnett and Coulson [9] in 1956 using radial orbitals
(s-orbitals) and was called the zeta function method because of expansions in terms of
successive derivatives with respect to exponents.
The method has similarities with the alpha function method of Lowdin [10]. Harris and
Michels [41] extended the method to angular general orbitals in 1965. This method has
been used by Smeyers, Jones, Guseinov, Fernandez Rico et al, and others.
The idea is the translation of an orbital from one point to the other. The translation of
a spherical harmonic is a limited expansion, the translation of the radial part is nevertheless
an infinite expansion. This situation can be best explained with formula of Guseinov [42]:
n 1 l
n,l,m (, rA ) = Vnlm,n l m (, RAB ) n ,l ,m (, rB ), (12)
n =1 l =0 m =l
where V are the coefficients of the expansion. The method is very stable but it requires com-
putation of a lot of terms to obtain sufficient correct decimal digits, therefore this method
needs very long computational times.
7.2. Gaussian Expansion

This is the Boys-Shavitt method [43], which consist in solving some integrals over
Slater orbitals expanding them into a finite series of Gaussians:
NG
er = ci ei r ,
2
(13)
i=1
ci and i are obtained by minimizing the least squares. This method and some improve-
ments of this method are used at present in the program SMILES [25]. As NG is usually
larger than the number of the primitives when using only Gaussian basis sets, the number
of integrals to calculate is large. The method is very stable and robust. It requires lengthy
computational times to get accurate integral values.
7.3. Gaussian Transform Method

The Gaussian transform method by Shavitt and Karplus 1965 [44] has been probably
the most used method. It consists in the Laplace transform of the exponential function, here
exemplified by the simplest one i.e. a 1s orbital:
Z
2 /(4s)
2
er = s3/2 e ds esr . (14)
2 0
Every Slater exponential within the integral is transformed into a Gaussian one, for that one
has to solve the integrals over s which have a special form. This integral has to be solved
numerically. This is the disadvantage of the method.
7.4. Fourier-Transform Method

The B-functions Eq. (8) proposed by Filter and Steinborn in 1978 [35] have a highly
compact Fourier transform. The group of Steinborn has developed this method [24]. The
Figure 3. Transformation from polar to elliptical coordinates.
evaluation of integrals using B-functions leads to some integrals including a Bessel function
of first kind which is oscillatory:
Z
rn er Jl+1/2 (rx)dr. (15)
0
To evaluate these Safouhi [45,46] used the SD-transform, due to Sidi [47], which consists in
substituting this integral by a sine integral which has the same behavior. It needs numerical
integration.
7.5. Use of Sturmians

The Sturmians were proposed by Shull and Lowdin in 1956 [37]. Smeyers used the
Sturmians to evaluate three-center nuclear attraction integrals using the one-center expan-
sion [40]. Guseinov 2001 used also them [48]. The Sturmians Eq. (10) satisfy the Sturm-
Liouville theorem:

2n m
Sn,l =
2 m 2
Sn,l . (16)
r
The so-called Coulomb Sturmians orthogonalise the Coulomb potential in their argu-
ment. This generally applies to the attraction term, at least for one-electron functions.
Geminals useful for explicit correlation have also been used.
A seminal text by Avery gives more details to the interested reader on this subject [36].
7.6. Elliptic Coordinate Method

The elliptic coordinate method is the transformation of the polar orbital coordinates into
elliptical ones , according to Figure 3. The two coordinate systems pointed to each other
so that the elliptical angle coincides with polar angle . This transformation is:
R R
r1a = (1 + 1 ), r1b = (1 1 ), (17)
2 2
1 + 1 1 1 1 1
cos 1a = , cos 1b = , (18)
1 + 1 1 1
[(21 1)(1 21 )]1/2 [(21 1)(1 21 )]1/2

sin 1a = , sin 1a = , (19)
1 + 1 1 1
The volume element and the domain change are:
Z Z Z
R3
Z 2 Z +1 Z 2
r2 dr sin d d d1 d1 (21 21 ) d1 . (20)
0 0 0 8 1 1 0
The method has been used by numerous authors: Mulliken, Rieke, Orloff, Rudenberg,
Roothaan, Eyring, Randic, Saika, Yoshimine, Maslen and Trefry, Guseinov, Bosanac,
Randic, Harris, Fernandez Rico, Lopez, Ozdogan and many others. Some types of three-
electron integrals have been recently solved by Ozdogan and Ruiz using this method [49].
8. General Two-electron Exponential Type Orbital Integrals in

Poly-Atomics without Orbital Translations
8.1. Introduction
Now, the Coulomb resolution will be presented. This is a readily controlled approxima-
tion to separating the variables in the 1/r12 which, in recent work by Gill and by Hoggan is
shown to spell the end of exponential orbital translations and ensuing integral bottlenecks.
This section advocates the use of atomic orbitals which have direct physical interpreta-
tion, i.e. hydrogen-like orbitals. They are Exponential Type Orbitals (ETOs).
Until 2008, such orbital products on different atoms were difficult to manipulate for the
evaluation of two-electron integrals. The difficulty was mostly due to cumbersome orbital
translations involving slowly convergent infinite sums. These are completely eliminated
using Coulomb resolutions. They provide an excellent approximation that reduces these
integrals to a sum of one-electron overlap-like integral products that each involve orbitals
on at most two centers. Such two-center integrals are separable in prolate spheroidal co-
ordinates. They are thus readily evaluated. Only these integrals need to be re-evaluated to
change basis functions.
The above is still valid for three-center integrals. In four- center integrals, the resolu-
tions require translating one potential term per product. This is outlined here and detailed
elsewhere.
Numerical results are reported for the H2 dimer and CH3 F molecule.
The choice between Gaussian and exponential basis sets for molecules is usually made
for reasons of convenience at present. In fact, it appears to be constructive to regard them as
being complementary, depending on the specific physical property required from molecular
electronic structure calculations.
As regards exponential type orbitals (ETOs) such as Slater functions, it seems to be
difficult to evaluate two-electron integrals because the general three- and four-center inte-
grals evaluated by the usual methods require orbital translations. Some workers avoid the
problem using large Gaussian expansions, as in SMILES [50, 51].
It would be helpful to devise a separation of the variables of integration. This would

eliminate orbital translations, although some other translations remain involving a simple
analytic potential.
The present work describes a breakthrough in two-electron integral calculations, as a
result of Coulomb operator resolutions. This separates the independent variables of the
operator and gives rise to simple analytic potentials. The two-center integrals are replaced
by sums of overlap-like one-electron integral products. One potential term in these products
requires translation in four-center terms, which is significantly simpler to carry out than
that of the orbitals. This implies a speed-up for all basis sets, including Gaussians. The
improvement is most spectacular for exponential type orbitals. A change of basis set is
also facilitated as only these one-electron integrals need to be changed. The Gaussian and
exponential type orbital basis sets are, therefore interchangeable in a given program. The
timings of exponential type orbital calculations are no longer significantly greater than for
a Gaussian basis, when a given accuracy is sought for molecular electronic properties.
Numerical values for all two-electron integrals evaluated using Coulomb resolutions as
well as total energies will be tabulated for the H2 dimer and CH3 F molecule.
8.2. Basis Sets
Although the majority of electronic quantum chemistry uses Gaussian expansions of

atomic orbitals [13, 43], the present work uses exponential type orbital (ETO) basis sets
which satisfy Katos conditions for atomic orbitals: they possess a cusp at the nucleus and
decay exponentially at long distances from it [52]- [54]. It updates a real chemistry in-
terest beginning around 1970 and detailed elsewhere [3, 4, 15, 27, 44, 55, 56]. Slater type
orbitals (STOs) [57, 58] are considered here. STOs allow us to use routines from the STOP
package [23, 59] directly. The integrals may be evaluated after Gaussian expansion or ex-
pressed as overlaps to obtain speed up [60]. Exponents may be optimized solving a secular
determinant as in [61].
8.3. Programming Strategy

Firstly, the ideal ab initio code would rapidly switch from one type of basis function to
another. Secondly, the chemistry of molecular electronic structure must be used to the very
fullest extent. This implies using atoms in molecules (AIM) and diatomics in molecules
(DIM) from the outset, following Bader (in an implementation due to Rico et al [50]) and
Tully [62] implemented in our previous work [59, 63], respectively. The natural choice of
atomic orbitals, i.e. the Sturmians or hydrogen-like orbitals lend themselves to the AIM
approach. To a good approximation, core eigenfunctions for the atomic hamiltonian remain
unchanged in the molecule. Otherwise, atom pairs are the natural choice, particularly if
the Coulomb resolution recently advocated by Gill is used. This leads us to products of
auxiliary overlaps which are either literally one- or two- centered, or have one factor of the
product where a simple potential function is translated to one atomic center.
The Slater basis set nightmare of the Gegenbauer addition theorem is completely
avoided. Naturally, the series of products required for, say a four-center two-electron inte-
gral may require 10 or even 20 terms to converge to chemical accuracy, when at least one
atom pair is bound but the auxiliaries are easy to evaluate recursively and re-use. Unbound
pairs may be treated using approximate methods.
Now, the proposed switch in basis set may also be accomplished just by re-evaluating
the auxiliary overlaps. Furthermore, the exchange integrals are greatly simplified in that the
products of overlaps just involve a two-orbital product instead of a homogeneous density.
The resulting cpu-time growth of the calculation is n2 for SCF, rather than n4 . Further gains
may be obtained by extending the procedure to post-Hartree-Fock techniques involving
explicit correlation, since the r12 1 integrals involving more than two electrons, that pre-
viously soon led to bottlenecks, are also just products of overlaps. This Coulomb resolution
is diagonal in Fourier space in some cases.
8.4. Avoiding ETO Translations for Two-Electron Integrals

over Three and Four Centers
Previous work on separation of integration variables is difficult to apply, in contrast to
the case for Gaussians [64, 65]. Recent work by Gill et al [66] proposes a resolution of the
Coulomb operator, in terms of potential functions i , which are characterized by examining
Poissons equation. In addition, they must ensure rapid convergence of the implied sum in
the resulting expression for Coulomb integrals J12 as products of auxiliaries i.e. overlap
integrals, as detailed in [66]:
J12 = h(r1 ) i (r1 )i hi (r2 ) (r2 )i, with implied summation over i. (21)
This technique can be readily generalized to exchange and multi-center two-electron inte-
grals. For two-center terms it is helpful to define structure harmonics by Fourier transforms,
limiting evaluation to non-zero terms [67].
Note, however, that in four-center integrals, the origin of one of the potential functions
only may be chosen to coincide with an atomic (nuclear) position.
Define the potential functions [67]:
i = 23/2 n l (r)Ylm (, )
.
Omitting the spherical harmonic term gives radial factors:
Z +
n l (r) = hn (x) jl (rx)dx, with jl (x) denoting the spherical Bessel function. (22)
0
Here, hn (x) is the nth member of any set of functions that are complete and orthonormal
on the interval [0, +), such as the nth order polynomial function (i.e. polynomial factor
of an exponential). The choice made in [66] is to use parabolic cylinder functions (see
also another application [51]), i.e. functions with the even order Hermite polynomials as a
factor. This is not the only possibility and a more natural and convenient choice is based on
the Laguerre polynomials Ln (x): Define:

hn (x) = 2 Ln (2 x)ex . (23)
These polynomial functions are easy to use and lead to the following analytical expressions
for the first two terms in the potential defined in (22):
tan1 (r)
V00 (r) = 2 , (24)
r
tan1 (r) 2
V10 (r) = 2[ ], (25)
r (1 + r2 )
Furthermore, higher n expressions of Vn0 (r) all resemble (25) (see [67] eq (23)):
1 n
sin(2 k tan1 (r))
Vn0 (r) = 2 (tan1 (r) + (1)k ), (26)
r 1 k
and analytical expressions of Vnl (r) with non-zero l are also readily obtained by recurrence.
These radial potentials can generally be expressed in terms of hypergeometric functions,
whether the choice of polynomial is the present one, i.e. Laguerre, or Hermite polynomi-
als, as in [66]. This structure has been used to confirm the results of [67] using a rapid
code in C [68]. Spherical harmonics are translated using Talmans approach [69]. The dis-
placed potential in one factor of the product of auxiliaries, from four-center integrals is
readily expanded in two-center overlaps, after applying Eulers hypergeometric transforma-
tion. [70, 71].
The auxiliary overlap integrals h(r1 ) i (r1 )i and hi (r2 ) (r2 )i will involve densities
obtained from atomic orbitals centered on two different atoms in exchange multi-center
two-electron integrals. The overlap integrals required in an ETO basis are thus of the type:
max
ha (r1 ) b (r1 ) i (r1 )i = N (n1 , n2 , ni , li , |mi | ) s(n1, l1 , m, n2, l2 , ), (27)
=0
with: = 1 R and = 2 R. Slater exponents. In three-center overlaps, N is a normalised

Racah coefficient [71]. In two-center cases the sum reduces to a single normalisation term,
N0 . A Fourier transform approach is also being investigated, extending [67].
The real space core overlaps then take the form:

1 1
s(n1 , l1 , m, n2 , l2 , , ) = Dl1 ,l2 ,m Yij Ai ( + ) B j ( ) , (28)
ij 2 2
Yij is a matrix with integer elements uniquely determined from n, l and m.

Dl1 ,l2 ,m is a coefficient that is independent of the principal quantum number. It is ob-
tained upon expanding the product of two Legendre functions in this co-ordinate system.
Symmetry conditions imply that only m1 = m2 = m lead to non-zero coefficients:
Z
1 1
Ai ( + ) = exp ( + ) i d, (29)
2 1 2
Z 1
1 1
Bj ( ) = exp ( ) j d. (30)
2 1 2
Here, recurrence relations on the auxiliary integrals A and B lead to those for the requi-
site core integrals [72, 73]. These integrals may be pre-calculated and stored.
Such integrals appear for two-center exchange integrals and three- and four-center in-
tegrals (although just in one factor for three-center Coulomb terms). Note that exchange
integrals require distinct orbitals a and b . In the atomic case, they must have different
values for at least one of n, l, m or . In the two-center case, the functions centered at a
and b may be the same. The product does not correspond to a single-center density: it is
two-centered. Equation (27) then illustrates the relationship to the one-electron two-center
overlap integral, although it clearly includes the extra potential term from the Coulomb
operator resolution.
This assumes tacitly that the potential obtained from the Coulomb operator resolution
be centered on one of the atoms. Whilst this choice can be made for one pair in a four-center
product, it cannot for the second. There remains a single translation for this potential in one
auxiliary of the two in a product representing a four-center integral and none otherwise.
This method obviates the need to evaluate infinite series that arise from the orbital trans-
lations efficiently. They have been eliminated in the Coulomb operator resolution approach,
since only orbitals on two centers remain in the one-electron overlap-like auxiliaries. These
can be evaluated with no orbital translation, in prolate spheroidal co-ordinates, or by Fourier
transformation [67, 71].
8.5. Numerical Results of Coulomb Resolutions: Efficiency

First a test system is studied, built up of four hydrogen atoms. The second example is
the full RHF calculation of CH3 F using the Coulomb resolutions.
Consider the H2 molecule and its dimer/agregates. In an s-orbital basis, all two-center
integrals are known analytically, because they can be integrated by separating the variables
in prolate spheroidal co-ordinates. A modest s-orbital basis is therefore chosen, simply for
accuracy demonstration on a rapid calculation, for which some experimental data could be
corroborated.
The purpose of this section is to compare evaluations using the Coulomb resolution to
the exact values, obtained analytically. The IBM Fortran compiler used is assumed to be
reliable to 14 decimals in double precision. The worst values in the Coulomb resolution
approximation have 10 correct decimals for two-center integrals with a 25-term sum.
Timings are then compared for translation of a Slater type orbital basis to a single cen-
ter (STOP) [59] with the Poisson equation solution using a DIM (Diatomics in molecules
or atom pair) strategy and finally to show that the overlap auxiliary method is by far the
fastest approach, for a given accuracy (the choice adopted is a sufficient six decimals, for
convenient, reliable output).
H2 molecule with interatomic distance of 1.402 atomic units (a.u.). One and two-center
Coulomb integrals may be obtained analytically and Coulomb resolution values compare
well with them [66].
The two-center exchange integrals are dominated by an exponential of the interatomic
distance and thus all have values close to 0.3. The table is not the full set. All index 15
terms, involving 1sa1 (1) 1sb1 (2) are given, to illustrate symmetry relations.
Note that this is by no means the best possible basis set for H2 , since it is limited to
Table 1. Atomic exchange integrals (6 distinct single center values between pairs of
different AOs).
AOs (zeta) Label [a(1)b(2)a (2)b (1)] Value

1sa1 1.042 999 1 1212 0.720 716
1sa2 1.599 999 2 1313 0.585 172
2sa1 1.615 000 3 1414 0.610 192
2sa2 1.784 059 4 2323 0.557 878
1sb1 1.042 999 5 2424 0.607 927
1sb2 1.599 999 6 3434 0.602 141
2sb1 1.615 000 7 2121 0.720 716
2sb2 1.784 059 8 3232 0.557 878
Table 2. Two-center exchange integrals. All pair permutations possible. Some are
identical by symmetry.
Labels Value
1515 0.319 902
1516 0.285 009
1517 0.325 644
1518 0.324 917
1527 0.291 743
1528 0.293 736
1538 0.329 543
2525 0.260 034
2516 0.254 814
2517 0.290 533
2518 0.290 149
l = 0 functions (simply to ensure that even the two-center exchange integral has an analytic
closed form).
The total energy obtained for the isolated H2 molecule is -1.1284436 a.u. as compared
to a Hartree-Fock limit estimate of -1.1336296 a.u. Nevertheless, the Van der Waals well,
observed at 6.4 au with a depth of 0.057 kcal/mol (from Raman studies) is quite reasonably
reproduced [74].
Dimer geometry: rectangular and planar. Distance between two hydrogen atoms of
neighboring molecules: 6 a.u. Note that this alone justifies the expression dimer, the geo-
metry corresponds to two almost completely separate molecules. However, the method
is applicable in any geometry (for 3 a.u. all three- and four-center integrals evaluated by
Coulomb resolution agree with those of STOP to at least 6 decimals).
Timings on an IBM RS6000 Power 6 workstation, for the dimer (all four-center integrals
in msec): STOP: 12 POISSON: 10 OVERLAP: 2. Total dimer energy: -2.256998 a.u. This
corresponds to a well-depth of 0.069 Kcal/mol, which may be considered reasonable in
Table 3a. Orbital exponents.
AO No. n l m zeta
01 1 0 0 5.6727
02 2 0 0 1.6083
3-5 2 1 m 1.5679
06 1 0 0 8.5600
07 2 0 0 2.5600
8-10 2 1 m 2.5200
H 1 0 0 1.2400
Table 3b. Selected examples of three-center exchange integrals.
Integral Value Integral Value

h2sC 2sF |2sC 1sHa i 0.4970 48510 101 h2sF 1sHa |1sF 2sC i 0.1014 05594 102
h2sC 2sF |2sC 1sHa i 0.8420 56635 102 h2sF 1sHa |2sF 2sC i 0.9341 35949 102
h2sC 1sF |1sC 1sHa i 0.5737 90540 103 h2sF 1sHa |2pzF 2sC i -0.8442 95091 102
h2sC 1sF |2sC 1sHa i 0.3789 18525 102 h2sF 1sHa |1sF 2pzC i 0.1813 23479 102
h1sC 2pzF |2pzC 1sHa i 0.1587 58344 102 h2sF 1sHa |2sF 2pzC i 0.1379 64387 101
h2sC 2pzF |2pzC 1sHa i 0.5258 34208 102 h2sF 1sHa |2pzF 2pzC i -0.1135 01125 101
h2pzC 1sF |1sC 1sHa i 0.1025 32536 102 h1sHa 2sF |1sHa 2sC i 0.1252 319411 101
h2pzC 1sF |2sC 1sHa i 0.6772 76818 102 h1sHa 2sF |1sHa 2pzC i -0.1591 49899 102
h1sC 1sF |1sC 1sHa i 0.1099 00118 106 h1sHa 2pzF |1sHa 2pzC i 0.1772 90873 102
h1sC 1sF |2sC 1sHa i 0.6794 54131 106 h1sF 1sHb |2sF 1sC i 0.2287 77210 104
h1sC 2sF |1sC 1sHa i 0.1446 31297 102 h1sHb 2sF |1sHb 1sC i 0.1939 63837 102
h1sC 2sF |2sC 1sHa i 0.4235 59085 102 h2sC 1sHa |1sC 1sHb i 0.2034 841982 101
h2pzC 2sF |1sC 1sHa i 0.1112 10955 101 h1sC 1sHa |1sC 1sHb i 0.7154 932331 102
h2pzC 2sF |1sC 1sHa i 0.6738 14908 101 h2sC 1sHa |2sC 1sHb i 0.1137 390852
view of the basis set.
8.6. Selected Exchange Integrals for the CH3 F Molecule (Evaluated Using
the Coulomb Resolution)
Geometry and exponents are those of previous work [75]: Tetrahedral angles, with C-H
2.067 and C-F 2.618 a.u.
No symmetry is assumed but geometric relationships are observed, as well as those due
to m values, at least to the nano-Hartree accuracy chosen.
For illustrative purposes, three-center exchange integrals are tabulated in a real basis.
Timings on IBM RS6000 Power 6 workstation for all two-electron integrals: STOP: 1.21 s,
OVERLAP: 0.17 s.
All the two-electron integrals are identical to better than six significant figures with
those obtained using the STOP software package [59].
The factor limiting precision in this study is the accuracy of input. The values of Slater
exponents and geometric parameters are required to at least the accuracy demanded of the
integrals and the fundamental constants are needed to greater precision.
8.7. Conclusions
A remarkable gain in simplicity is provided by Coulomb operator resolutions [66], that
now enables the exponential type orbital translations to be completely avoided in ab initio
molecular electronic structure calculations.
This breakthrough that Coulomb resolutions represent (in particular with the conve-
nient choice of Laguerre polynomials) in the ETO algorithm strategy stems from a well-
controlled approximation, analogous to the resolution of the identity. The convergence has
been shown to be rapid in all cases [67].
The applications to H2 dimer Van der Waals complexes and CH3 F uses a general code
within the STOP package [59]. They show the Coulomb resolution can be used to give
fast and accurate results for basis sets of s and p Slater type orbitals. Generalisation is in
progress.
Numerical vales for the H2 dimer geometry and interaction energy agree well with
complete ab initio potential energy surfaces obtained using very large Gaussian basis sets
and data from vibrational spectroscopy [74].
9. Explicitly Correlated Methods for Molecules

The application and development of such methods to determine accurately the ground
and excited states, and properties of diatomic and triatomic molecules is very promising and
more interesting for the Computational Chemist than the atomic case. There is nowadays a
growing interest in this field. Subroutines and programs which perform these calculations
are often requested in the community.
The investigation of these integrals should be approached within the Molecular Orbital
method (MO) [76], because the MO wave function is the simplest wave function for a
molecular system. As Coulson [77] discussed, the MO method permits the visualization of
electrons and nuclei and interpretation of individual electrons and their orbital exponents
better than the wave functions written in elliptical coordinates.
The wave functions constructed with elliptical orbitals are of two types, the so-called
James-Coodlige [78] wave functions (one-alpha exponent), recently extended to the two-
alpha case [33], and Kolos-Wolniewick [79,80] wave functions (with both orbital exponents
alpha, and beta ). Both have been applied to the H2 molecule.
The elliptical wave functions are the natural representation of a two-center problem but
for three-center and larger molecules the use of the MO method becomes necessary. Frost
[81] used the MO method and the Correlated Molecular Method (CMO) in H2 calculations.
About the extension of the method he wrote: The extension of CMO-type wave functions
to more complex molecules does not seem feasible at the present time. The new integrals
which will be introduced would involve more than two centers if more nuclei were involved
and higher atomic orbitals than 1s if more electrons were considered, and their evaluation
would be extremely difficult.
Recently, impressive calculations using Hylleraas wave functions have been done for
H2 , see Table 4. Hylleraas [33], the Iterative Complement Iteration method (ICI) [82], and
explicitly correlated Gaussian (ECG) [83] calculations of the hydrogen molecule, Hylleraas
calculations on HeH+ and some other species [84] leading to 2.9710784698 a.u. using
9576 configurations and calculations of He2 using 4800 optimized ECG configurations with
energy 5.80748359014 a.u. [83] achieved the highest known accuracy in molecules (pico-
hartree accuracy is more than that of chemical measurements, e.g. a micro cm1 , a nano eV
or micro cal/mol. Although one must recall that in the calculation of properties according
to Drake [85], only half of the digits of the energy are kept).
Note also that input exponents, distances and some fundamental constants may limit
accuracy of calculations compared with measurements and that molecules may not be rigid.
Eventually, dynamics and the effect of the Born-Oppenheimer approximation should be
included.
Hylleraas-CI (Hy-CI) was applied in 1976 to LiH molecule by Clary [32] using elliptical
STOs. For two-center molecules the three-electron and four-electron integrals occurring in
the Hy-CI have been developed by Budzinski [39].
Another type of explicitly correlated wave functions are the ones that use Gaussian
orbitals. Clementi et al extended the Hy-CI to molecules using Gaussian orbitals [86],
and applied it to the calculation of H3 . The ECG wave function is appropriate also for
molecules [83, 87], as the inter-electronic distance r12 is a Gaussian exponent. This leads to
results, which are comparable with Hylleraas calculations [83].
The R12 -wave function proposed by Kutzelnigg and Klopper [88, 89] has the merits
to fulfill the cusp condition, to use Gaussian functions avoiding the three- and four-center
integration problems, and to include precisely r12 , involving electrons 1 and 2, close to
the nucleus, where the probability that r12 = 0 is larger, also these electrons are present at
any system starting from helium atom. The r12 variation influences energy. The R12 wave
function, developed for molecular calculations is nowadays widely used and combined with
all kinds of methods. The occurring three- and four-electron integrals are calculated in terms
of two-electron ones. Due to the use of a single r12 value, the accuracy achieved for atomic
calculations is lower than the accuracy of Hy and Hy-CI calculations. Recent improvements
of the method [90]- [92] can achieve microhartree accurate energy results for chemically
interesting systems.
Table 4. Highly accurate calculations on the H2 molecule with different types of wave
functions at R=1.4011 a.u.
Authors type w. f. Confs. Energy (a.u.)

1933 James and Coolidge JC 5 -1.1735
1960 Kolos and Roothaan KR -1.17214
1968 Kolos and Wolniewicz KW -1.174475
1995 Wolniewicz KW 833 -1.17447467
2006 Sims and Hagstrom JC 7034 -1.17447593139984
2007 Nakatsuji ICI 6776 -1.17447571400027
2008 Cencek and Szalewicz ECG,opt 4800 -1.17447571400135
Short wave function expansions lead to very good results. When a large number of
configurations are used (up to 10000) the energy results are beyond pico-hartree accuracy,
while the CI wave function would need in the order of millions of configurations.
10. Highly Accurate Calculations Using STOs

Another problem appearing in these calculations is the digital erosion. For many opera-
tions and subtraction numbers of similar value some digits can be lost leading to erroneous
results. Quadruple precision avoids this, about 30 decimal digits are correct on our com-
puter. Other possibility is high precision arithmetic software. Some programs are available
like Baileys MPFUN [93], the Brent and Miller program packages [94, 95].
One example of the use of Slater orbitals in the present are the highly accurate calcu-
lations of small molecules using explicitly correlated wave functions i.e. wave functions
where the inter-electronic coordinate ri j is included explicitly in the wave function. These
are the Hylleraas and Hylleraas-CI wave functions, ICI method, compared with the explicit
correlated Gaussians ECG and the R12 method.
11. Closing Remarks

We conclude with the words of G. Berthier: GTOs are like medicine, you have to use
them as long as they are healing, but once they dont work any more, you much change
them, Gaston Berthier, Interview, Paris, 2nd June 1997.
Recently, a whole book Recent Advances in Computational Chemistry: Molecular
Integrals over Slater Orbitals was dedicated to a mathematical review of methods of inte-
gration over Slater orbitals and Hylleraas wave functions [96].
Acknowledgements
The authors would like to thank very much Profs. Milan Randic, Ante Graovac, Roberto
Todeschini and Peter Otto for their interest in Slater orbitals.
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Chapter 5
T UNNELING DYNAMICS AND I TS S IGNATURES

IN C OUPLED S YSTEMS
S. Ghosh and S.P. Bhattacharyya

Department of Physical
Chemistry Indian Association for the Cultivation of Science
Jadavpur, Calcutta 700 032, INDIA
Abstract
It has been demonstrated through numerical experiments that tunneling in a symmetric

double well may be either suppressed or enhanced by a Morse oscillator coupled to it
depending on the form of coupling. An external time varying electric field that causes
0+ 0 transition in the double well affects the tunneling rate. A well defined mini-
mum in the rate is observed for = c for which maximum energy transfer from the
double well to the Morse mode takes place. If the field is chosen to cause 0 1 tran-
sition in the Morse mode, the dissociation probability is influenced by the tunneling
mode, being maximized for a particular value = c . In the uncoupled system, field
with similar intensity practically fails to cause any dissociation. The tunneling dynam-
ics is analyzed in a situation when the particle has a coordinate dependent mass as is
often assumed in the charge transport in hetero-structures. The tunneling time or rate
are seen to be very significantly affected by the nature of the coordinate dependence
of the tunneling mass.
1. Introduction
As a purely quantum phenomenon, tunneling is ubiquitous in microscopic systems. It
pervades all areas in physics, chemistry and biology and ever since its use in nuclear physics
in explaining the decay of particles from atomic nuclei, the importance of tunneling has
been increasingly recognized. The study of electron tunneling in condensed matter physics
has led to the Josephson effect and the tunneling diode [1] . The tunneling of proton or
hydrogen atom has often been invoked in chemistry to explain unusual features of chemical
E-mail address: pcspb@mahendra.iacs.res.in
92 S. Ghosh and S.P. Bhattacharyya
reaction rates or mechanisms. In fact, the atom tunneling phenomenon has been recog-
nized to be important in science of various types of materials and biology. Starting from
atom tunneling reactions in quantum solid hydrogen or in solid or liquid Helium, there
have been studies relating to rather unusual aspects of tunneling reactions of organic sub-
stances, tunneling insertion reaction of carbenes and heavy particle tunneling. The role
of atom tunneling reaction in vitamin-C in the suppression of mutation or of vitamin-E
in its antioxidant, pro-oxidant and regeneration reactions have attracted serious attention
from biologists. The possible occurrence of spontaneous tunneling elimination of hydrogen
molecules from hydrocarbon cations has led to serious questions about our conventional
idea of a stable chemical structure [2]. The relevance of tunneling in the interpretation of
molecular and crystal structure in very low temperature regimes can hardly be overesti-
mated. It would be appropriate therefore to review briefly how the idea of tunneling was
developed and exploited in different fields of science.
2. Historical Development
A. Tunneling in Physics
The theory of radioactivity proposed by Gamow [3] explained the law of exponential
decay P(t) = N(t) t by solving the Schrodinger equation for the particle inside the
N0 = e
nucleus where the attractive nuclear force and coulomb repulsion were assumed to provide
an effective barrier confining the particle. Gamow imposed the outgoing wave boundary
condition at large distances from the center of the nucleus and found that the Schrodinger
equation does not have solutions for the real energies while for complex energies, it had
solutions. Gamow interpreted the imaginary part of the energy as the decay width 2 and
obtained a relation between 2 and the energy of the emitted particle. The use of com-
plex energy meant the use of a non-hermitian hamiltonian and the idea was criticized as
quantum mechanics worked with hermitian operators. The same result was later obtained
by Bohr by considering states with real energies and working with a hermitian hamiltonian
[4]. The idea of resonant tunneling was introduced by Gurney who realized that particles
with low energies that match with quasi-stationary energies of the nucleus could easily pen-
etrate the barrier [5]. The importance of the idea in artificial disintegration can hardly be
overestimated.
The idea of tunneling was soon exploited in other areas of physics. Notably, many at-
tempts were made to relate the dynamics of electron current in the metal semi-conductor
systems to the tunneling of electrons in solids. The discovery of transistors in 1947 rekin-
dled interest in the tunneling of electrons in solids the occurrence of which was conclusively
proved by L. Esaki (1957) who discovered the tunneling diode [6]. Close on the heels of the
discovery of tunneling diode, Giaever found if one or both the metals are superconducting,
the voltage-current plots could lead to measurement of energy gaps in superconductors [7].
Josephson discovered that the superconductors separated by a thin layer of insulating oxide
provide a system in which a second current (over and the above the Giaevers current), the
so-called supercurrent, exists and that it is caused by tunneling of electrons in pairs [8]
Dynamics and Its Signature 93
B. Tunneling in Chemistry
Tunneling has a long history in chemical kinetics. Traditionally, curvature in Arrhe-

nius plots of rate constants has been interpreted as a signature of tunneling. It is generally
very difficult to observe such curvatures in Arrhenius plots for gas phase chemical reactions
while such curvatures are a common-place occurrence in chemical reactions in condensed
phases below 100 K. Accurate theoretical calculations, however, indicate that tunneling can
contributes significantly to the reaction rates even at room temperature where the Arrhe-
nius plots are very nearly linear [8]. In fact, tunneling can be taken to be synonymous
with a chemical reaction occurring at energies less than the barrier energy (Ea ). The barrier
arises on the 3N 6 dimensional potential energy surface in the Born-Oppenheimer ap-
proximation as the nuclei of the N atom reactive system move breaking and making bonds.
Traditionally one identifies the one dimensional minimum energy path (x) as the reaction
path along which an effective potential energy Ve f f (x) is defined by adding the vibrational
energies (x) along the reaction path associated with the nuclear motion perpendicular to
it [9]. This vibrationally adiabatic approximation reduces the multidimensional problem
into a one dimensional problem, for which tunneling has a unique definition. The tunneling
probabilities calculated using the idea described above are generally a bit too small due to
the neglect of the reaction path curvature. Several alternative approaches have been ex-
plored for better representation of the tunneling path, for example, the least action ground
state method [10] and the tunneling tube method [11]. The barrier energy on the reaction
Ea
path can be identified with the activation energy (Ea ) in the Arrhenius rate law k = Ae Kb T
which has been recognized as the central law of chemical kinetics.
Many attempts have been made to derive the central law of chemical kinetics. The
transition state theory (TST) of Eyring [12] was the first attempt in this direction. The
TST was derived assuming complete thermodynamic equilibrium wherein the possibility
of reverse transition was neglected, which was later taken care of in an ad hoc manner by
introducing a transmission coefficient in the pre-exponential factor. Kramers [13] treated
elementary rate process in the presence of a medium as a generalized Brownian motion in a
potential field and showed how the rate constant would be influenced by the viscosity of the
medium. Kramers results have been derived from the TST applied to an extended system
of the reactants and reservoir of oscillators which provide a frictional force and a random
force along the reactive mode [14]. Kim and Hynes [15], Truhler etal. [16] introduced
additional coordinates describing the dynamics of the solvent mode along with the reagent
mode within the framework of TST and derived results equivalent to those obtained by
Kramers. Chemical reactions at sufficiently low temperatures are marked by remarkably
special features.
Goldanski [17], showed that the rate constant of a chemical process has a low tem-
perature limit (non-zero) as T 0 and introduced the concept of crossover temperature
(Tc )which divides the whole temperature interval into over and under barrier regimes. Gol-
danskii assumed that the tunneling particle moves through the saddle point for obtaining
TC . A tunneling particle may not, however move in the traditional classical manner along
the adiabatic reaction coordinate through the first order saddle point, but take a short cut
wherein it experiences a higher barrier, but a shorter tunneling length. In the absence of
highly precise data for the reaction systems, numerical calculations for obtaining the tun-
neling rate constant become difficult. One is then left with the alternative of relating the
special features of tunneling chemical reactions to the changes in the reaction barrier due to
the vibrations (intermolecular) [18].
Atom transfer reactions are the most thoroughly investigated reactions [19]. Here the
transferring atom moves between the two potential wells. A reversible transfers leads to
tunneling level splitting (spectral signature of tunneling) and an irreversible transfer pre-
cipitates chemical reactions (signature of tunneling dynamics). If the period of inter-well
quantum oscillation is smaller than the relaxation time, coherent transfer takes place while
the process is incoherent if the opposite situation is encountered. If the two time scales
are comparable, the process is better described by density matrix methods. Ivanov and
Kozhushner [20] showed that the time period of oscillation (1 ) and the particle trans-
fer time (the tunneling time ) play an important role. If << 1, the particle transfer is
instantaneous and takes place at predetermined positions of the reagents. If >> 1, the
transfer takes place at average positions of the reagents and the surrounding molecules. If
= 1, the tunneling particle adjusts its positions corresponding to those of the reagents
and the surroundings. The synchronous motion of the reagent and the surroundings may
either hasten or delay the particle transfer rate [22]. In a tunneling reaction we have three
subsystems taking part of which the electronic and the intramolecular subsystem constitute
the fast variables and the inter subsystem variables constitute the slow variable. Using the
Fermi Golden rule, and a modified theory of radiationles transition, an expression for the
tunneling rate constant has been obtained [21]
2
ktunneling = Ai h f |V (R)|i i2 (~ f + E ~i ).
~ f
The transition matrix element delicately depends on the distance between the reagents
and that means intermolecular vibrations play a dominant role in shaping the tunneling rate
constant. Such vibrations cause variations in the tunneling distance. Vibrations that bring
the reagent closer are called promotive modes which are taken into account by invoking
either the Einstein or the Debye model of promotive modes [22-24], depending upon the
situation. It has been shown that in atom tunneling reactions in the solid phase the low
temperature limit of ktunneling exists for nonendothermic processes only.
Along with inter-molecular vibrations (which can change inter-reagent separation), me-
dium reorganization and under barrier friction play significant roles in determining temper-
ature and pressure dependence of tunneling rate constants. The effect of reorganization of
the medium alone leads to a temperature dependence that is independent of the form of the
barrier. We note that the tunneling particle is assumed to interact with phonons only in the
initial and final states, but not during the course of tunneling. The interaction of the tunnel-
ing particle with phonons in the underbarrier regimes lead to the appearance of frictional
effects that depend rather sensitively on the form of the barrier and its modulations, if any.
C. Tunneling in Coupled Systems

With the preceeding background in view, our purpose in this chapter has been to inves-
tigate typical signatures of tunneling dynamics in several coupled systems. In one of these,
the tunneling mode is described by a symmetric double well potential which is coupled to,
let us say, a bond stretching mode. The latter is represented by a typical Morse potential
and the form and strength of the coupling are assumed to vary. We propose to investigate
how the mode of coupling with bond stretching mode influences the tunneling dynamics in
the double well and vice versa. If the bond stretching mode is externally driven, how does
it affect the tunneling dynamics? These questions are addressed in subsequent sections.
Normally, the tunneling particle is assumed to have a fixed mass- fixed in space and
time. However, in charge transfer and tunneling of electrons through heterostructures, the
effective mass of the electron is often assumed to be coordinate dependent. Could the
coordinate dependence of the mass of the tunneling particle have a typical signature on the
tunneling dynamics? We have investigated the question through numerical experiments.
Let us now focus on the general methodology used in our explorations.
3. The Method
For the calculations, we have used time dependent Fourier grid hamiltonian method
[25-19]. The basic framework of the approach adopted in the present series of calculations
is described in this section.
A. Dynamics of the Coupled System in the Absence of Driving

Let H0 (x, y) be the hamiltonian of a particle of mass m moving on the x y plane in a
potential V0 (x, y), where V0 (x, y) is assumed to be additively separable into a double well
potential V0 (x) and a Morse potential V0 (y) . Thus
H0 (x, y) = T0 (x) + T0 (y) +V0 (x, y)

= T0 (x) +V1 (x) + T0 (y) +V2 (y) = H0 (x) + H0 (y). (1)
Let us assume that x represents the tunneling coordinate and y stands for a bond stretching
coordinate. To be more specific, we may take H0 (x) is taken to represent the Hamiltonian
describing the motion of a quantum particle in a asymmetric double well potential V1 (x)
while H0 (y) is assumed to represent the motion along a bond stretching coordinate described
by an appropriate Morse potential V2 (y) . We may now introduce a coupling between the
two modes by using the interaction potential Vint (x, y) so that the total hamiltonian H(x, y)
that describes the coupled system can be written as
H(x, y) = H0 (x, y) + Vint (x, y). (2)
being the strength of the coupling between the tunneling and bond stretching coordinates.
The purpose of the present study has been to investigate how the tunneling dynamics gets
affected by the coupling with the bond stretching mode. Let us assume that the eigen
functions i (x) of H0 (x) and i (y) of H0 (y) are known to start with. The states of the
coupled system can be described by superposition of the products of the eigenstates of the
uncoupled system [H0 (x) and H0 (y)]. Thus we may write
ni n j
|(x, y,t)i = ci j (t)|i (x) j (y)i. (3)
i j
The product functions generated by the eigenfunction of the uncoupled system de-
scribed by the hamiltonians.H0 (x) and H0 (y) serve as the basis of the coupled system. The
introduction of the coupling term Vint (x, y) would cause the superposition in equation 3 to
evolve in time. The combination coefficients ci j s are therefore taken to be time depen-
dent. Time evolution equations for the combining coefficients are obtained from the time
dependent Schrodinger equation by following the standard procedures and are given by
mx ,my
dci j
i~
dt
= ckl hxk yl |H0 (x, y)|xi yj i (4)
k,l
for i = 1, mx , j = 1, ny
We may call it a time dependent configuration interaction type of formalism. To find
out the time independent basis functions |i (x)i and | j (y)i we make use of the Fourier grid
hamiltonian (FGH) technique [29] and compute the eigenfunctions and eigenvalues of the
uncoupled model systems as follows
H0 (x)|i (x) = xi |i (x)i, (5)
where
nx
|i (x)i = wxpi |x p ix, (6)
p=1
and
H0 (y)i (y) = yi |i (y)i, (7)
where
ny
|yi i = wyqi |yq iy. (8)
q=1
wxp,i and wyq,i are the corresponding grid point amplitudes along x and y coordinates, respec-
tively. We note that the coordinates are uniformly discretized, x and y being the uniform
grid spacing along the x and y coordinate, respectively. Using equations (6) and (8) the
time evolution equations of the combining coefficients ci j (i = 1, nx ; j = 1, ny ) of equation
4 reduce to
nx ,ny
dci j
i~ = ckl wxpi wyq j H(x p , yq )wxpk wyql (xy)2 = ckl Hi j,kl . (9)
dt k,l p,q k,l
In matrix form equation 9 can be written as

= HC(t).
i~C(t) (10)
The time integration may be done by employing sixth order Runge-Kutta method. When a
quantum mechanical particle moves in a double well there is a nonzero probability that the
particle tunnels from one well to the other well whatever be its energy relative to the barrier
top. Let us suppose the particle was initially localized in the left well of the uncoupled
symmetric double well. The lowest energy localized states (L and R ) can be described
by linear combinations of the two lowest energy eigen-states of even (+ 0 ) and odd parity

(0 ), respectively
1
L = (+ 0 + 0 ),

(11)
2
1
R = (+ 0 0 ),

(12)
2
where L and R represent the states localized in the left and the right well, respectively.
In the absence of any coupling between the tunneling mode and the bond stretching mode
the particle tunnels coherently from the left well to the right well. If one takes L to be
the initial state, tunneling probability is obtained by calculating the probability of finding
the particle in the right well at energies less than the barrier energy. The corresponding
probability PR (t) at any particular instance is given by (the barrier is located at x = 0)
Z
PR (t) = |(x,t)|2 dx. (13)
0
In the two dimensional case, the corresponding probability can be computed by using
Z + Z +
PR (t) = |(x, y,t)|2 dxdy. (14)
y= x=0
In the CI formalism used by us in the FGH basis, equation 14 can be written as
ni ,n j nx ny
PR (t) = |ci j |2 wxpi wyq j xy.
nx 1
(15)
i, j q=1
2
The rate of tunneling can then be obtained from the average slope of the PR (t) - t plot.
Alternatively, the tunneling rate can be calculated from the average rate of the change of
the hx(t)i with time plot, where hx(t)i is given by
hx(t)i = h(x, y,t)|x|(x, y,t)i. (16)
Substituting the expression for h(x, y,t)| from equation (4) we get
hx(t)i = ci j (t)ck j (t)hxi |x|xk i (17)
i, j,k
nx
= ci j ck j wxpi x p wxpk . (18)
i, j,k p
The computed rate of tunneling is related to the tunneling splitting in the double well [30].
When the double well gets coupled to a bond stretching mode described by a Morse oscil-
lator, we may envisage three probabilities:
(a) The bond stretching mode enhances the tunneling rate. We may call it a promoting
mode.
(b) The bond stretching mode reduces the tunneling rate. We call it a suppressing mode
(c) The bond stretching mode does not affect the tunneling rate at all. It acts as a passive
mode
We anticipate that the type of the effect could depend on the nature of the coupling (see
later).
B. Dynamics of the Coupled System in the Presence of External Driving

When a spatially homogeneous external electric field is applied along the x direction
the perturbed hamiltonian H(x,t) can be represented as
H(x,t) = T (x) +V1 (x) +V (x,t) (19)

= H0 (x) +V (x,t), (20)
where
V (x,t) = xex sin(t). (21)
is the field intensity and e represents the charge carried by an electron. Similarly, with an
electric field applied along y direction
H(y,t) = H0 (y) +V (y,t), (22)
where
V (y,t) = yey sin(t). (23)
The time evolution equations now turn out to be (with field along x direction)
nx ,ny
dci j
i~ = ckl wxpi wyq j (H(x p ,t) + H0 (yq ) + Vint (x p , yq ))wxpk wyql (xy)2 (24)
dt k,l p,q
for i = 1, nx ; j = 1, ny .
These equations can be integrated numerically over ckl s at t = 0 are provided.
4. Results and Discussion

A. Tunneling in the Coupled System in Absence of External Driving
We take the model potentials
V1 (x) = ax4 bx2 + c, (25)

((yye )) 2
V(2) (y) = D(1 e ) . (26)
The system parameters are listed in table-1. FGH calculations have been done with
151 grid points in each coordinate. The grid lengths along x axis and y axis are 6 a.u and
10 a.u, respectively. When V1 (x) and V2 (y) are coupled through an interaction potential
Vint (x, y) and the coupling strength . the shape of the two dimensional potential energy
surface (PES) gets modified depending on the functional form of V (x, y) and strength .
Figure 1a shows the two dimensional potential energy surface (PES) when V1 (x) and V2 (y)
are uncoupled, i.e. = 0. Figure 1b shows the two dimensional PES for Vint (x, y) = xy,
( = 0.001). Evidently, for the particular functional form the symmetry of the double well
potential gradually gets distorted (along the y axis). The left well becomes deeper than
the right well. By increasing the coupling strength the asymmetry between the two wells
Figure 1. Potential Energy Surfaces for different forms of interaction potentials Vint (x, y).
(a) Vint (x, y) = 0; (b) Vint (x, y) = xy; (c) interaction potential Vint (x, y) = x2 y2 ; (d)
Vint (x, y) = (x2 y + xy2 ).
increases and the coherence in the tunneling process is progressively disturbed. Figure 2a
shows the plot of the computed tunneling rate versus the coupling strength. The initial wave
function (x, y,t = 0) corresponds to the state in which the Morse mode and the tunneling
mode are both in the ground state.
From figure 2a we can clearly conclude that the tunneling rate decreases almost linearly
with increasing coupling strength for the particular functional form of interaction potential
Vint (x, y) = xy. Figures 1c and 1d show the two dimensional PES for the functional forms
Vint (x, y) = x2 y2 and Vint (x, y) = (x2 y + y2 x), respectively (with = 0.001). In figure
1c the symmetry of the double well potential remains intact but the barrier height of the
double well decreases (along y axis). As we go on increasing with the functional form
Vint (x, y) = x2 y2 the barrier height gradually decreases and as a consequence the tunneling
rate increases almost linearly which is very clearly reflected in figure 2b. If Vint (x, y) is taken
to have the form Vint (x, y) = (x2 y+y2 x), the PES (figure 1d) is obtained in which the barrier
height of the double well potential increases as well as the symmetry of the double well po-
tential is lost. The tunneling rate decreases (figure 2c) as increases. These results indicate
that the form (Vint (x, y)) and strength () of the interaction potential between the symmet-
ric double well (tunneling mode) and the Morse oscillator (bond stretching mode)are very
important in determining the nature and the extent of the influence that the coupling could
Figure 2. Tunneling rate in the coupled systen in absence of external driving when (a)
Vint (x, y) = xy; (b) Vint (x, y) = x2 y2 ; (c) V (x, y) = (x2 y + xy2 ).
have on the tunneling dynamics in the double well.
B. Tunneling Dynamics in the Coupled System in the Presence of an External

Electric Field Coupled to the Tunneling Coordinate
We apply an external time varying electric field along the tunneling coordinate with an
intensity of 0.01 a.u and frequency of 0.00227 a.u. The specific frequency matches with
the 0 1 transition frequency (01 )of the double well. We take the product of the lowest
even parity state the double well and the ground state of the Morse oscillator, as the initial
state;
(x, y,t = 0) = +
0 1 . (27)
For the uncoupled composite system, = 0 and we see the particle execute a to and fro
movement between the two wells. Figure 3a shows the plot of < x > vs t for the uncoupled
double well Morse oscillator system. The variation of < x > seems to be very regular and
periodic in nature. The corresponding quantum phase space diagram (figure 3b) shows that
Figure 3. Tunneling dynamics in the presence of an external time varying field coupled
to the tunneling coordinate x with Vint (x, y) = xy (a) < x > versus t profile at = 0; (b)
Quantum phase space diagram along = 0 for the tunneling mode; (c) < x > versus t
profile at = 0.0001; (d) Quantum phase space diagram along = 0.0001 for the tunnel-
ing coordinate; (e) Quantum phase space diagram for = 0.0001 for the bond stretching
mode.
the particle is symmetrically distributed in the two wells ( the symmetry about < x >= 0
line is maintained). Tunneling rate is calculated from the average slope of < x > versus t
plots. When the symmetrical double well system gets coupled to the Morse oscillator with a
coupling term Vint (x, y) = xy the dynamics gets modified. We have shown the variation of
< x > with t for = 0.0001 for such a system in figure 3c which is substantially different
from the corresponding picture of the uncoupled system (figure 3a). However, figure 3c
also exhibits regularity and periodicity. The quantum phase space picture (figure 3d) is
still symmetric about the < x >= 0 line, but the area occupied in the phase space diagram
has decreased substantially.
It indicates transfer of some energy from the tunneling to the bond stretching mode. Fig-
ure 3e displays the quantum phase space structure along y direction (the bond stretching
mode). The occupied region of the phase space in figure 3e is rather small which indicates
that the energy transfer from the x mode to the y mode (i.e. from the tunneling to the bond
stretching or the Morse mode) is also small for = 0.0001. However, because of this small
energy transfer the tunneling rate gets reduced. We have investigated the dynamics at dif-
ferent values of and we have found that the energy transfer from the x mode to the y mode
becomes maximum at = 0.003. The tunneling rate in turn passes through a minima for
= 0.003 (figure 4a). Figure 4b shows the variation of < x > with time for = 0.003. At
this value the quantum phase space diagram for the Morse mode occupies a larger area
which again indicates that the energy transfer (figure 4d) from the tunneling to the Morse
mode for the given value of is higher. The population of the first excited state of the
Morse oscillator grows (figure 4d) with oscillations which is reflected in the increase of the
amplitude of the oscillation of the average bond length < y > (figure 4e).
It is clear therefore that direct excitations by external field coupled to the tunneling
mode can influence the bond stretching mode coupled to it.
C. Tunneling Dynamics in the Presence of External Field Coupled to the Bond

Stretching Mode
If we locally excite the Morse mode with an external time varying electricfield of in-
tensity 0.01 a.u, and frequency 01 (y) (frequency of the 0 1 transition in the Morse
mode), we do not observe any significant probability of bond dissociation in the uncoupled
system. But if we introduce an interaction potential Vint (x, y) = xy, the dissociation prob-
ability slowly rises as increases. Table-3 shows the values of the computed dissociation
probability and tunneling rate for various values of coupling strength ().
At = 0.004 we observe a dissociation probability of 0.37 which is the maximum for
the given intensity. From table-3 it is clear that tunneling is strongly impeded when the
tunneling mode gets coupled to a stretching mode that is locally excited. Quantum phase
space picture along the tunneling coordinate at = 0.004 is depicted in figure 5a. Figure
5b exhibits the corresponding picture for the stretching mode at = 0.004. The growth of
dissociation probability attains a maximum at = 0.004 (Table-3). Figures 5c and 5d show
the quantum phase space diagrams for the stretching mode for = 0.001 and = 0.006,
respectively. In both the cases the area occupied in the phase space is smaller compared to
what is observed for = 0.004 (figure 5b). It indicates that the maximum energy transfer
from the symmetric double well to the Morse mode takes place at = 0.004 which is
Figure 4. Tunneling dynamics in the presence of an external time varying field coupled to
the tunneling coordinate with Vint (x, y) = xy (a) Tunneling rate versus coupling strength ;
(b) < x > versus t profile for = 0.003 along the tunneling coordinate; (c) Quantum phase
space diagram for = 0.003; (d) Population of the ground and the first excited states of
the bond stretching mode for = 0.003; (e) < x > versus t profile at = 0.003 for the bond
stretching mode.
Figure 5. Tunneling dynamics in the presence of an external time varying field coupled
to the bond stretching coordinate with Vint (x, y) = xy (a) Quantum phase space diagram
for = 0.004 along the tunneling coordinate; (b) Quantum phase space diagram for =
0.004 along the bond stretching coordinate; (c) Quantum phase space diagram for =
0.001 along the bond stretching coordinate; (d) Quantum phase space diagram for =
0.006 along the bond stretching coordinate; (e) Dissociation probability versus time for
= 0.004.
reflected in the relatively high dissociation probability achieved at the given intensity of the
external field . Figure 5e shows the plot of the computed dissociation probability against
time at = 0.004 a.u. The dissociation probability grows fast and attains a relatively high
value. The tunneling, on the other hand gets quenched completely. Thus, excitations in the
non-tunneling mode in the coupled system can be exploited for controlling tunneling.
D. Tunneling Dynamics of a Particle with Coordinate Dependent Mass

Tunneling of electron through heterostructures is complicated by the interaction of the
tunneling particles with many centres of scattering. Instead of taking these complexities
directly into account in the calculation, it is often expedient to replace the real system by
a model one in which the tunneling potential remains unaffected, but the tunneling particle
is assumed to have coordinate dependent mass. The question that arises now concerns the
signature of the coupling of the tunneling particle with the lattice or equivalently of the
coordinate dependent mass [31], on the dynamics of the tunneling. We have carried out a
series of experiments within the framework of the basic methodology described in Section-
II. The numerical experiments are done with a symmetric double well potential and are
subdivided into two classes.
1. The mass of the tunneling particle varies symmetrically along the tunneling coordi-
nate.
2. The mass variation is asymmetric
Figure 6. Pattern of coordinate dependent mass variation (a) mass distribution is gaussian;
(b)mass distribution has a minima at the barrier top.
Under category 1 three possibilities have been investigated: (a) the tunneling mass is
constant m0 everywhere, (b) the tunneling particle has mass m0 at x = 0 where the barrier
height is maximum while away from the barrier top, the mass decreases. More specifically,
2
the mass has a gaussian profile along the tunneling coordinate (figure 6a), m(x) = m0 ex ,
and (c) the tunneling mass is m0 at the bottom of the left or right well and it decreases as
2 2
it approaches the barrier top at x = 0 (figure 6b) i.e m(x) = m0 e(x a ) . x = a being
the location of the well minima. Figure 7a shows how the dynamics appears to be when
the tunneling mass (m0 ) is fixed along x. It is perfectly coherent and the particle oscillates
back and forth between the right and the left wells. When the tunneling mass is higher in the
Figure 7. The pattern of tunneling dynamics displayed when (a) tunneling mass is indepen-
dent of x i.e. m(x) = m0 ; (b) tunneling mass has a maxima at the bottom of the wells; (c)
tunneling mass has a maxima on the barrier top.
Figure 8. The mass distribution plot when it is sharply peaked at x = .
wells and lower in the barrier, the tunneling becomes slower, still remaining coherent (figure
7b). However, if the tunneling mass is lower in the well and increases as it approaches
the barrier, the tunneling rate is increased very significantly and the coherent oscillation
frequency becomes much larger (figure 7c). In such a situation very significant increase in
tunneling rate through heterostructure should be seen. It is clear that mass concentration in
the well lowers the tunneling rate while mass concentration in the barrier region enhances
tunneling.
Under category-2, we have considered an asymmetric distribution of the tunneling mass
along the tunneling coordinate by assuming
m0
m(x) = . (28)
|x + |
The function is peaked at x = (figure 8). The larger the value of the larger is the shift
of the peak towords the region x < 0. Figure-8 shows the mass variation pattern along the
tunneling coordinate for different values of . The tunneling time [32] has been computed
for each value of with m0 being assumed to be the proton mass and reported in table-IV. It
is clearly seen that tunneling time increases as increases meaning thereby that the rate of
tunneling decreases. The asymmetric mass variation of the type displayed in figure 8 along
the tunneling coordinate could lead to quenching tunneling. The coupling with the lattice
(environment) can therefore modulate tunneling current in hetero structures.
Table 1. Morse and Symmetric double well potential parameters used in model
calculations
Parameters Values (a.u)
a 0.1
b 0.12
c 0.04
D 0.135
0.731
xe 2.23
250.0
Table 2. Energies of the Morse and the double well oscillators
double well Morse Oscillator

1st state energy(a.u) 0.02270 0.00439
2nd state energy (a.u) 0.02496 0.01267
Table 3. Computed dissociation probability and tunneling rate in a symmetric double

well and Morse oscillator system for various strength of coupling parameters
Dissociation probability Tunneling rate(au1 )

0 0.04 0.000769
0.001 0.05 0
0.002 0.1 0
0.003 0.18 0
0.004 0.37 0
0.005 0.05 0
0.006 0.05 0
Table 4. Computed tunneling time for various
Tunneling time
5.0 105 0.5
1.0 106 1.0
3.3 106 1.5
5. Conclusion
In a tunneling system where the tunneling motion of the particle along the coordinate
gets coupled to non-tunneling motion along another coordinate, the coupling leaves its sig-
nature on the dynamics in different ways. It can quench tunneling, depending upon the
strength and form of coupling. Similarly the tunneling motion can also affect the dynamics
along the non-tunneling (e.g. bond stretching) coordinate. Experimentally, little seems to
be known about the possible impact that excitation in the tunneling coordinate could have
on the bond stretching and the dissociation dynamics of a mode coupled to the tunneling
coordinate and vice-versa. Work along these lines could enrich our knowledge about the
dynamics of coupled quantum system.
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Chapter 6
THEORETICAL CALCULATION OF THE LOW LAYING

ELECTRONIC STATES OF THE MOLECULAR ION
CSH+ WITH SPIN-ORBIT EFFECTS
M. Korek* and H. Jawhari

Faculty of Science, Physics Department, Beirut Arab University,
P.O.Box 11-5020 Riad El Solh, Beirut 1107 2809, Lebanon
Abstract
Research studies on ultracold molecules are a current and great challenge in the spectroscopic
study of alkali dimers, because of their importance in the cooling and trapping of atoms and
molecules, their role in high precision spectroscopy and Bose-Einstein condensation (BEC).
Using the high reliability of the ab initio technique combined with the easily amenable
phenomenology core polarization concept, the theoretical calculation of the electronic
structure of the molecular ion CsH+ has been performed. This ion is treated as a one electron
system where the interaction between the outer electron and the atomic core of Cs+ is
modulated through non empirical relativistic effective one-electron core potential. The lowest
2
71 electronic states for the ion CsH+ have been calculated for the molecular states (+) and
and dissociating into the 16 asymptotes considered, i.e. up to 16 states 2+, 9 states 2, 4
states 2, 25 states =1/2, 13 states =3/2 and 4 states =5/2. Some avoided crossings are
pointed out for the symmetries 2+, 2, =1/2 and =3/2, their positions rAC and the energy
difference EAC at these positions have been determined. For 19 bound states, the harmonic
vibrational constant e, the internuclear distance re and the electronic transition energy with
respect to the ground Te have been calculated. Using the canonical functions approach, we
calculate in the present work Ev, Bv and Dv of the molecular ion CsH+ up to the vibrational
levels v = 19 for 17 electronic states. From the calculated values of Ev for a given vibrational
level v and by using a cubic spline interpolation between each 2 consecutive points of the
potential energy curves, the rmin and rmax of the turning points have been investigated for
a
these bound states. Permanent dipole moments M a (r) as well as all non-zero transition
dipole moments M ab (r) (ab ) have been calculated for each electronic state (a,b) under
*
E-mail address: fkorek@cyberia.net.lb
112 M. Korek and H. Jawhari
consideration and in the whole range of r investigated here. The comparison of the present
results with those available in literature shows a very good agreement.
1. Introduction
Beginning in the late 1980s, methods to use laser light to cool and confine atoms at
unprecedented temperatures have made a dramatic impact on atomic physics. The cooling and
manipulation of cold molecules is likely opening up new branches of research. As a gas of
molecules is cooled, their average velocity is decreased and the spread of their molecular
velocities narrowed. This is important not only for studying molecular physics, but also for
studying fundamental physics. The internal structure of certain molecules provides an ideal
laboratory for sensitive measurements of fundamental physical quantities. Ultracold
molecules are of a current and great challenge in the spectroscopic study of alkali dimers,
because of their importance in the cooling and trapping of atoms [1,2] and molecules [3],
their role in high precision spectroscopy [4], Bose-Einstein condensation (BEC) [5], atomic
clocks, ultrasensitive isotope detection, quantum information, and processing ultracold
collisions. At ultracold temperatures, the collisions of atoms, which may be characterized by
s-wave scattering lengths, have received considerable attention because of their importance in
cooling and trapping of atoms and molecules [6] and their role in high precision spectroscopy
[7]. Collisions of ions involve higher-order partial waves because of the long-range attractive
polarization forces and because of the possibility of charge transfer. Ion-atom charge transfer
collisions are of great interest both theoretically and experimentally. Another especially
promising area will be the study of collisions between ultracold molecules, in a regime where
they behave like waves, perhaps giving rise to a new chemistry [8]. They may also allow for
the study of collective quantum effects in molecular systems, including BEC [9].
There are proposed experiments to study polar molecular systems in order to measure the
electrons permanent electric dipole moment (EDM), the lifetime of long-lived energy levels,
and the effects of the dipole-dipole interactions on the molecular samples properties [10].
Ultracold polar molecules interact with each other via highly anisotropic electric dipole-
dipole forces providing access to qualitatively new regimes previously unavailable by
ultracold homonuclear_nonpolar systems [11-12]. Novel phenomena are expected from
ultracold polar molecules as new features in phase diagrams of degenerate states [13] and
anisotropic collisions caused by anisotropic dipole-dipole interaction [14]. The sympathetic
cooling of these mixtures has led to the achievement of simultaneous quantum degeneracy of
bosonic and fermionic species, producing BEC and Fermi-Bose mixtures [15-16]. Theory
groups developed the methods to map problems, such as the BEC-BCS crossover, superfluid
phases, Bose glasses and spin-charge separation from solid state quantum systems to the pure
world of degenerate quantum gases [17-19]. Meanwhile, a growing community developed the
technique of atom chips. From this dataset and the experience of three generations of atom
chip experiments on hand, a truly next-generation experiment was designed. Furthermore, the
interaction of bosons and fermions with attractive and repulsive interactions can be studied
without the need of a Feshbach resonance, as the interaction between Rb and Li is repulsive
and the interaction between Rb and K is attractive [20]. Recent advances in precision control
of the optical spectrum emitted by a femtosecond laser have made a revolutionary impact on
the fields of optical frequency metrology (via self-referenced, ultra-broad bandwidth
Theoretical Calculation of the Low Laying Electronic States 113
frequency combs) and ultrafast optical science (via carrier-envelope phase stabilized pulse
trains). These advances have, in effect, provided an entirely new class of optical sources
available for experimental investigations which is the Femtosecond lasers+cold
atoms/molecules.
In the three past decades a limited number of theoretical studies have been performed for
the molecular ions AH+(where A is an alkaline atom). The potential energy curves of these
molecular ions are well needed to understand ion-atom collision [21] and to serve as input for
diatomics-in-diatomics studies of the potential energy surfaces for A+H2 collisions [22].
These systems are interesting for the theory of chemical bonding since each involves a single
valence electron. Interest in alkali dimers is closely related to developments in the ultra-cold
alkali dimers atom trapping, which are at the root of photoassociation spectroscopy. The
charge transfer in collision of neutral alkaline atoms with protons affects the ionization
balance in the atmospheres of planets, dwarf stars, and the interstellar medium [23-27]. At
low temperature, such as in ultracold experiments, collision energies are much les than 1eV,
and radiative charge transfer may become dominant over nonradiative charge transfer.
Neutralization of H+ is of interest in the area of plasma fusion as a method of energetic
neutral beam injection in fusion reactors. At lower energies, this charge exchange process is
used to make metastable [H(2s)] hydrogen used for atomic experiments [28,29] and for the
creation of spin polarized proton beam for injection into large accelerators [30]. Due to these
results, the lack of the theoretical calculation on a certain number of alkali dimers, and
because of its use particularly in the domain of quantum computer to create the qubite [31],
we investigated recently theoretical calculation of these molecules and their ions [32-38].
Using an improvement on the ab initio pseudo-potential method [39-45], we investigate in
this chapter the lowest 29 electronic states of -representation (neglect spin-orbit effect), the
lowest 42 electronic states of -representation (including spin-orbit effect), and the
spectroscopic constants of the regularly bound states. Based on the canonical functions
approach [46-48], a rovibrational study has been done to calculate the eigenvalue energies Ev,
the rotational constants Bv, the centrifugal distortion constants Dv, and the abscissas of the
turning points (rmin, rmax) for 17 electronic states. Moreover, the dipole moment functions and
the transition dipole moment are calculated for many of the states in the -representation.
2. The Theory
A. Ab initio Calculation
For the molecular ion CsH+ the energies for the molecular states including the spin-orbit
effect =1/2, 3/2, and 5/2 have been obtained from the treatment of the total Hamiltonian
Ht=He+WSO where He is the Hamiltonian in the Born-Openheimer approximation for the
calculation of the energies for the molecular states labelled 2S+1(+/-) and WSO is the spin-orbit
pseudo-potential. The Spin-orbit (SO) effects are considered for Cs while they are neglected
for H. The CsH+ ion is treated as a one electron system where the interaction between the
outer electron and the atomic core of Cs+ is modulated through non empirical relativistic
effective one-electron core potential of the Durand and Barthelat type [42-44]. The electron-
core interaction is represented by the effective potential
2
V[r ] = U [r ]P
=0
where is the orbital angular momentum and P corresponds to the projection operator on the
subspace defined by the Ym spherical harmonies with a given . U[r] is written as:
2
U [ r ] = ci r ni e r
2
i
i =1
with c, n and adjusted to fit the energy and wave functions of the valence Hartree-Fock
orbitals. Core valence effects including core-polarization and core valence correlation are
taken into account by using an -dependent core-polarization potential of the Foucrault et al.
type [49]
1
Vcpp = k f k . f k
2 k
where the index k labels the ionic cores, k is the static dipole polarizability of the ionic core,
fk is the electric field action on the ionic core k due to the valence electrons and the other
core. The -dependent form proposed by Foucrault et al [49]
m=+
fk = F (r ik , rk ) m > kk < m
=0 m =
with m>k are spherical harmonic centered on the core k and rk are cut-off parameters. For
l
the one-valence-electron atom Cs the parameters rk have been determined in order to
reproduce the experimental values of the ionization potential IP, as well as the transition
energies for the atomic. In this way rl has been obtained for l = 0, 1, 2 and we have chosen
rk2 = rk3 . [50] The parameters defining the core-polarization potentials and the comparison of
the calculated IPs and atomic transition energies with the experimental values of the atom Cs
are given in Ref. [51] The core-core interaction is evaluated as the ground state energy for the
molecular ion RbH2+ instead of the approximation 1/r which not accurate enough for this
species, at least for small values of the internuclear distance. In the present calculation
including the spin-orbit effect the total Hamiltonian Ht is diagonalized in the basis of the S
states yielding the relativistic adiabatic states. The symmetry used in this calculation is
being Cv with a common set of molecular orbitals for all symmetries. Semi-empirical spin-
orbit pseudo-potentials have been designed for Cs atom [52-53]. The present investigation of
the electronic structure including the spin-orbit effect for the molecular ion CsH+ has been
performed by using the package CIPSO (Configuration Interaction by Perturbation of a
multiconfiguration wave function with Spin-Orbit interaction) of the Laboratoire de Physique
Quantique Toulouse, France, which allows a full CI calculation as well as perturbative CI

calculations with SO effects.
B. Vibration Rotation Calculation
In the Rayleigh-Schrdinger perturbation theory the eigenvalue EvJ and the eigenfunction
vJ are given respectively by
E vJ = e n n (1)
n =0
vJ (r ) = n (r ) n (2)
n =0
where r is the internuclear distance, v and J are respectively the vibrational and rotational
quantum numbers, = J (J + 1) , and e0 = Ev, e1=Bv, e2 =- Dv , , 0 is the pure vibrational
wave function and n its rotational corrections. By replacing Eqs.(1) and (2) into the radial
Schrdinger equation [54-58]
d 2 2
2 + 2 (E vJ U(r )) 2 vJ (r ) = 0 (3)
dr r
one can write [36]
'0' (r ) + [e 0 U (r )] 0 (r ) = 0 (4)
1'' (r ) + [e 0 U(r )] 1 (r ) = [e1 R (r )] 0 (r ) (5-1)
2'' (r ) + [e0 U (r )]2 (r ) = [e1 R (r )]1 (r ) e2 0 (r ) (5-2)
n
'n' (r ) + [e 0 U(r )] n (r ) = R (r ) n 1 e m n m (r ) (5-n)
m =1
where R(r)=1/r2, the first equation is the pure vibrational Schrdinger equation and the
remaining equations are called the rotational Schrdinger equations. One may project Eqs.(5)
onto 0 and find [47]
1
< 0 | 0 > e1 =< 0 | | 0 > (6-1)
r2
1
< 0 | 0 > e 2 =< 0 | | 1 > e1 < 0 | 1 > (6-2)
r2
1 n 1
< 0 | 0 > e n =< 0 | 2
| n 1 > e m < n m | 0 > (6-n)
r m =1
Once e0 is calculated from Eq.(4), e1, e2, e3 can be obtained by using alternatively
Eqs.(5) and (6).
3. The Results
Atomic Calculation
The electronic structure of the molecular ion CsH+ is studied with and without the spin-
orbit (SO) coupling. The spin-orbit effects has been studied by using the package CIPSO
(Configuration Interaction by Perturbation including Spin-Orbit coupling) of the "laboratoire
de physique Quantique Toulouse-France". The values of the cut-off parameters involved in
the polarization potentials are given in Table 1 [38,59].
Table 1. Parameters for the polarization potential of the Cs and H atoms
Atom (ao3) rko(ao) rk1(ao) rk2(ao)

Cs 15.117 2.6915 1.8505 2.8070
H 1.000 1.000 1.000 1.000
Table 2. Energies of the lowest lying levels of the H-atom
Configuration Term J Etheoretical(cm-1) Eexperimental(cm-1) E/E%

2
1s S 1/2 0.00 0.00 0.00
2 0 1/2 82312.7386 82258.9206 0.07
2p P
3/2 82324.9802 82259.2865 0.08
2
2s S 1/2 82324.9802 82258.9559 0.08
2 0 1/2 97568.0092 97492.2130 0.08
3p P
3/2 97568.0092 97492.3214 0.08
2
3s S 1/2 97568.0092 97492.2235 0.08
2 3/2 97568.0092 97492.3212 0.08
3d D
5/2 97568.0092 97492.3574 0.08
2 0 1/2 102948.0576 102823.8505 0.12
4p P
3/2 102948.0576 102823.8962 0.12
2
4s S 1/2 102948.0576 102823.8549 0.12
2 3/2 102948.0576 102823.8961 0.12
4d D
5/2 102948.0576 102823.9114 0.12
Average relative error 0.09
By using the Gaussian basis set given in Ref. [32] for the cesium atom and the modified
basis cc-pv6z [60] for the hydrogen atom we calculate the energy levels up to 4d and 8s
respectively for H and Cs-atoms. The comparison of these values, in Tables 2 and 3, to those
obtained experimentally [61-63] shows an excellent agreement with an average relative error
E/E=0.09% for the H-atom and 0.01% for the Cs-atom. This agreement confirms the validity
and the accuracy of the chosen basis sets in this calculation.
Table 3. Energies of the lowest lying levels of the Cs-atom
Configuration Term J Etheoretical(cm-1) Eexperimental(cm-1) E/E%

2
6s S 1/2 0.00 0.00 0.00
2 0 1/2 11172.7488 11178.2686 0.04
6p P
3/2 11728.5025 11732.3079 0.03
2 3/2 14480.8502 14499.2584 0.12
5d D
5/2 14579.0300 14596.8423 0.12
2
7s S 1/2 18537.3276 18535.529 ~0.00
2 0
7p P 1/2 21837.0533 21765.35 0.32
3/2 22019.7714 21946.396 0.33
2
6d D 3/2 22776.7197 22588.8210 0.83
5/2 22818.5012 22631.6863 0.82
2
8s S 1/2 24354.4958 24317.0185 0.01
3.3. Spin-Orbit Effects Neglected
For the molecular ion CsH+ the potential energy curves (PECs) of the 2(+) states have
been investigated in the range 3.0a0r60a0 of the internuclear distance and dissociating into
the 16 asymptotes considered up to the dissociation limit H+(4d 2D3/2,5/2)+ Cs(1S0); i.e. up to
16 states 2+, 9 states 2, 4 states 2, as displayed in Table 4. This table also reports the
calculated energies at the dissociation limits; the comparison of these values to those obtained
experimentally [62-63] shows a very good agreement with an average relative error of 0.06
%. The PECs versus the internuclear distance for the 2(+)-states are plotted respectively in
the Figs1-3. Among the calculated 29 PECs 22 states are proved to be attractive. For each
bound state the harmonic vibrational constant e, the rotational constant Be, the internuclear
distance at equilibrium re and the electronic transition energy with respect to the ground state
Te are calculated by fitting the energy data around the equilibrium position to a polynomial in
terms of the internuclear distance r, these values are given in Table 5. The comparison of our
calculated values of re and Be of the ground state with those available in literature shows a
good agreement with relative errors 3.6% and 7.5% respectively. Double minima potentials
are obtained for the states (14)2+, (16)2+, and (9)2, the minima of these potentials are
given in Table 5. No comparison for the other results since they are given here for the first
time.
Table 4. Numbering of the various -states of the CsH+ correlated adiabatically to the
16 lowest dissociation limits
2
Cs H + 2
2
Etheoretical(cm-1) Eexperimental(cm-1) E/E%
1 2
S0 1s S1/2 1 0 0 0.00
6s 2S1/2 1
S0 2 78268.9598 78268.9598 0.00
1 2
S0 2p P1/2,3/2 3 1 82318.8594 82259.1035 0.07
1
S0 2s 2S1/2 4 82324.9802 82258.9559 0.08
2 1
6p P1/2,3/2 S0 5 2 89719.5854 89724.2480 ~0.00
5d 2D3/2,5/2 1
S0 6 3 1 92798.8999 92817.0101 0.02
7s 2S1/2 1
S0 7 96806.2874 96804.4888 ~0.00
1
S0 3s 2S1/2 8 97568.0092 97492.2235 0.08
1
S0 3p 2P1/2,3/2 9 4 97568.0092 97492.2672 0.08
1
S0 3d 2D3/2,5/2 10 5 2 97568.0092 97492.3393 0.08
7p 2P1/2,3/2 1
S0 11 6 100197.3722 100124.8328 0.07
6d 2D3/2,5/2 1
S0 12 7 3 101066.5703 100879.2135 0.18
8s 2S1/2 1
S0 13 102623.4556 102585.9783 0.03
1
S0 4s 2S1/2 14 102948.0576 102823.8549 0.12
1
S0 4p 2P1/2,3/2 15 8 102948.0576 102823.8733 0.12
1
S0 4d 2D3/2,5/2 16 9 4 102948.0576 102823.9037 0.12
460000
440000
E(cm-1)
420000
400000
0 10 20 30 40 50 60
R(Bohr)
Figure 1. Continued on next page.

400000
300000
E(cm-1)
200000
100000
0
0 10 20 30 40 50 60
R(Bohr)
Figure 1. Potential energy curves of the states 2+ of the molecule CsH+.
460000
440000
E(cm-1)
420000
400000
0 10 20 30 40 50 60
R(Bohr)
Figure 2. Potential energy curves of the states 2 of the molecule CsH+.

Table 5. Calculated spectroscopic constants for the various [(k)2] states of CsH+
[(k)2s+1] Te(cm-1) re() e(cm-1) Be(cm-1)

3.372 1.479
[(1)2+] 0.00 460.350
3.25a 1.59a
[(2)2+] 204220.06 3.467 409.50 1.402
2 +
[(3) ] 401701.74 4.611 263.99 0.792
2 +
[(4) ] 414566.28 5.178 129.26 0.628
[(5)2+] 418211.74 7.854 115.45 0.273
2 +
[(6) ] 423296.11 9.699 96.250 0.179
2 +
[(7) ] 428459.83 11.65 81.54 0.124
2 +
[(8) ] 432489.77 15.185 41.21 0.073
2 +
[(9) ] 433523.86 24.742 6.017 0.029
2 +
[(10) ] 435366.04 16.978 46.20 0.058
2 +
[(11) ] 438110.28 19.817 40.05 0.042
[(12)2+] 441472.00 11.932 66.71 0.117
444554.93 13.921 62.13 0.086
[(14)2+] Max 444583.4 At r=14.4
443451.88 23.834 32.93 0.029
2 +
[(15) ] 444571.45 17.765 72.78 0.053
447113.83 15.030 78.56 0.074
[(16)2+] Max 447239.8 At r=16.6
447111.94 25.870 7.20 0.025
2
[(1) ] 204796.07 3.519 344.80 1.359
2
[(2) ] 414065.64 3.425 457.16 1.437
[(3)2] 424463.77 6.946 53.227 0.344
[(4)2] 429363.48 9.583 59.41 0.183
2
[(6) ] 438641.40 14.171 36.11 0.083
[(8)2] 444031.66 18.80 17.15 0.047
447229.32 13.270 46.83 0.095
[(9)2] Max 447249.3 At r=14
447118.05 23.338 7.14 0.030
(a) Ref. [64].
These PECs present avoided crossings in quite complex forms (humps and wells) at short
and large value of the internuclear distance which are due to either crossings or avoided
crossings. The internuclear distance at the avoided crossing RAC with the energy difference
EAC between two corresponding states at these points for the different states are given in
Table 6. We show avoided crossing between the states (9)2+ and (8)2+ in Figs 4 as
illustration.
460000
440000
E(cm )
-1
420000
400000
0 10 20 30 40 50 60
R(Bohr)
Figure 3. Potential energy curves of the states 2 of the molecule CsH+.
Table 6. Some avoided crossing between 2+ states of the molecular ion CsH+
(n+1)State / (n)State rAC(Bohr) EAC(cm-1)
(8)2+/(7)2+ 12.4 1573.97

(9)2+/(8)2+ 10.4 1461.58
(9)2+/(8)2+ 18.4 33.14
(12)2+/(11)2+ 8.3 543.19
(12)2+/(11)2+ 11.5 547.72
(12)2+/(11)2+ 20.6 504.07
2 + 2 +
(15) /(14) 6.4 357.90
2 + 2 +
(15) /(14) 17.8 473.14
2 + 2 +
(15) /(14) 32 118.38
2 + 2 +
(16) /(15) 10.6 154.25
(5) 2/(4) 2 8.2 1886.88
(9) 2/(8) 2 8.3 1630.83
434400
(8)
(9)
E(cm-1) 434300
434200
434100
434000
18.1 18.3 18.5 18.7
R(Bohr)
Figure 4. Avoided crossing between (9)2+ and (8)2+states of the molecule CsH+.
3.4. Spin-Orbit Effects Included
Energy calculation for the -representation is performed for the states corresponding to
the 16 lowest dissociation limits, i.e. up to H+(4d 2D3/2,5/2)+ Cs+(1S0) is the range of
internuclear distance r from 3ao to 60ao. Consequently 25 states of =1/2, 13 states of =3/2
and 4 states of =5/2 are correlated adiabatically as shown in Table 7. The PECs of these
states are displayed in Figs 7, 8 and 9 respectively. Among these calculated PECs 24 states
are proved to be attractive and the other are repulsive.
Table 7. Numbering of the various -states of CsH+ correlated adiabatically to the 25

lowest dissociation limits
Cs H+ =1/2 =3/2 =5/2

1 2
S0 1s S1/2 1
6s 2S1/2 1
S0 2
1 2
S0 2p P1/2,3/2 3,4 1
1
S0 2s 2S1/2 5
2 1
6p P1/2,3/2 S0 6,7 2
5d 2D3/2,5/2 1
S0 8,9 3,4 1
7s 2S1/2 1
S0 10
1 2
S0 3s S1/2 11
1
S0 3p 2P1/2,3/2 12,13 5
Table 7. Continued
Cs H+ =1/2 =3/2 =5/2

1
S0 3d 2D3/2,5/2 14,15 6,7 2
2 1
7p P1/2,3/2 S0 16,17 8
6d 2D3/2,5/2 1
S0 18,19 9,10 3
8s 2S1/2 1
S0 20
1
S0 4s 2S1/2 21
1
S0 4p 2P1/2,3/2 22,23 11
1
S0 4d 2D3/2,5/2 24,25 12,13 4
For each bound state the harmonic vibrational constant e, the rotational constant Be, the
internuclear distance at equilibrium re and the electronic transition energy with respect to the
ground state Te are calculated by fitting the energy data around the equilibrium position to a
polynomial in terms of the internuclear distance r, these values are given in Tables 8 and 9
respectively along with the main parents 2(+) of the states =1/2 and =3/2 near the
equilibrium positions. It should be noticed that, such identification was not possible for other
states since their minima are situated close to the crossings between 2(+) states.
460000
440000
E(cm-1)
420000
400000
0 10 20 30 40 50 60
R(Bohr)

400000
300000
E(cm-1)
200000
100000
0
0 10 20 30 40 50 60
R(Bohr)
Figure 7. Potential energy curves of the states =1/2 of CsH+.
460000
440000
E(cm-1)
420000
400000
0 10 20 30 40 50 60
R(Bohr)

400000
E(cm-1) 300000
200000
100000
0
0 10 20 30 40 50 60
R(Bohr)
Figure 8. Potential energy curves of the states =3/2 of the molecule CsH+.
460000
440000
E(cm-1)
420000
400000
0 10 20 30 40 50 60
R(Bohr)
Figure 9. Potential energy curves of the states =5/2 of CsH+.
Since the spin orbit coupling has no effect on the state we compare these results with
those available in literature without spin orbit. This comparison shows a very good agreement
with a relative errors 3.6% and 7.5% respectively for re and Be for the ground state. No
comparison for the other results since they are given here for the first time.
Table 8. Calculated spectroscopic constants for the various (n)=1/2 states of CsH+
n[(k)2s+1] Te(cm-1) re() e(cm-1) Be(cm-1)

3.372 1.479
(1) [(1)2+] 0.00 460.356
3.25a 1.59a
(2) [(2)2+] 204220.06 3.467 409.473 1.402
(3) [(1)2] 204795.65 3.519 345.114 1.359
(4) [(3)2+] 401700.63 4.611 263.463 0.792
2
(5) [(2) ] 414063.89 3.426 456.004 1.437
Max 414752.7 At r=3.9
(5) [(4)2+] 414565.97 5.177 129.213 0.628
(6) 414792.88 4.169 480.602 0.974
(7) [(5)2+] 418211.24 7.855 115.627 0.272
2 +
(8) [(6) ] 423222.19 9.696 96.473 0.179
(9) [(3)2] 424450.23 7.574 1105.84 0.541
(10) [(7)2+] 428383.70 11.694 78.041 0.123
2
(11) [(4) ] 429284.02 10.256 58.061 0.159
(12) [(8)2+] 432489.53 15.182 41.239 0.073
(15) [(10)2+] 435366.45 16.977 46.185 0.058
(16) 438617.06 12.252 26.045 0.082
Max 438026.4 At r=13.7
(16) [(11)2+] 438110.06 19.815 40.064 0.042
2
(17) [(6) ] 438666.78 15.846 95.567 0.066
(18) [(12)2+] 441471.64 11.934 66.424 0.117
2 +
(21) [(14) ] 443451.88 23.834 32.939 0.029
(22) 444555.10 12.624 92.079 0.085
Max 444583.4 At r=13.8
(22) [(8)2] 444026.53 17.430 58.353 0.044
(23) [(15)2+] 444571.46 17.765 72.777 0.053
Max 444632.2 At r=18.5
(23) 444080.58 30.278 15.702 0.017
2 +
(24) [(16) ] 447113.96 15.019 79.332 0.075
(25) 447237.12 12.224 67.025 0.081
Max 447249.2 At r=13.5
(25) [(9)2] 447225.70 15.187 225.477 0.042
Max 447239.8 At r=15.9
(25) [(9)2] 447118.11 23.973 102.062 0.028
(a) Ref.[64].
Double minima potentials are obtained for the states (5)=1/2, (16)=1/2, (22)=1/2,
(23)=1/2 and (13)=3/2, while the (25)=1/2 is a triple well potential state.
Table 9. Calculated spectroscopic constants for the various (n) =3/2 states of CsH+
n[(k)2s+1] Te(cm-1) re() e(cm-1) Be(cm-1)
(1) [(1)2] 204796.49 3.519 344.896 1.359

2
(2) [(2) ] 414067.25 3.424 458.206 1.438
2
(4) [(3) ] 424505.55 7.170 14.270 0.295
(5) 414565.97 5.177 129.213 0.628
(8) [(6)2] 438666.91 14.144 36.317 0.084
2
(11) [(8) ] 444033.05 18.801 17.144 0.047
2
(13) [(9) ] 447229.54 13.272 46.757 0.095
Max 447249.4 At r=13.4
(13) [(9)2] 447118.05 23.337 7.246 0.030
At the internuclear distance at equilibrium re, the SO splitting for the states (1, 2, 3, 6, 8,
9)2 have been identified and evaluated, the difference between the lowest and highest
energy are 0.84cm-1, 3.36cm-1, 0.13cm-1, 6.52cm-1, 3.84cm-1 and 0.6cm-1 respectively. In the
-representation the PECs present avoided crossings in quite complex forms (humps and
wells) at short and large value of the internuclear distance which are due to either crossings or
avoided crossings of the -states. The internuclear distance at the avoided crossing rAC with
the energy difference EAC between two corresponding states at these points are given in
Tables 10 and 11. These avoided crossings are drawn, as illustration, in figures 10 and 11.
Table 10. Some avoided crossings between =1/2 states of CsH+ . rAC and EAC are
respectively the internuclear distance and the energy difference at the avoided crossing
between the two corresponding states
Crossing between Aviod crossing

(n+1) =1/2/(n)=1/2 rAC(Bohr) EAC(cm-1)
(n)state/(m)state (n)state/(m)state
(3)=1/2/(2) =1/2 5.1 25.18 (2)2+/(1)2
(5)=1/2/(4) =1/2 4.7 169.97 (3)2+/(2)2
(6)=1/2/(5) =1/2 7.7 46.92 (4)2+/(2)2
(8)=1/2/(7) =1/2 5.2 137.64 (5)2+/(3)2
(9)=1/2/(8) =1/2 13.9 109.66 (6)2+/(3)2
(11)=1/2/(10) =1/2 17.7 378.17 (7)2+/(4)2
6.1 8.87 (8)2+/(5)2
(13)=1/2/(12) =1/2 12.1 81.59 (8)2+/(5)2
18.8 18.14 (9)2+/(5)2
(14)=1/2/(13) =1/2 18.2 52.56 (9)2+/(5)2
Table 10. Continued
Crossing between Aviod crossing

(n+1) =1/2/(n)=1/2 rAC(Bohr) EAC(cm-1)
(16)=1/2/(15) =1/2 11.4 65.71 (10)2+/(6)2
(17)=1/2/(16) =1/2 29.4 66.70 (11)2+/(6)2
8.8 3.26 (11)2+/(7)2
(18)=1/2/(17) =1/2 11.5 519.22 (12)2+/(11)2+
20.6 502.78 (12)2+/(11)2+
8.3 545.70 (12)2+/(11)2+
11.1 121.37 (12)2+/(7)2
(19)=1/2/(18) =1/2 12 88.07 (12)2+/(7)2
17.7 4.62 (12)2+/(7)2
34.5 62.83 (12)2+/(7)2
(21)=1/2/(20) =1/2 16 44.80 (13)2+/(8)2
21.7 18.20 (14)2+/(8)2
(22)=1/2/(21) =1/2 25.8 6.20 (14)2+/(8)2
35 73.10 (14)2+/(8)2
32.2 163 (15)2+/(14)2+
(23)=1/2/(22) =1/2
56.5 5.5 (15)2+/(8)2
26.4 8.5 (16)2+/(9)2
(25)=1/2/(24) =1/2
31 13.5 (16)2+/(9)2
Table 11. Some avoided crossings between =3/2 states of CsH+
Crossing between Avoid crossing

(n+1) =3/2/(n)=3/2 rAC(Bohr) EAC(cm-1)
(6) =3/2/(5)=3/2 9 63.07 (4)2/(2)2
(7) =3/2/(6)=3/2 8.2 1848.77 (5)2/(4)2
(8) =3/2/(7)=3/2 4.6 14.75 (5)2/(3)2
(9) =3/2/(8)=3/2 7.4 20.47 (6)2/(3)2
(12) =3/2/(11)=3/2 11.8 26.63 (8)2/(4)2
Each -state, except for few ones, has more than one main parent -state. This is proved
in Tables 12 and 13 by showing the percentage of parent -states over a certain range of the
internuclear distance of -states.
425000
(8)=1/2
(9)=1/2
424800 (6)+
(3)
424600
E(cm-1)
424400
424200
424000
13.2 13.4 13.6 13.8 14 14.2 14.4 14.6
R(Bohr)
Figure 10. Avoided crossing between (8)=1/2 and (9)=1/2 is due to crossing between (6)2+ and
(3)2.
445200
(22)=1/2
(23)=1/2
(14)+
(15)+
444800
E(cm-1)
444400
444000
30 31 32 33 34 35
R(Bohr)
Figure 11. Avoided crossing between (22) =1/2 and (23) =1/2 is due to avoided crossing between
(14) 2+ and (15) 2+.
Table 12. Parent states for the potential energy curves of (n)=1/2
% % %
(n) From to From to From to
State State State
100%
(1) 3 60.5
(1)2+
3.4% 96.5%
(2) 3 5 5 60.5
(1)2 (2)2+
3.4% 96.5%
(3) 3 5 5 60.5
(2)2+ (1)2
2.9% 97%
(4) 3 4.7 4.7 60.5
(2)2 (3)2+
2.9% 5.5% 91.5%
(5) 3 4.7 4.7 7.9 7.9 60.5
(3)2+ (2)2 (4)2+
8.3% 91.6%
(6) 3 7.8 7.8 60.5
(4)2+ (2)2
3.4% 96.5%
(7) 3 5 5 60.5
(3)2 (5)2+
3.6% 15.4% 80.9%
(8) 3 5.1 5.1 14 14 60.5
(5)2+ (3)2 (6)2+
2.9% 16% 81.1%
(9) 3 4.7 4.7 13.9 13.9 60.5
(4)2 (6)2+ (3)2
2.9% 22.4% 74.6%
(10) 3 4.7 4.7 17.6 17.6 60.5
(6)2+ (4)2 (7)2+
Table 12. Continued
% % %
State State State
25.3% 74.6%
(11) 3 17.6 17.6 60.5
(7)2+ (4)2
5.2% 10.4% 84.3%
(12) 3 6 6 12 12 60.5
(8)2+ (5)2 (8)2+
5.2% 11.1% 83.6%
(13) 3 6 6 12.4 12.4 60.5
(5)2 (8)2+ (5)2
100%
(14) 3 60.5
(9)2+
14.7% 85.2%
(15) 3 11.5 11.5 60.5
(6)2 (10)2+
2.9% 11.4% 85.6%
(16) 3 4.7 4.7 11.3 11.3 60.5
(7)2 (10)2+ (6)2
3.4% 6.4% 90.1%
(17) 3 5 5 8.7 8.7 60.5
(10)2+ (7)2 (11)2+
10% 89.9%
(18) 3 8.8 8.8 60.5
(11)2+ (7)2
100%
(19) 3 60.5
(12)2+
5.7% 9% 7.3%
3 6.6 6.6 11.8 11.8 16
(8)2 (13)2+ (8)2
(20)
77.9%
16 60.5
(13)2+
Table 12. Continued
% % %
State State State
6.4% 8.3% 7.8%
3 6.7 6.7 11.5 11.5 16
(13)2+ (8)2 (13)2+
(21)
77.4%
16 60.5
(8)2
1.2% 2.6% 28.5%
3 3.7 3.7 5.2 5.2 21.6
(13)2+ (9)2 (14)2+
(22)
67.6%
21.6 60.5
(8)2
3.8% 14% 82.1%
(23) 3 5.2 5.2 13.3 13.3 60.5
(14)2+ (9)2 (15)2+
17.9% 22.7% 9.7%
3 13.3 13.3 26.4 26.4 32
(15)2+ (9)2 (16)2+
(24)
20.8% 28.8%
32 44 44 60.5
(9)2 (16)2+
41% 8% 22.6%
3 26.4 26.4 31 31 44
(15)2+ (9)2 (15)2+
(25)
28.3%
44 60.5
(9)2
Table 13. Parent states for the potential energy curves of (n)=3/2
% % %
State State State
100%
(1) 3 60.5
(1)2
100%
(2) 3 60.5
(2)2
100%
(3) 3 60.5
(1)2
100%
(4) 3 60.5
(3)2
10.4% 89.5%
(5) 3 9 9 60.5
(2)2 (4)2
10.4% 89.5%
(6) 3 9 9 60.5
(4)2 (2)2
32.6% 67.3%
(7) 3 21.8 21.8 60.5
(5)2 (2)2
2.6% 4.6% 92.7%
(8) 3 4.5 4.5 7.2 7.2 60.5
(5)2 (3)2 (6)2
7.3% 92.6%
(9) 3 7.2 7.2 60.5
(6)2 (3)2
100%
(10) 3 60.5
(7)2
15.1% 84.8%
(11) 3 11.7 11.7 60.5
(4)2 (8)2
15.1% 84.8%
(12) 3 11.7 11.7 60.5
(8)2 (4)2
100%
(13) 3 60.5
(9)2
3.5. The Vibration-Rotation Calculation
The canonical functions approach [1, 2, 3] enables us to calculate the eigenvalue energy
Ev, the rotational constant Bv, the centrifugal distortion constant Dv at any vibrational level
even near dissociation. However, this approach fails if avoided crossings between states occur
because of the break down of the Born-Oppenheimer approximation at these points. Here for
the alkali dimmer CsH+, these constants have been calculated for 8 states in -representation
and 9 states in the -representation up to vibrational level v=19. From the cubic spline
interpolation between each two consecutive energy values of the PECs, and by using
eigenvalue energies Ev, the abscissas of the turning points (rmin, rmax) of the above mentioned
states have been calculated. These constants for the states (1, 2, 3)2+ are reported in the
Tables 14 to 16, and the other are given in Ref. [59]. No comparison of these values with
other results since they are given here for the first time.
Table 14. Values for the eigenvalues (Ev), the abscissas of the turning points (rmin, rmax),
the rotational constant (Bv), and the centrifugal distortion constant (Dv) for the state
(1)2+ of the molecular ion CsH+
v Ev(cm-1) rmin() rmax() Bv(cm-1) Dv10+5(cm-1)

0 214.728 3.156 3.716 1.423 7.036
1 587.566 3.049 4.131 1.276 9.568
2 873.605 2.997 4.552 1.326 11.934
3 1089.894 2.966 5.035 0.971 14.5043
the rotational constant (Bv), and the centrifugal distortion constant (Dv) for the state (2)
2 +
of the molecular ion CsH+

0 190.687 3.240 3.849 1.3260 7.9254
1 501.900 3.134 4.319 1.1693 10.5019
2 737.346 3.083 4.795 1.0219 11.8595
3 921.226 3.051 5.287 0.8949 12.8388
the rotational constant (Bv), and the centrifugal distortion constant (Dv) for the state (3)
2 +
of the molecular ion CsH+

0 129.638 4.290 5.014 0.7785 2.9326
1 377.385 4.096 5.384 0.7490 3.0982
2 608.215 3.981 5.696 0.7169 3.3159
3 820.972 3.899 5.999 0.6819 3.5967
4 1014.498 3.835 6.314 0.6435 3.9675
Table 16. Continued

5 1187.593 3.785 6.655 0.6011 4.4562
6 1339.148 3.745 7.038 0.5544 5.0841
7 1468.346 3.714 7.484 0.5031 5.8789
8 1574.907 3.690 8.018 0.4475 6.8411
9 1659.412 3.761 8.676 0.3887 7.9306
10 1723.533 3.658 9.504 0.3287 9.0650
11 1769.979 3.648 10.564 0.2700 10.1569
12 1802.086 3.641 11.938 0.2149 11.1810
3.6. Dipole Moment
Knowledge of the permanent or transition dipole moment is essential. For the

molecular ion CsH+ we calculate the transition electric dipole moment and the permanent
electric dipole moment values of the different bound -states as functions of the
internuclear distance r. This data provides us information about the most efficient scheme
of forming the CsH+ molecular ion. Moreover, our ab initio potentials for the excited states
can be used to identify the complex behavior of the transition dipole moment as function of
a
r. Permanent dipole moments M a (r) as well as all non-zero transition dipole moments
M ab (r)
M ab = ea | e (r ) | eb
have been calculated for each electronic states (a, b) under consideration and in the whole
range of r investigated here. e and e are respectively the electronic wave functions of two
a b
different electronic states and e(r) is the permanent electronic dipole moment. This dipole
moment function has been calculated for most of the -states [59]. In Fig 14 we show, as
illustration, the transition dipole moment between the states (22)=1/2 (21)=1/2. The
three peaks at 21.7, 25.8 and 35.0 Bohr respectively, correspond to crossing or avoid crossing
between the states (14)2+ and (8)2 as shown in these figure15, 16 and 17and given in
Table 10.
3
Re(r)
0
20 22 24 26 28 30 32 34 36 38 40
R(Bohr)
Figure 15. Variation dipole moment between (22) =1/2 (21) =1/2 states.
445600
(21)=1/2
(22)=1/2
(14)+
445400
(8)
E(cm-1)
445200
445000
444800
21 21.4 21.8 22.2 22.6
R(Bohr)
Figure 16. Crossing between (14)2+ and (8)2 states.

444800
(21)=1/2
(22)=1/2
444700
(14)+
(8)
444600
E(cm-1)
444500
444400
444300
24.8 25.2 25.6 26 26.4 26.8
R(Bohr)
444600
(21)=1/2
(22)=1/2
444400
(14)+
(8)
444200
E(cm-1)
444000
443800
443600
33 34 35 36 37 38
R(Bohr)

4. Conclusion
Using an ab initio approach the potential energy has been calculated for 16 states 2+, 9
states 2, 4 states 2, 25 states =1/2, 13 states =3/2 and 4 states =5/2 of the molecular
ion CsH+. For 19 bound states the harmonic vibrational constant e, the internuclear distance
re and the electronic transition energy with respect to the ground Te have been calculated.
Based on the canonical functions methods Ev, Bv and Dv have been calculated up to the
vibrational levels v = 19 for 17 electronic states. From the calculated values of Ev for a given
vibrational level v and by using a cubic spline interpolation between each two consecutive
points of the potential energy curves the rmin and rmax of the turning points have been
a
investigated for these bound states. Permanent dipole moments M a (r) as well as all non-
b
zero transition dipole moments M a (r) (ab ) have been calculated for each electronic states
(a,b) under consideration and in the whole range of r investigated here. The comparison of the
present results with those available in literature shows a very good agreement.
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Chapter 7
THEORETICAL EXPLANATION OF LIGHT

AMPLIFYING BY POLYETHYLENE FOIL
Vjekoslav Sajfert1a,, Duan Popov2,b, Stevo Jacimovski3,c

and Bratislav Tosic4,d
1
Technical Faculty Mihajlo Pupin Zrenjanin, Serbia
2
Universitatea Politehnica, Timisoara, Romania
3
Police Academy Belgrade, Serbia
4
Vojvodina Academy of Science and Arts Novi Sad, Serbia
Abstract
In connection with the experimental result which stated that polyethylene foil amplifies about
three times the penetrated light, we propose two theoretical explanations of this phenomenon.
One of them is that several amplified peaks are the consequence of the forming of solitons in a
polyethylene chain whose velocities are close to the velocity of sound. Forming of solitons,
together with boundary conditions in a polyethylene macromolecules chain, which contain
about thirty monomers, lead to the amplification of light. The second explanation requires
introduction of homeopolar excitons in polymer macromolecules. Both energy gap of
homeopolar excitons and width of homeopolar exciton zone are of the same order of
magnitude. It means that transitions in a very wide zone give light quanta which are able to
amplify the initial light.
In order to avoid some confusion and misunderstandings, we wish to point out the
following. Atoms and molecules as the whole are treated classically (transition through
potential barriers, for example, etc.). The exception to this rule are phonon theories of crystals
where the phonon is considered as a quanta of boson field, i.e., it means that, in the theory of
mechanical oscillations, molecules and atoms as the whole are treated quantum mechanically.
On the other hand, elementary excitations in crystals such as excitons, vibrons, spin waves,
and ferroelectric excitations, etc., which arise from changes of some parts of atoms or
molecules are treated quantum mechanically exclusively.
a
E-mail address: sajfertv@ptt.yu.
b
E-mail address: dusan_popov@yahoo.co.uk. Correspondent author.
c
E-mail address: maskovicm@yahoo.co.uk.
d
E-mail address: btosic@yahoo.com.
142 Vjekoslav Sajfert, Duan Popov, Stevo Jacimovski et al.
In the analyses of this work, the excitations of an individual molecule subsystem (i.e. the
quantum objects) would serve as an explanation of the light amplification by a polymer chain.
1. Introduction
In some previous works [1,2] it was experimentally found that the polyethylene foil
noticeably amplifies intensity of light, and that amplification is proportional to the foil
thickness. It was separated seven lines from mercury lamp and each of them was amplified.
The experimental procedure is described in detail in [1], and therefore it will not be repeated
here. We shall quote only the results of the experiment. The seven lines of mercury lamp were
amplified 34 times after passing the light through a polyethylene foil. The wavelengths of
amplified peaks were 254, 315, 366, 436, 506, 577 and 624 nanometers. Seven initial lines
which are separated, are the more probable consequence of impurities of Hg, since in the foil
of absolutely pure Hg exists only one level at = 253.7 nm.
We shall try to explain the amplification of incident peaks in the frames of two models.
One model is based on the idea that solitons, whose velocity is close to the velocity of
sound appearing in polyethylene molecular chains, create the conditions for light
amplification.
The second model requires introducing homeopolar excitons in the system of possible
excitations in the polyethylene chain. In this case, amplification of light by polyethylene
arises as a consequence of the fact that the width of homeopolar exciton zone is of the same
order of amplitude as the energy of excitation of individual polyethylene monomer.
The amplifications of peaks were produced by one polyethylene foil whose thickness was
2 mm. The peaks were amplified 34 times by this foil. The amplifications produced by two
foils (thickness: 4 mm) could not be registered since the devices were not able to register
highness of peaks. It means that amplifications sharply increase with respect to the thickness
of polyethylene foil.
The theoretical explanation of this amplification of light intensity, given in [1], was based
on inverse population of electrons. Namely, it was assumed that in the polyethylene chain
exist metastable energy levels where electrons gathered and that they coherently transit to
ground state. This coherent transition, as in a laser, leads to the energy amplification.
In the work [2], the amplification was explained by exciton and soliton transitions. The
excitons were not of dipole-dipole type, but of exchange (homeopolar) type, since
polyethylene monomers are forming linear polyethylene macromolecules (polyethylene
chains) by homeopolar forces whose potentials are of the order of magnitude of excitation
energy of an electron in isolated monomer. The behavior of such excitons will be analyzed in
this work with the goal to explain amplification of the light.
2. Excitons and Solitons in Infinite Polyethylene Chains

Frenkel excitons [3] more often appear in a molecular crystal where dipole-dipole
interactions propagate excitations of an isolated molecule produced by visible light.
Excitation energy of an isolated molecule lies between 2.5 eV and 5 eV, while energies of
Theoretical Explanation of Light Amplifying by Polyethylene Foil 143
dipole-dipole interactions are 50100 times lower. In such situation, energy of exciton and
energy of visible photons are practically identical.
For forming polyethylene linear chain made of monomers C2H4 are responsible exchange
forces (covalent connection of monomers) [4,5]. Since potential energies between two
electrons are reflexive, the potential energy is of positive sign. On the other hand if electron
spins are parallel, the configurationally parts of wave function must be antisymmetric and this
leads to negative exchange integrals which are binding monomers in chain. Consequently, if
one isolated monomer of chain is excited by quanta of visible light this excitation propagates
along the chain in covalent forces field. The matrix elements of covalent potential are of the
order of five electronvolts. It means that they are of approximately of same magnitude as
excitations of an isolated molecule. It is essential difference with respect to excitons in
molecular crystals. In polyethylene chains wideness of exciton zone is practically same as the
energy of excitation of an isolated monomer. It means that in polyethylene chains can appear
excitons whose energy is two or three times higher than energy of visible light which
produces excitons. This amplifying is registered in experiment described in the previous
section.
The mechanical oscillations interacting with excitons lead to forming of new
quasiparticles - solitons [6], which can have higher energy than exciton. Besides, the solitons
are qusiparticles of stable form moving superfluidely and having higher luminescence time
8
than excitons. Luminescence time for singlet excitons is about 10 s, for triplet excitons
3 2 1
(corresponding to parallel electron-spins) 10 s [7] and for solitons about 10 s - 10 s [8].
The long times of luminescence means that metastable state are lasting sufficiently long to
cause coherent illumination.
The upper ideas will be demonstrated on the simple case of two level monomer
excitation. The electronic Hamiltonian of monomer chain can be written in the following
way:
1
H = s ans+ ans +
n,s 2
W (s , s , s , s )a
n, m
nm 1 2 3 4
+
ns 1
+
ams a ans 2
3 ms 4
(1)
s1 , s 2 , s 3 , s 4
where a are Fermi operators of electrons localized in monomer and (which are of the
order 2.5 -5 eV) are energies of excitations of an isolated monomer. The matrix element W
include Coulomb and exchange forces and they are given by
( ) ( ) n e m ( ) ( )
2
Wnm = d 3 n d 3 m s*1 n s*3 m s4 m s2 n (2)
where are internal coordinates of monomers. Because we consider two-level scheme,

indices s1, s2 , s3 , s4 must have only two values: 0 - corresponding to ground state and f -
corresponding to excited state.
Here and below, for reasons of simplifying the writing of equations, we will use in the
denominator the following notation: n m n m .
+ + +
Introducing the operators of monomers excitations P = a f a0 and P = a0 a f we
easily concluded that they are closed in electron subspace 10 ,0 f ( ) ( )
and 00 ,1 f . The
+
operators P and P are Pauli operators which in the lowest ASQ approximation can be
+
substituted by Bose operators B and B .
+
Extracting from the Hamiltonian P only quadratic terms in P and substituting P with
Bose operators B , we obtain the following excitonic Hamiltonian in ASQ approximation
+ +
(ground state terms as well as the terms proportional to P P and PP are omitted):
V ( f , f ,0,0) + V (0,0, f , f ) +
H = f 0 V (0,0,0,0) + Bn Bn
n 2
1
+ 2 [Wnm ( f ,0,0, f ) + Wnm (0, f , f ,0)]Bn+ Bm (3)
n, m
where V = Wn m .
m
It will be now shown that W ( f , f ,0,0 ) and W (0,0, f , f ) are positive Coulomb terms
while W ( f ,0,0, f ) and W (0, f , f ,0) are negative exchange terms.
The antisymmetric electron pair function is given by:
nm =
1
2
[ ( ) ( ) ( ) ( )]
f n 0 m f m 0 n (4)
and, as a consequence of this fact, the integral of the electron-electron interaction
e2

3 3 *
d n d m nm nm
nm
consists from four integrals:
d 3 n d 3 m nm*
e2
nm
1
2
( ) ( )
nm = { d 3 n d 3 m f* n 0* m
e2
nm
0 m f n ( ) ( )
( ) ( ) n e m ( ) ( )
2
+ d 3 n d 3 m 0* n f* m f m 0 n
( ) ( ) n e m ( ) ( ) }
2
d 3 n d 3 m 0* n f* m 0 m f n
1
= [Wnm ( f , f ,0,0) + Wnm (0,0, f , f ) + Wnm ( f ,0,0, f ) + Wnm (0, f , f ,0)] (5)
2
Introducing notations
= f 0
V ( f , f ,0,0 ) + V (0,0, f , f )
D= V (0,0,0,0)
2
1
Wnm = [Wnm ( f ,0,0, f ) + Wnm (0, f , f ,0)] (6)
2
and taking the nearest neighboring approximation ( Wn, n 1 = W ), the Hamiltonian (3) can be
written as (see [5,6]):
H exc = ( + D ) Bn+ Bn W Bn+ (Bn +1 + Bn 1 ) ; W > 0 (7)

n n
By means of Fourier transformations
1
Bn =
N
eikan Bk (8)
k
the Hamiltonian (7) goes over to
H exc = Ek Bk+ Bk (9)

k
where
Eexc (k ) = + D 2W cos ak (10)
Now we can estimate exciton energy in polymer chain with exchange interaction. We
will take = 3 eV , D = 1 eV (matrix elements W ( f , f ,0,0 ) are bigger than matrix
elements W (0,0,0,0 ) and W ~2.5 eV. The maximal energy of excitons for ak = is 9 eV
and it is 3 times higher than energy excitations (energy of photons). This corresponds to the
results of quoted experiment. In the case of dipole-dipole interaction we can
take D 2W cos ak = 0.06 eV , so that Eexc (k )max = 3.06 eV . This example points out a
sharp difference between exciton energies in systems with dipole-dipole interactions with
respect to those energies in systems with exchange interactions.
At the end, we shortly expose the soliton characteristics of this exciton system. To the
excitonic Hamiltonian we add the phonon Hamiltonian:
1 C
H ph = pn2 + (un un 1 )2 (11)
2M n 2 n
where M is the mass of monomer, C is the Hook's constant of monomer chain, un are
displacements of monomers and pn = u are corresponding momenta. The exciton phonon
Hamiltonian is given as follows:
D + W + u
H ep = 2 Bn Bn Bn (Bn +1 + Bn 1 ) a (12)
n a a (na )
Using complete Hamiltonian of the system
H = H exc + H ph + H ep (13)
and equations of motion for B we obtain
D W
EBn = ( + D )Bn W (Bn +1 + Bn 1 ) + 2 Bn (Bn +1 + Bn 1 ) a u (14)
a a (na )
and
2u n C
= (un +1 + un 1 2un ) (15)
dt 2 M
The equations can be averaged by coherent states
< ep e n (Bn Bn )Bn e n (Bn Bn ) ep >=< ep e n (Bn Bn )Bn+ e n (Bn Bn ) ep >= n

+ + + +
ep >= nexc > n ph > ; *n = n (16)

and
n n
pn pn
< ep ei u ne
i ep >= n ; * = (17)
After that we go over to continual variable na x and to common variable = x vt ,

where v is velocity of soliton. After quoted operations, the equation (15) goes over to:
(v )dd = 0
2
2
s2 2
(18)
where
C
s2 = a2 (19)
M
is the square velocity of sound in the chain. The boundary condition for this equation is
d
(0 ) = 0 , =0 = M 1 p0 (20)
d
where p0 is the beginning momentum which produce mechanical oscillations. By the way,
one of explanations of appearance of tsunami is based on such beginning conditions.
By means of conditions (20) we obtain
d M 2 p02
= (21)
d v 2 s 2
The equation (14), written in continuum, after the substitution (21), becomes:
2aM 2 p 2 V W
E + D 2W + 2 2 0
d 2 v s a a
= =0 (22)
d 2 W
a 2 W + a
a
If the coefficient in second term of (22) is positive the solution of (22) is
= c1 cosh Q = c1 cosh Q( x vt ) (23)
where
2aM 2 p 2 V W
E + D 2W + 2 2 0
v s a a
Q= (24)
W
a 2 W + a
a
The details of further calculations one can find in ref. [6, pp. 27-31]. Here they will not
be quoted. For our aims it is important to say that the wave function of soliton is proportional
to reciprocal value of , i.e.
c2 1
sol = = (25)
cosh Q( x vt )
The function sol is taken as sol = cosh

1
[Q(x vt )] since Q contains arbitrary
parameter soliton energy E. Soliton energy Esol can be determined from normalization
condition:
+
1

2
d sol = 1 (26)
a
which reduces to
2
=1 (27)
aQ
wherefrom we obtain
2aM 2 p02 V W W
E = + D + 2W + + 4a (28)
v 2 s 2 a a a
Soliton wave function (25) is of the stable form and propagates practically superfluidly.
Comparing (26) with (10) we see that soliton energy is some higher than the exciton one, but
when s v , i.e. when soliton velocity becomes close to sound velocity then soliton energy
becomes noticeably higher than exciton energy. It means that in the soliton model of
excitations in polyethylene, amplification can be considered as a consequence of sharp
increase of soliton energies when velocity of solitons becomes very close to the velocity of
sound.
3. Greens Function of Homeopolar Excitons

The general form of electron Hamiltonian, where overlapping of electron wave functions
of neighbor molecules is weak, is given by
N 8
1 N
H = s ans+ ans + Wn m ( s1 , s2 , s3 , s4 )ans+ 1 ans 2 ans+ 3 ans 4 (29)
n=0 s 2 n, m = 0 s1 , s 2 , s3 , s 4 = 0
+
Here a and are a electron operators, s is energy of electron in an isolated monomer
e2
and W are matrix elements of reflexive electron potential taken over products of
nm
configuration electron functions and spin electron functions. For two electrons forming bonds
between two monomers spin functions is even (it corresponds to parallel spins) while the
configurationally function must be odd. It gives attractive transition potentials between
monomers whose order of magnitude is 5 eV, i.e. of the same order of magnitude as
excitation energies of electrons in an isolated monomer. It should be noted that in the case of
dipole-dipole interactions (Frenkel excitons) attractive potentials between molecules are of
the order of 10-2 eV.
Using the well known procedure, taken from the theory of Frenkel excitons for two level
schemes of electron excitations [3, 4] and going over to approximate second quantization
approach, we can write the Hamiltonian (29) in the nearest-neighboring approximation as:
N N N
H = Bn+ Bn + (Dn , n +1 + Dn , n 1 )Bn+ Bn Bn+ (J n , n +1Bn +1 + J n , n 1 Bn 1 ) (30)
n=0 n=0 n=0
where
Wn , n 1 ( f , f ,0,0) + Wn , n 1 (0,0, f , f )
= f 0 ; Dn, n 1 = Wn , n 1 (0,0,0,0) (31)
2
Wn , n 1 ( f ,0,0, f ) + Wn , n 1 (0, f , f ,0)

J n, n 1 = ; D > 0, J > 0
2
Here f denotes energy of excited electron, while 0 denotes electron energy in ground
state.
Assuming that polyethylene linear chain has N monomers (N is 30-50 monomers) we
must introduce the boundary conditions
D0, 1 = DN , N +1 = 0 ; J 0, 1 = J N , N +1 = 0 (32)
The exciton system with Hamiltonian (2) will be analyzed by means of the real space
Greens function method. The double-time Greens functions are
1, n = m
[ ]
Gnm (t ) =<< Bn (t ) | Bm+ (0) >>= (t ) < Bn (t ), Bm+ (0) > ; (t ) = (33)
0 , n m
where [, ] is the commutator, < > is the thermal average over the grand canonical
ensemble and (t ) is the Heaviside function.
Using the equations of motion for Bose operators B and taking into account the boundary
conditions (32) we will obtain, after Fourier transformations time-frequency, the system of
three difference equations defining Greens functions,
J [Gn +1, m ( ) + Gn 1, m ( )] + Gn , m ( ) =
i
n, m ; 1 n N 1 (34)
2
i
JG1, m ( ) + ( + D)G0, m ( ) = 0, m ; n = 0 (35)
2
i
JGN 1, m ( ) + ( + D)GN , m ( ) = N ,m ; n = N (36)
2
where
= E 2D (37)
It can be shown that the system of equations (34) - (36) reduces into unique equation (39)
by the substitution:
N +1
Gn,m ( ) = A (m, ) F (n) (38)
=1
and
N
i
(2 J cos + )A (m, ) F (n) = 2
=0
n,m ; n = 0, 1, 2,, N (39)
where
D
F (n) = sin(n + 1) sin n (40)
J
Parameters are the solutions of the transcendental equation
2
D D
sin( N + 2) 2 sin( N + 1) + sin N = 0 (41)
J J
The Kronecker symbol will be represented as follows
N +1
n, m = F (n) (m) ; n, m {0, 1, 2,, N } (42)
=1
Putting equation (42) into (39) we obtain
A ( n , ) = ( n ) g ( ) (43)
where
i 1
g ( ) = (44)
2
After substituting the equations (42) - (44) into equation (39), we get
E
= ; E = + 2 D 2 J cos (45)
The spectral intensity of Greens functions:
i N F (n) (m)
Gn , m ( ) =
2 = 0
(46)
is given by [5, 6]
N +1
F (n) (m)
I n, m ( ) = ( ) (47)
=1
e k BT
1
By means of the formula (3.19 ) we can determine the correlation function
i
N +1
F (n) (m) E t
Cn , m (t ) =< Bm+ (0) Bn (t ) >= d e i t I n , m ( ) = E e (48)
=1
e k BT
1
and the concentration of excitons
N +1
F (n) (m)
Cn , m (0) =< Bm+ (0) Bn (0) >= E
(49)
=1
e k BT
1
This formula gives the exciton energies in analysed polyethylene chain.
4. The Exciton Wave Function of Polyethylene Chain

The equation (45) gives the energies of excitons in polymer chain. Using this formula we
can find the transitions whose wavelenghts correspond to experimentally obtained
wavelenghts , which are quoted in Introduction.
Besides these wavelenghts, we shall determine the probabilities of finding of exciton at
given energy level, as well as the probabilities of exciton transition between two energy
levels. These probabilities can be find out by means of exciton one particle wave function
N +1
| >= A (n) Bn+ | 0 > (50)
n =1
On the basis of equations motion and boundary conditions, it is obtained the system of
homogeneous diference equations for coefficients A(n):
An +1 + An 1 + An = 0 ; 1 n N 1
D
A1 + + A0 = 0 ; n=0 (51)
W
D
AN 1 + + AN = 0 ; n=N
W
which, by the substitution
N +1
D N +1
An = A sin( n + 1) sin n = A F ( n) (52)
=1 J =1
goes over to the unique equation
N +1
(2 J cos + )F (n) = 0 ;
=1
n (0,1, 2,, N ) (53)
where F (n) is given by (40) and parameters are real solutions of the equation (41).
Consequently, finally we have
N
B+ | 0 >= F (n)Bn+ | 0 > (54)
n=0
Multiplying equation (54) with (m), summing both sides of obtained equality over
and taking into account (42), we obtain:
N +1
Bn+ | 0 >= (n)B+ | 0 > (55)
=1
+
The normalised function Bn 0 is given by
N
1
B+ | 0 >=
N F (n)B +
n |0> (56)
F (n) 2 n =0
n =0
+
while normalised function B 0 is:
N +1
1
Bn+ | 0 >=
N +1 (n)B +
|0> (57)
(n) 2 =1
=1
The dependence of exciton energies with respect to , which are obtained from (17) for
values = 3 eV; D = 2.5 eV; J = 2.7 eV, is given in Figure 1.
Figure 1. The energy levels of excitons in polyethilen chain.
Table 1. Experimental and theoretical wavelengths of transitions leading

to amplifications
exp (nm) theor (nm) Transition Amplification

' factor
254 256 32 18 4.46
315 314 27 18 4.16
366 363 24 17 3.81
436 439 32 22 4.46
506 503 23 18 3.67
577 574 30 23 4.39
624 625 29 23 4.33
Experimental and theoretical wavelenghts of peaks as well as the theoretical amplifying

of peaks are given in the Table 1. The theoretical values are determined as
hc (E E ) ; > .
1
On the other hand, the probabilities of finding excitons on levels before luminiscence are
given Table 2.
1 31
Table 2. The probabilities of existence at stable levels where = (n )
32 n = 0
2
P P = N +1 P (%)
2
=1
P23 0.299281 8.956
P22 0.072849 0.531
P18 0.265614 7.055
P17 0.152059 2.312
Table 3. The transition probabilities of exciton to stable levels

P , = N +1 P , (%)

=1
2
P32;18 3.454
P30;23 7.794
P32;23 6.289
P27;18 0,796
P32;22 0.947
P24;17 3.652
P23;18 7.949
Similarly, the transitions probabilities from higher level E to the stable levels E
quoted in the previous Table 2. are presented in the Table 3.
Conclusion
In this work are analyzed two possible mechanisms of light amplification by polyethylene
foil, registered in experiments with a mercury lamp. In these experiments the light, after
transition through polyethylene foil was about 3 times more intensive than in the cases when
the foil is absent.
In the first model it was assumed that in the polymer chain solitons are forming whose
velocities were close to the velocity of sound and this caused the light amplification.
In the second model was introduced the concept of homeopolar excitons having
approximately equal gap and zone width. The analyses by means of Green's function as well
as the wave of homeopolar excitons wave function were determined metastable levels of
homeopolar excitons and probabilities of transition levels to ground state. Calculated
theoretical values of mentioned probabilities were in good agreement with experimental data.
Acknowledgements
This work was supported by the Serbian Ministry of Science and Technology: Grant No
141044, by Vojvodina Academy of Sciences and Arts, and by the Provincial Secretariat for
Science and Technological Development of the Autonomous Province of Vojvodina (Project
114-451-00615/2007-06).
References
[1] Janji J. D., Toi B. S., Scientific Bulletin of the Politehnica University of
Timisoara, ROMANIA, Transactions on Mathematics and Physics 2006, 51, 80.
[2] Janji J. D., Toi B. S., Sajfert V., "Luminescence Mechanism of Light Amplyfing by
Polyethylene, Bulletin of the Politehnica University of Timisoara, ROMANIA,
Transactions on Mathematics and Physics 2008, 53, 91.
[3] Agranovich V.M., JETP 1959, 37, 430.
[4] Agranovich V. M., Theory of Excitons; Nauka: Moscow, RUSSIA, 1978.
[5] yablikov S.V., Methods in the Quantum Theory in Magnetism, Plenum Press: New
York, USA, 1967.
[6] Toi B. S., Statistical Physics, Faculty of Natural Sciences, Novi Sad, SERBIA, 1978.
(in Serbian)
[7] Masterson W. W., Hurley C. N., Chemical Principles and Reactions, Saunders College
Publishing, Phyladelphia, USA, 1993; pp. 579.
[8] Brown, W.H., Introduction in Organic Chemistry, Saunders College Publishing
Phyladelphia, USA, 1997; pp. 428.
Chapter 8
ANHARMONIC EFFECTS IN NORMAL MODE

VIBRATIONS: THEIR ROLE IN BIOLOGICAL SYSTEMS
Attila Bende*
Molecular and Biomolecular Physics Department, National Institute for Research and
Development of Isotopic and Molecular Technologies, Donath street,
No: 65 103, Ro-400293, Cluj-Napoca, ROMANIA
Abstract
The intra- and intermolecular hydrogen-bond dynamics plays an important role in thermal
stability and molecular functionality of biomolecules like DNA base pairs and proteins. The
phenomena of thermal relaxation, conformational changes as well as the ultrafast non-
radiative decays in molecules, especially in biomolecules are realized among other physical
effects also with the help of molecular vibrations. Intermolecular hydrogen- or weak chemical
bonds (covalent bond including H atoms) usually present large anharmonic normal mode
vibrations. The anharmonic effects of normal mode vibrations for some small molecular
model systems (formamide and urea) as well as for guanine-cytosine and adenine-thymine
DNA base pairs are presented considering DFT and ab initio second order Mller-Plesset
(MP2) theoretical methods. The role of basis set superposition errors in harmonic and
anharmonic frequency calculations is briefly discussed. It was observed that anharmonic
effects can significantly change the blue- or red-shifted harmonic frequency values. Large
anharmonic effects were found in the case of protonated molecular structures, especial for
Hoogsteen conformation of guanine-cytosine base pairs.
1. Introduction
Hydrogen bonding is ubiquitous in nature and governs a wide array of chemical and
biological processes ranging from local structure in molecular liquids to the structure and
folding dynamics of proteins [1, 2]. Although the hydrogen bond is well studied, its low-
frequency vibrationsthe large-amplitude motions involving stretching and bending along
the actual hydrogen-bond coordinateshave been rarely investigated [3]. Information about
*
E-mail addresses: bende@itim-cj.ro, attlbende@gmail.com
158 Attila Bende
these vibrations offers exceptional insight into the potential energy surface of the interaction
and so further enhances our understanding of the hydrogen bond and its impact on molecular
structure and dynamics. The C=OH-N type hydrogen-bond (H-bond) is one of the most
frequently occurring Van der Waals (VdW) bonds in the biological systems. They can be
found as a main component of the DNA bases pairs interaction systems or in protein -helix
and -sheets. In this sense, not only is the cognition of molecular structures important, but
also their dynamics, which in essence represent their biological functionality.
Vibrational spectroscopy is a powerful tool for getting information about the complex
dynamics of atoms in H-bonds. In particular, such calculations provide sensitive information
on the potential energy surfaces of these systems [4, 5]. In the case of infrared (IR)
spectroscopic studies, the most evident effect of hydrogen bonding are the red shift of the
high-frequency XHY stretching mode, its intensity increase and band broadening; the
latter is often accompanied by the development of peculiar band-shapes. The large increase of
the bandwidth, the band asymmetry, the appearance of subsidiary absorption maxima and
minima, such as Evans windows, peculiar isotope and temperature effects and the similarity
of features of the line shape when passing from the condensed to the gas phase [6, 7] are the
challenge for theories of H-bonds. Computational studies are essential in this context since
comparison of calculations to the measured spectroscopic data provides a test of the potential
surface [811]. While calculations at the level of the harmonic approximation are very useful,
they are often not of sufficient accuracy [8, 9, 1214]. One approach is to apply empirical
scaling factors in order to represent the anharmonic effects [15, 16]. However, such an
approach, while useful in many cases, has no fundamental (quantum mechanical) basis.
Moreover, it does not provide any insights into the nature of the anharmonic part of the
potential, which itself is of great interest. Calculations of the spectra of large molecules
beyond the harmonic approximation remain a major challenge.
The goal of this Chapter is to give an accurate description of intermolecular normal
modes and to present different intermolecular interaction effects which could influence the
monomer type vibrations, considering the formamide and urea dimer cases and the guanine-
cytosine DNA base pair molecular system.
2. Theoretical Background and Computational Methods

Regarding the theoretical methods, it is well established that for an accurate description
of HBs, ab initio techniques which include the electronic correlation level are needed, i.e.
with an error bar of less than 0.04 eV (1 kcal/mol) for predicting the HB strength. Thus the
observed underestimation of the HB strength by the Hartree-Fock (HF) calculations (where
the electron correlation effects are missing) is overcome using correlated methods like second
order Mller-Plesset perturbation theory (MP2) or coupled cluster (CC) methods. But it is
necessary to use very large high quality basis sets to expand the wave function and to get
reliable HB properties. This fact and the necessity of correlated methods to accurately
describe HBs make such studies computationally too expensive and only applicable to
molecular complexes of at most a few tens of atoms. Therefore strategies to study HBs with
similar accuracy to MP2 or higher levels of theory but computationally less expensive are
needed. In this vein, density functional theory (DFT) is a method that includes electronic
correlation. Unfortunately the accuracy of DFT to describe the HB interaction relies on the
Anharmonic Effects in Normal Mode Vibrations 159
applied functional to approximate the electronic exchange - correlation (XC) contribution. To

overcome this problem, first we try to find those XC functionals which could describe HBs
with an approximate accuracy as MP2. In the last few years a number of significant works
could be found in the literature, which compared the efficiency of different DFT functionals
with those obtained using MP2 method.
Besides of the accurate electron correlation methods, based on the perturbational,
coupled-cluster or Kohn-Sham (KS) scheme, the basis set superposition errors (BSSE)
present a very important source of discrepancies. Many papers have indicated that the impact
of BSSE on the geometries of weakly bound systems is smaller for DFT methods than those
for ab initio methods such as MP2, but their influence even in case of DFT could not be
neglected [1719]. The reason why BSSE is similar in HF and KS methods is that the KS
method does not require the high oscillatory basis functions which are needed to describe
electron correlation in traditional electronic structure methods, and which are virtually
impossible to include at saturation.
2.1. The BSSE Problem
The BSSE is a pure mathematical effect and it is an important problem to solve when
we study a weakly bonded molecular complex. This effect appears only as a result of the use
of finite basis sets, because the description of the monomer is actually better within the
supermolecule than that which one has for the free monomers by applying the same basis set,
so thus leads to incomplete description in the individual monomers. Due to BSSE, the
calculated interaction energies show too deep minima and the computed potential energy
surface (PES) is distorted. The most important and straightforward a posteriori correction
scheme, the so-called function counterpoise (CP), or simply the BoysBernardi method,
was introduced by Jansen and Ross [20] and, independently, by Boys and Bernardi [21] in
1969/1970. In this CP scheme, the monomer energies are recalculated by using the whole
supermolecular basis set and these corrected monomers are used in the molecular interaction
energy calculations. A conceptually different way to handle the BSSE problem is to apply the
chemical Hamiltonian approach (CHA) for the case of intermolecular complexes proposed
by Mayer [22] in 1983. (For a detailed review on CHA, see Ref. [23].) By using the a priori
CHA method one can eliminate the nonphysical terms of the Hamiltonian, which leads to
wave functions free from the nonphysical delocalizations caused by BSSE. Using this CHA
scheme, several approaches have been developed both at the HF [2437] and correlated [38
45] levels of theory to study the structures and interaction energies for different van der
Waals and H-bonded systems.
The CP Scheme
The simplest definition of the uncorrected interaction energy between two molecules is
the difference of the supermolecular energy and the sum of the free monomer energies, each
calculated in its own basis set:
E AB
unc
= E AB ( AB ) E A ( A) EB (B ) , (1)
160 Attila Bende
where EAB(AB), EA(A), and EB(B) denote the total energy of the AB supermolecule and the
energy of the A and B monomers, respectively. The notations in parentheses indicate that
basis sets corresponding to (sub)system A, B, and AB, respectively, were used. To compute
the correct value of the interaction energy E AB
unc
, we need to use (nearly) complete basis sets
on the supermolecule and on each monomer, which is usually impossible in practice.
In the CP scheme, the interaction energy E ABCP
is defined as the difference of the
supermolecule and monomer energies, all computed in the same supermolecule basis set:
E AB
CP
= E AB ( AB ) E A ( AB ) EB ( AB ) (2)
Using Eqs. (1) and (2), one can define the BSSE content in the interaction energy as
EBSSE = E AB
unc
E AB
CP
(3)
= E A ( AB ) E A ( A) + EB ( AB ) EB (B )
According to Eq. (3), the CP-corrected potential energy surface (PES) of the dimer
becomes
E CP ( AB ) = E AB
unc
E BSSE
(4)
= E AB
unc
E A ( AB ) + E A ( A) E B ( AB ) + E B (B )
Equation (4) shows that by considering only the intermolecular internal coordinates as
optimized parameters one has to calculate three different total energies to determine the CP-
corrected PES.
The CHA Scheme
In the alternative a priori CHA scheme introduced by Mayer [22, 23] one can omit the
BSSE caused terms of the Hamiltonian, which is a conceptually different way of handling the
BSSE problem. The CHA procedure permits the supermolecule calculations to remain
consistent with those for the free monomer performed in their original basis sets. The basic
idea of Mayers scheme is that one can divide the BornOppenheimer Hamiltonian into two
parts:
H BO = H CHA + H BSSE (5)
where H CHA is the BSSE-free part of the Hamiltonian and H BSSE is the unphysical part of
the Hamiltonian that is responsible for the BSSE. The only difficulty of this scheme is that the
resulting physical Hamiltonian H CHA is not Hermitical, so one cannot expect the BSSE-
free Hamiltonian H CHA to be Hermitical either. Based on this CHA Hamiltonian, Mayer and
Vibk developed different SCF-type equations [28]:
H CHA CHA = CHA , (6)
CHA H BO CHA
ECHA / CE = . (7)
CHA CHA
In the CHA framework [3235] described by Eqs. (6)(7) the non-Hermitical CHA
Hamiltonian H CHA is used only to provide the BSSE-free wave function (or a perturbative
approximation to it) but the energy should be calculated by using the conventional
(Hermitical) Born Oppenheimer Hamiltonian H BO , making not trivial the question of how
one should calculate the second-order energy correction.
The 0th-order Hamiltonian is defined in terms of the CHA Fockian [45]:
H 0 = ~
p
p
+
p

p , (8)
where p+ and ~p are the creation and annihilation operators.

To obtain the first-order wave function in the perturbation theory, the non-Hermitical
CHA Hamiltonian could be partitioned as
H CHA = H 0 + VCHA , (9)
0
where H defined by Eq. (8), is the MllerPlesset type unperturbed Hamiltonian, which is
also non-Hermitical, and VCHA represents the perturbation. At the same time, the perturbation
energy could be obtained considering the following partition of the BornOppenheimer
Hamiltonian H BO :
H BO = H 0 + V (10)
Then the energy up to second order could be presented as
0 H BO 0
(2 )
E = + J2 , (11)
0 0
where J2 is the generalized Hylleraas functional:

162 Attila Bende
J2 =
1
0 0
[ ( ) (
2 Re Q 1 V 0 Re 1 H 0 E0 1 , )] (12)
Here 0 is the unperturbed wave function, E0 is the zero order energy ( H 0 =

0
= E0 0 ), 1 is the first order wave function of the perturbation, and Q is the projection
operator on to the orthogonal complement to 0 . These equations define our working formula
at the second-order perturbation level. This formalism is called CHA/MP2 theory [40].
2.2. Anharmonic Approach of Normal Mode Vibrations
Computation of harmonic force field and implicit the harmonic vibrational frequencies
many times give results which are very far from the experimentally measured values. The
explanation seems to be quite simple. Beyond of harmonic approximation, many other
contributions like solvent effects, anharmonic corrections or cluster effects, are not taken into
account. Usually, all of these corrections were considered by multiplying the harmonic
frequency values with a scaling factor. Unfortunately, the collective contribution of different
approximations could not always be fitted into the previous scaling scheme. So, it is very
important to study them separately considering different theoretical models which describe
these effects.
The linear relationship between normal coordinates Q and Cartesian displacement X
coordinates are:
Q = L+ M 1 2 X , (13)
where, by convention, all the components of Q and X vanish at the reference geometry, M is
the diagonal matrix of atomic masses, and L is the matrix of (columwise) eigenvectors of the
mass weighted Cartesian force constant matrix
M-1/2FM-1/2. The second-derivative matrix over normal coordinates, is
= L+ M 1 2 FM 1 2 L (14)
and is diagonal when evaluated at the equilibrium geometry with eigenvalues proportional
to the squares of harmonic vibrational frequencies . In this way we can evaluate the third
and fourth order energy derivatives with respect to normal coordinates by numerical
differentiations of analytical Hessian matrices at geometries displaced by small increments
Q from the reference geometry [46, 47]:
1 (Qi ) jk ( Qi ) ki (Q j ) ki ( Q j ) ij (Qk ) ij ( Qk ) (15)

ijk = jk + +
3 2Qi 2Q j 2Qk

ij (Qk ) + ij ( Qk ) 2 ij (0 )
ijkk = (16)
Qk2
1 (Qk ) + ii ( Qk ) 2 ii (0 ) kk (Qi ) + kk ( Qi ) 2kk (0)

iikk = ii + (17)
2 Qk2 Qi2
In case of nonlinear molecules these computations require at most the Hessian matrices at
6N-11 different points, N being the number of atoms in molecules.
Expanding the vibrational Hamiltonian Hvib using the vibrational wavefunctions in the
framework of the second-order perturbation theory, one can obtain the following expression:
1 1 1
vi H vib vi = 0 + n + 2 + n + 2 n
i i
i j
ij i j +
2
(18)
where the constants are simple functions of the cubic and quartic force constants.
2.3. Density-Fitting Local Perturbation Methods
Hyper-accurate quantum chemical techniques, suffer from high-degree polynomial

scaling. For example, CCSD scales as O(N6) and MP2 scales as O(N5) where N is some
measure of system size. In this sense, to develop new techniques which reduce their high-
degree polynomial scaling are very important in order to describe larger molecular systems.
In the last decade were developed two important methods (density fitting and local
perturbational or coupled cluster approximation) which all together can change the high-
degree scaling and reduce them close to the linear dependency. In this way, medium sized
molecular systems (60 80 atoms) can be treated at triple-zeta basis set quality level.
Density Fitting
In the HF theory, calculations of electron repulsion integrals (ERI)
G G p (1) q (1) r (2) s (2 )

* *

1
pr r qs = pq rs = dr1 dr2
12 (19)
r12
are the most expensive computational procedures. The computational effort for ERI valuation
and transformation can be reduced by 12 orders of magnitude using density fitting (DF)
methods [48 51]. In this approach the one-electron charge densities in the ERIs, which are
binary products of orbitals, are approximated by linear expansions in an auxiliary basis set
| pq ) | ~
pq ) = DApq | A) (20)
164 Attila Bende
This leads to a decomposition of the 4-index ERIs in terms of 2- and 3-index ERIs, and
the O(N4) dependence of the computational cost is reduced to O(N3)
( pq | rs ) ( ~pq | ~r s ) = DApq J AB DBrs , (21)
where
G G A(1)B(2)

J AB = dr1 dr1
r12
(22)
Local Approximation
In the LMP2 method the occupied space is spanned by localized molecular orbitals
(LMOs), which can be obtained from the canonical orbitals by standard localization
procedures as proposed by Boys [52] or Pipek and Mezey[53]. The virtual space is spanned
by a basis of non-orthogonal projected atomic orbitals (PAOs),
1 = Tabij ijab (23)
which are obtained from the AO basis functions by projecting out the occupied orbital space
1 = [ T]
i , jP ab i , j
ij
ab ijab (24)
In the following, PAOs will be labeled a,b. Since these functions are inherently local, one
can introduce two approximations: First, excitations from a pair of occupied LMOs can be
restricted to subsets of PAOs that are spatially close to the two LMOs. The number of
functions Nij in each of these subsets (pair domains) is independent of the molecular size, and
the number of excitations for each electron pair reduces from Nvirt2 to Nij2. Second, the
integrals (ai|bj) for distant orbitals i and j can be approximated by multipole expansions [54]
or neglected. The remaining number of non-distant orbital pairs (ij), and therefore the total
number of excitations, scales linearly with molecular size.
3. Results and Discussions

3.1. Formamide Dimers
Formamide (FA) is the simplest molecule that contains a peptide linkage built by the
carbonyl and amino groups; therefore, we can consider the formamide dimer (FAFA) as the
simplest model of the pairing of nucleic acids and the formamidewater (FAWA) complex
as a hydration of proteins, respectively. Geometry structures [3, 5564] and vibrational
spectra [3, 56, 60, 6568] of the FAFA and FAWA dimers have been the subject of many
studies using different ab initio [HF and MP2] methods, which give valuable information
about the structure and dynamics of the H-bonds in molecular systems.
The standard HF, MP2, and CP-corrected HF/MP2 calculations were performed using the
Gaussian 03 computer code [69]. The CHA/CE- and CHA/MP2-type calculations were done
by generating the input data (integrals and RHF orbitals) with a slightly modified version of
HONDO-8 [70]. In these calculations the CHA/SCF code [2527] and the CHA/MP2
program of Mayer and Valiron [40, 42] were used. For the frequency calculations based on
Wilsons G-F method, the program written by Beu [71] was applied.
We considered six different basis sets: 6-31G, 6-31G**, 6-31G**++, D95V, D95V**,
and D95V++**. 6-31G to 6-31G**++ are standard Pople basis sets; D95V to D95V++** are
Dunning/Huzinaga valence basis sets.
The conventional supermolecule geometries were optimized at both the HF and MP2
levels, applying the analytical gradient method included in the Gaussian 03; the CHA- and
CP-corrected geometries were calculated by using a numerical gradient method [inverse
parabolic interpolation (IPI) [72]] in internal coordinates including only internal coordinates
with intermolecular character (one bond, two angles, and three torsion angles). The reason for
this choice is that the CPU time of MP2-CHA program is fairly big. To test the applicability
of our numerical gradient method we performed several sample calculations using both the
IPI method and the analytical gradient built into Gaussian 03. There is practically no
difference between them. For conventional uncorrected cases we also performed similar
calculations to check the values of the force constants and harmonic vibrational frequencies.
The uncorrected HF and MP2 results for the force constants (in internal coordinates) and for
the harmonic vibrational frequencies were obtained by using the standard routines of the
Gaussian 03 program. As for the CHA- and CP-corrected calculations, at first the numerical
second derivatives of the energies were calculated to obtain the CHA and CP force constants
and then the NOMAD program [71] was applied to obtain the appropriate CHA and CP
harmonic vibrational frequencies. As we are interested in the BSSE content in the molecular
interaction energies, only those components of the force constant matrix were recalculated
that correspond to intermolecular internal coordinates. The anharmonic frequencies were
obtained using the standard full-CP method implemented in Gaussian 03.
The Geometry Structure
Table I shows the optimized geometry parameters for the FAFA complex (Figure 1),
using the conventional (Uncorr.), CHA, and CP schemes at both the HF and MP2 levels. The
FAFA dimer has planar geometry configuration: the global minimum for the dimer is a
cyclic structure of C2h symmetry involving two equivalents N-HO=C intermolecular
hydrogen bonds.
Two other planar minima has been identified [56, 62, 73] that establish a single N-HO=C
HB building up the linear and zig-zag configurations. In the work we consider just the planar
cyclic dimer configuration, for which the BSSE-corrected geometrical parameters are
presented. Once this assumption is made, the only variables left are the rHO bond length and
two angles, NHO and HOC, which could be associated with the in-plane vibration normal
modes, while all three torsion angles having intermolecular character are kept constant, their
normal modes representing out-of-plane vibrations. The results show that only the rHO bond
length has an important BSSE correction (0.06 for MP2-CHA/6-31++G**, 0.08 for
MP2-CHA/D95V++**, and 0.06 for MP2-CP/6-31++G** and MP2-CP/D95V++**),
which increase the bond size. Furthermore the change in the NHO and HOC angle values is
166 Attila Bende
insignificant but their corresponding force constants also include BSSE effects.
Unfortunately, the experimental value for rHO bond length presented in Ref. [63] does not
have the desired precision, so we could not compare with high precision the uncorrected
values and the given BSSE corrected bond lengths. Both the corrected and the uncorrected
values are close to the experimental value, 1.9 (1.87 for MP2/D95V++** and 1.9 for
MP2/6-31++G** in the uncorrected case; 1.95 for the CHA- and CP-corrected cases).
However, we can compare our calculated result for the rNO intermolecular distance with the
experimental values obtained by Itoh and Shimanouchi [66].
Table 1. Intermolecular coordinate for the FAFA dimer computed at the HF and
second-order MllerPlesset perturbation theory (Uncorr., CHA, CP) level, using D95V,
D95V**, D95V++**, 6-31G, 6-31G**, and 6-31++G** basis sets
rHO ()a HOC (Deg.) NHO (Deg.)

Basis Method RHF MP2 RHF MP2 RHF MP2
D95V Uncorr. 1.904 1.872 129.7 125.9 165.6 169.3
b
(66) CHA 1.950 1.936 128.9 125.1 166.3 170.1
CP 1.943 1.960 129.4 125.7 165.8 169.5
D95V** Uncorr. 2.002 1.862 125.7 122.1 168.9 172.6
(120) CHA 2.029 1.912 125.0 122.1 169.6 172.6
CP 2.019 1.924 124.9 121.8 169.7 172.8
D95V++** Uncorr. 2.021 1.874 125.2 120.9 169.4 173.7
(150) CHA 2.039 1.915 125.2 122.5 169.4 172.1
CP 2.034 1.936 125.2 122.4 169.4 172.2
6-31G Uncorr. 1.919 1.912 126.8 122.0 168.0 172.4
(66) CHA 1.934 1.923 126.8 123.0 168.0 171.3
CP 1.939 1.965 127.6 123.7 167.3 170.7
6-31G** Uncorr. 1.998 1.887 122.7 119.0 171.5 175.0
(120) CHA 2.007 1.898 123.6 120.9 170.5 173.0
CP 2.025 1.947 123.6 120.4 170.6 173.6
6-31++G** Uncorr. 2.017 1.899 125.4 121.7 169.2 172.8
(150) CHA 2.034 1.954 125.1 122.6 169.4 171.9
CP 2.038 1.954 125.2 122.5 169.3 172.1
a
Experimental value 1.9 , taken from Ref. [63].
b
The number of basis functions are given in parenthesis.
The calculated lengths are 2.895 for the uncorrected case, 2.970 for CHA-type, and
2.955 for CP-type BSSE-corrected cases, while the X-ray data for the formamide crystal
[66] gives 2.935 for the rNO intermolecular distance. If we suppose that the intermolecular
bond length in the crystal phase is a bit shorter than in the gas phase, it can be considered that
the corrected values are very close to the experimental.
Figure 1. The formamide dimer.
Table 2. Interaction energiesa (in kcal/mol) for different FAFA dimer geometry
computed at the HF and second-order MllerPlesset perturbation theory (Uncorr.,
CHA, CP) level, using D95V, D95V**, D95V++**, 6-31G, 6-31G**, and
6-31++G** basis sets
Basis D95V D95V** D96V++**

Method RHF MP2 RHF MP2 RHF MP2
Uncorr. -17.018 -18.370 -12.912 -16.921 -12.043 -15.903
CHA -15.279 -14.511 -12.086 -13.971 -11.567 -13.140
CP -15.185 -14.046 -11.886 -13.552 -11.547 -13.201
Basis 6-31G 6-31G** 6-31++G**
Method RHF MP2 RHF MP2 RHF MP2
Uncorr. -17.387 -18.799 -14.212 -18.330 -12.385 -15.365
CHA -15.580 -14.496 -12.576 -13.851 -11.965 -13.228
CP -14.956 -13.705 -12.032 -13.492 -11.837 -13.399
a
Experimental value -13.967 kcal/mol; taken from Ref. [63].
In Table 2 we present the calculated intermolecular binding energies, considering the

optimized geometry in the given basis and using the given methods (uncorrected, CHA, and
CP) and levels of theory (RHF and MP2). The experimental value was obtained using
Rydberg electron transfer technique between laser-excited atoms; the molecular system [63]
is 606 meV, which corresponds to 13.967 kcal/mol. Our BSSE-corrected results (13.288
kcal/mol for MP2-CHA/6-31++G**, 13.399 kcal/mol for MP2-CP/6-31++G**, 13.140
168 Attila Bende
kcal/mol for MP2-CHA/D95V++**, and 13.201 for MP2-CP/D95V++**) are very close to
experimental values, whereas the uncorrected results show more than 1.4 kcal/mol difference.
Moreover, we can obtain reasonable binding energy value even if we use the 6-31G and
D95V bases without diffuse or polarization functions, applying BSSE correction for
uncorrected geometry at the same time.
Harmonic and Anharmonic Frequencies
The FAFA dimer has 30 vibrational normal modes from among which 24 (12 for each
monomer) vibrations are characteristic to the monomer-type vibrational motion, while six
modes have a pure intermolecular character.
Table 3. The uncorrected and CP-corrected harmonic () and diagonal anharmonic (x)
frequency of FAFA dimer computed at MP2 level of theory,
using 6-31++G** basis set
Nr. dim CP mon xdim xCP xmon Assign.

intramolecular
3770.0 3770.3 -32.5 -32.4
1 3814.1 -40.5 N-N a.
3769.9 3770.1 -32.9 -32.8
3465.8 3467.5 -49.9 -49.2
2 3660.9 -36.1 N-N s.
3424.8 3426.4 -58.9 -57.8
3103.9 3104.2 -33.0 -33.0
3 3083.9 -67.7 C-H
3101.6 3101.9 -33.1 -33.1
1795.5 1796.4 -24.0 -24.4
4 1794.9 -6.6 C=O
1773.9 1774.4 -22.3 ???
1677.0 1677.2 -9.5 -9.4
5 1654.2 -8.5 H-N-H
1666.6 1667.9 -3.9 -4.0
1444.0 1446.7 -3.8 -3.9
6 1444.0 -9.1 O=C-H
1444.8 1445.8 -3.9 -3.9
1367.7 1367.4 -2.9 -2.8
7 1295.9 -5.0 C-N
1353.1 1352.4 -2.6 -2.6
1112.1 1111.6 -0.8 -0.8
8 1075.2 -1.3 C-N-H
1106.0 1105.6 -0.7 -0.7
1060.2 1067.7 0.5 -1.1
9 1041.0 -1.3 OofP
1046.2 1056.1 1.1 -0.7
824.3 827.8 -15.5 -20.7
10 628.1 -15.9 Torsion
785.1 789.7 -6.5 -8.3
622.8 621.2 -0.6 -0.6
11 565.6 1.2 O=C-N
605.7 604.8 -0.2 0.3
413.9 425.5 17.8 12.9
12 276.1 -462.7 Torsion
394.5 404.4 28.2 24.8
Table 3. Continued
Nr. dim CP mon xdim xCP xmon Assign.

intermolecular
1 47.5 118.3 451.2 47.6 OofP
2 29.6 99.7 2101.0 11.0 OofP
3 9.2 49.0 16800.0 1.5 OofP
4 171.8 176.2 -3.1 -2.3 HO
5 212.6 217.3 -1.8 -1.2 HH
6 136.4 136.2 -0.2 -0.1 OO
Usually the vibration frequencies of molecular complex are evaluated at the harmonic
approximation applying the Wilson F-G analysis and using the BSSE-uncorrected Hessians.
On the other hand, the vibrational frequencies, in particular there with an intermolecular
character, contain considerable anharmonic effects and therefore it is difficult to follow these
two important corrections in a distinct way. Considering the monomer-type vibrations (Table
3) it can be found that two different dimer frequencies correspond to the similar monomer
vibrations, but their values are usually shifted due to the intermolecular interaction. Taking in
to account the full CP-corrected values in the dimer calculations, we found another frequency
shift, but in this case due to the BSSE effects. Moreover, the frequency values show an
important basis size effect at the MP2 level, which implies the shifts in dimer frequency
values will change. The results of the anharmonic frequency corrections show a more
complex picture. Because of the large numbers of the anharmonic frequencies in Table 3 only
the diagonal elements of anharmonic frequency matrix are presented.
The most important effect in the anharmonic values is given by the influence of the
adjacent molecule, which generates substantial shifts in the anharmonicity of different
monomer normal modes within the dimer system. Although the above-mentioned cluster
effect is quite uniform, the basis size effects become much more complicated. In the case of
hydrogen bond stretching (NH, CH) and angle-bending vibrations, changes in the
anharmonic frequency are not so important, but the torsion angle and C=O stretching modes
show very dissimilar results. Considering the full CP-corrected BSSE-free anharmonic
frequency calculations, no major corrections can be found for the monomer-type vibrations,
which in practice mean that their effects could be generally neglected for the FAFA dimer.
Regarding the intermolecular normal modes, in addition to the cluster and basis size effects,
the BSSE corrections become very important, especially for out of plane normal modes (see
MP2/6-31++G**). After these, considering the collective effects of basis size and BSSE
corrections on the intermolecular vibration frequencies, it can be concluded that major
corrections are obtained in the cases of the harmonic approximation given by the quality
(applying polarization and diffuse basis sets) and the BSSE of the applied basis sets, which is
followed by the similar correction of the anharmonic approximation. With respect to the
intermolecular normal modes, the out-of-plane vibration with low frequencies usually shows
a very dissimilar and unrealistic anharmonic correction, especially for the MP2/6-31++G**
CP-corrected case. This phenomenon may be related to many facts: i) in the CP method the
PES is very flat, the intermolecular force constants are very small [74] and the numerical
170 Attila Bende
calculations could give significant errors; ii) the role of the well-balanced basis set is very
important, therefore we consider that the 6-31++G** does not give us adequate results. For
example, the 6-31++G(2d, 2p) basis set could be a more suitable choice, but the available
computer capacity does not allow us to perform such full-CP anharmonic calculations.
3.2. Urea Dimer
The urea dimer presents to some extent a good similarity with the formamide-formamide
system. The difference between these two systems is the existence of the second cyclic
system in the urea dimer. In the case of the urea dimer one of the HBs is the weak C-NH-N
hydrogen bond. The planarity (or nonplanarity) of the urea dimer system has been the focus
of a number of studies. Masunov and Dannenberg [75, 76] considered different levels of
theory (HF, MP2 and DFT with and without BSSE corrections), and the most stable
conformation was found to be the non-planar structure (using the MP2 method with the
D95++** basis set). However, they accentuate that inclusion of vibrational and thermal
corrections in the calculations of the molecular structure might give an effectively planar
structure. We consider the papers of Rousseau and Keuleers [77, 78] as very important work
in elucidating the urea structure, where detailed descriptions of vibrational spectra of urea
both in gas and crystal phase are presented. Their concisely conclusion was that the
vibrational analysis of solid urea and of the gas phase of urea are not comparable, which is
mostly due to the different planar or non-planar conformation of urea in different states.
The goal of this study is to give an accurate description of intermolecular normal modes
and to present different intermolecular interaction effects which could influence the monomer
type vibrations, considering the cyclic urea dimer case. Accordingly, several DFT functionals
were tested by comparing them with the corresponding MP2 results. The BSSE was corrected
using the counterpoise (CP) method [20, 21] as implemented in the Gaussian03 package suite
[69]. The uncorrected and BSSE-corrected energies, geometries, harmonic frequencies and
their anharmonic corrections [79, 80] were calculated for MP2 and DFT levels of theory
using D95V, D95V** and D95V**++ basis sets [81]. The combined local and density fitting
approximations for MP2 and Coupled-Cluster methods (DF-LMP2 and DF-LCCSD(T)) were
taken into account considering Molpro program package suite [82].
In Table 4 we list the interaction energies (given in kcal/mol) and intermolecular HB

distances (in ) obtained for the cyclic urea dimer structure with MP2 method and six
different DFT XC functionals (both in uncorrected and CP-corrected cases) using D95V**++
basis set. In the last five rows of Table 4 the same interaction energy and intermolecular HB
distance obtained with DF-LMP2 method using D95V**++ and cc-pVQZ basis sets are also
shown, as well as the interaction energy obtained using DF-LCCSD(T) method. The cyclic
urea dimer is bonded by two equivalent C=OH-N HBs presented in Figure 2.
Table 4. The he interaction energies (in kcal/mol) and R intermolecular distances (in
) in case of cyclic urea dimer structure, optimized at different levels of theory and
considering the D95V**++ and cc-pVQZ basis sets
Method Cyclic
ROH
a
MP2 NoCP -16.53 1.86
b
CP -13.18 1.93
BLYP NoCP -14.15 1.84
CP -13.52 1.86
B3LYP NoCP -15.04 1.84
CP -14.43 1.85
PBE NoCP -16.81 1.79
CP -16.12 1.80
HTCH407 NoCP -12.33 1.96
CP -11.76 1.98
KMLYP NoCP -20.74 1.75
CP -20.08 1.75
c
BHLYP NoCP -15.59 1.81
CP -15.01 1.86
DF-LMP2 - -13.26 1.93
LMP 2
E disp - -2.21 -
d
DF-LMP2/vqz - -14.83 1.86
LMP 2
E disp /vqz - -3.56 -
DF-LCCSD(T)e/vqz - -14.29 -
a
Without counterpoise correction
b
With counterpoise correction
c
BHandHLYP
d
cc-pVQZ
e
The LMP2 optimized geometry was used.
Figure 2. The urea cyclic dimer.

172 Attila Bende
Table 5. The harmonic () and anharmonic (a) frequencies (in cm-1) of intramolecular
normal modes (H N: 1 4 and O=C: 5,6 bond stretching) of cyclic urea dimer
obtained at MP2, B3LYP and BHLYP levels of theory with and without BSSE
correction and using the D95V++** basis set
dim dim dim dim

No Meth NCP CP mon a NCP aCP a mon exp
1 3782.5 3784.1 3608.7 3610.5
MP2 3770.1 3596.1
3782.4 3784.0 3608.7 3610.4
3712.1 3712.6 3546.4 3546.7 3450a
B3LYP 3706.8 3544.5
3712.1 3712.6 3546.4 3546.7 3348b
3848.3 3848.8 3688.1 3688.6
BHLYP 3841.3 3658.4
3848.3 3848.8 3688.0 3688.6
2 3752.3 3759.4 3584.7 3592.6
MP2 37701 3596.3
3751.7 3758.6 3584.3 3592.2
3657.4 3675.9 3512.3 3514.3 3444
B3LYP 3706.6 3543.9
3675.7 3675.3 3511.7 3513.3 3435
3813.7 3814.7 3652.1 3653.8
BHLYP 3841.1 3684.8
3813.4 3814.4 3652.1 3653.8
3 3649.7 3651.1 3493.6 3495.3
MP2 3641.5 3484.3
3649.7 3651.0 3493.7 3495.2
3589.9 3590.2 3441.9 3442.1 3349
B3LYP 3578.8 3438.9
3589.9 3590.1 3441.8 3442.0 3345
3723.5 3723.8 3580.2 3580.6
BHLYP 3720.1 3580.3
3723.5 3723.7 3580.0 3580.3
4 3457.8 3509.0 3229.3 3388.8
MP2 3638.9 3482.3
3419.6 3480.0 3149.0 3370.4
3340.0 3348.9 3144.0 3148.1 3331
B3LYP 3582.5 3435.3
3297.2 3307.3 3008.5 2984.4 3330
3510.8 3518.2 3322.0 3307.5
BHLYP 3715.1 3575.3
3478.8 3483.2 3305.0 3325.0
5 1798.3 1801.2 1764.9 1765.6
MP2 1853.2 1782.1
1777.9 1781.0 1729.1 1740.9
1768.6 1769.4 1722.6 1723.9 1683
B3LYP 1797.0 1751.5
1743.7 1744.3 1769.3 1700.5 1683
1855.9 1856.6 1813.0 1800.9
BHLYP 1887.4 1841.4
1825.3 1825.6 1781.8 1782.6
6 1693.2 1693.1 1648.3 1647.3
MP2 1823.2 1728.1
1684.7 1687.4 1650.1 1646.6
1656.9 1659.1 1619.9 1622.3 1625
B3LYP 1629.0 1589.4
1651.0 1653.5 1602.4 1610.6 1627
1722.7 1724.3 1681.6 1683.7
BHLYP 1696.2 1659.0
1721.6 1723.3 1682.4 1685.4
a
At T = 20 C
b
At T = -196 C
The interaction energy and HB distance values show that a good fitting of DFT values
with MP2 results are not obvious for any of the selected XC functionals. In the case of cyclic
structure one can observe that the best agreement for the intermolecular interaction energies
and intermolecular RO...H distances are given by the BHLYP and B3LYP XC functionals. The
interaction energy values are: -15.04 kcal/mol for B3LYP, -15.59 kcal/mol for BHLYP and -
16.53 kcal/mol for MP2, while the intermolecular distance for RO...H is: 1.84 (B3LYP), 1.85
(BHLYP) and 1.86 (MP2). At the same time, reasonable values could be also obtained
applying the BLYP functional, while in the case of KMLYP, PBE and HTCH407 the energy
and geometry parameter results are quite different from the MP2 values. If we compare the
same and R values at DF-LMP2 level of theory, but obtained with different basis sets
(D95V**++ versus cc-pVQZ), one could see that the energy results increase with 1.58 and
2.39 kcal/mol, respectively, while for the R distance we get smaller values with 0.06 and 0.07
, respectively.
Focusing on the dispersion part of the intermolecular interaction energy, significant
dispersion energy growth can be found (1.35 kcal/mol for cyclic dimer and 1.71 kcal/mol for
asymmetric case), when the larger cc-pVQZ basis set is used against the D95V**+ one.
These represent the major contribution to the total interaction energy increase. In order to
consider higher correlation effects, other than those included in the MP2, the interaction
energies were computed applying the DF-LCCSD(T) method, using the same cc-pVQZ basis
set and taking into account the DF-LMP2 optimized geometry.
The cyclic urea dimer has 42 vibrational normal modes from which a number of 36 (18
for each monomer) vibrations are characteristic to monomer-type vibrational motion. The last
6 normal modes with the lowest frequency values have purely intermolecular character. These
18 monomer frequencies of dimer structure are split in a form of frequency pairs (doublets).
For the whole theoretical IR spectra, see Figure 3. Compared to the individual monomer lines
they present different frequency shifts and their magnitudes depend very much on the dimer
molecular symmetry.
Figure 3. The theoretical IR spectra of urea cyclic dimer obtained at MP2-CP, DF-LMP2 and B3LYP-
CP levels of theory, using D95V**++ basis set.
174 Attila Bende
In Table 5 were collected the harmonic frequencies (doublets) and their anharmonic
corrections for those monomer type normal modes of which vibrational motions are
substantially perturbed by the adjoining molecule. They were determined in advance by
identifying the frequency value which corresponds to each normal mode vibration and by
visualization of their vibrational characters [83].
It was found that, the 1, 2 and 3 intramolecular normal modes are N-H bond stretching
vibrations where the H atoms do not take part in intermolecular HB formations. The 4, 5 and
6 are one N-H and two C=O bond stretching vibrations located at the N-HO=C
intermolecular HBs. It can be observed that the doublet frequency splits for 1, 2 and 3
normal modes are almost irrelevant. More precisely, the frequency shifts, which are induced
by each monomer on the adjoining molecules, have the same magnitude. Only those normal
modes presents different frequency shifts and implicitly larger doublet splits where the
perturbation of HB vibration is present (4, 5 and 6). As it can be seen in Table 5 the dimer
frequency shift could be attributed to several effects like: anharmonic corrections, BSSE
effects, or intermolecular effects. It should be mentioned that BSSE is not a real physical
effect and normally it must be considered together with the intermolecular effects. But, in
order to see how important frequency shifts could the BSSE error induce we consider as a
separate effects.
Table 6. The harmonic () and anharmonic (a) frequencies (cm-1) of intermolecular

normal modes of cyclic urea dimer obtained at MP2, B3LYP and BHLYP levels of
theory with and without BSSE correction and using the D95V++** basis set
Cyclic
No. Meth. dim dim dim dim
NCP CP a NCP aCP
I MP2 159.3 141.5 151.9 132.4
B3LYP 157.8 150.6 155.2 150.1
BHLYP 158.4 156.0 151.5 153.1
II MP2 154.3 135.2 144.7 123.7
B3LYP 152.0 137.9 147.4 137.4
BHLYP 154.7 150.7 143.9 141.3
III MP2 126.8 121.9 121.6 117.6
B3LYP 134.6 127.2 135.0 132.6
BHLYP 133.4 133.4 127.0 132.6
IV MP2 94.4 89.9 80.5 75.3
B3LYP 93.7 81.5 93.8 80.7
BHLYP 93.7 94.1 78.7 80.7
V MP2 65.1 62.0 55.6 54.4
B3LYP 67.9 50.5 66.9 53.0
BHLYP 68.6 67.6 53.8 55.9
VI MP2 35.8 38.0 29.5 33.8
B3LYP 45.4 46.8 44.1 45.7
BHLYP 45.8 45.0 43.9 54.4
In the case of N-H bond stretching vibrations, the magnitudes of anharmonic corrections
(frequency red-shift) are quite large ( 150 - 170 cm-1 for 1, 2 and 3, and >200 cm-1 for 4,
respectively) while in the case of a1, a2 and a3 anharmonic corrections, for both of doublet
frequency values, the magnitude of frequency shifts are the same. For a4 correction the size of
doublet frequency shifts is different (ex. at MP2 level 4-a'4=3457.8 - 3229.3 cm-1 = 228.5
cm-1 and "4 - a"4 = 3419.6 - 3149.0 cm-1 = 270.6 cm -1). Regarding to 5 and 6 C=O
stretching modes one can see that the anharmonic corrections are much smaller than in the H-
N case, their shifts are about 30-40 cm-1 and the behavior of their frequency split is similar to
4 mode. The correction scheme for 4 and 5 is as follows:
4' : mon = 3638 .9 cm 1 dimer

dim anh. BSSE = 3388 .8 cm 1
anh BSSE

- - +1
1
:
"
4
mon
= 3638 .9 cm
dimer dim

anh.
anh
BSSE = 3370 .4 cm 1
BSSE
- - +2
1
:
'
5
mon
= 1853 .2 cm
dimer dim

anh.
anh
BSSE = 1765 .6 cm 1
BSSE
- - +0.
1
:
"
5
mon
= 1853 .2 cm
dimer dim

anh.
anh
BSSE = 1740 .9 cm 1
BSSE
- - +1
Considering the scheme of frequency corrections by dimer, anharmonic and BSSE effects
presented above, one could be observe that they bring different contributions in the case of
the 4 monomer frequency value (3638.9 cm-1), where finally we got a double-split
frequency pair ( 4' and 4" ) of 3370.4 cm-1 and 3388.8 cm-1 values. Similar situation can be
found for the 5 monomer frequency value where we have two frequency values with 24.7
cm-1 distance between them.
Beside of the monomer-type frequencies, the molecular association induces a group of
another six normal mode vibrations which can be called intermolecular normal modes. They
can be found in the very-far region (10250 cm-1) of the molecular IR spectra and show the
relative vibrations of two rigid urea monomers according to the six degree of freedom
which derive from the intermolecular coordinates. The frequency values of these
intermolecular normal mode vibrations are shown in Table 6 obtained both at MP2 and DFT
(B3LYP and BHLYP) levels of theory. They have strictly intermolecular character and show
only anharmonic and BSSE corrections. Scrutinizing the results of normal mode vibrations
for the cyclic dimer one can observe that there are three frequencies of which motion take
place in the supermolecular plane (I III) let calls them in-plane vibrations, while the
another three intermolecular normal modes (IV VI) show out-of-plane vibrations. If we
consider together the amount of anharmonic and BSSE corrections one can see that the in-
plane vibrations are more affected by these errors than out-of-plane normal modes. Yet
analyzing separately for only one mode, it can be seen that they have almost similar
magnitude, becoming equally relevant corrections for the intermolecular normal mode
vibrations. At the same time, if we consider the off-diagonal vibration couplings of these
normal modes, one can find that frequencies which belong to the group of in-plane or out-
of-plane their vibrations are strongly coupled inside the group, but much less coupled
between the groups. In the case of asymmetric urea dimer the separation of the above
mentioned in-plane and out-of-plane group of vibrations is not so obvious, but similarly
176 Attila Bende
to the cyclic dimer the BSSE and the anharmonic effects are equally relevant. In both cases of
dimer structures the collective effect of BSSE and anharmonic corrections presents about 10
15% from the frequency values.
The intra intermolecular normal mode couplings could give us more detailed
information about how strongly the intra- and intermolecular normal modes are coupled
between them. Since the intra- and intermolecular normal modes have very different
vibrational frequency values one should obtain a strong coupling only in some special cases.
Analyzing the anharmonic coupling matrix we found that in case of cyclic dimer the I III
intermolecular normal modes are coupled only with 4' and 4" (ex. x( 4" - I ) = +6.73 cm-1)
intramolecular vibrations, while couplings between 5' and 5" intra-normal modes and I
III inter-normal modes are almost missing. This could be explained with the fact that
molecular vibrations are performed in the same molecular plane and along the same
vibrational direction. In the case of asymmetric urea dimer neither for 4' and 4" , nor for 5'
and 5" so significant anharmonic coupling with the intermolecular normal modes could be
found than for the cyclic structure. In this case, the only relevant coupling is x( 5" - II ) = -3.86
cm-1.
If one compares the selected theoretical normal mode frequencies with the experimental
data (Table 5), the more appropriate values are obtained for the CP-corrected anharmonic
frequencies, both for cyclic and asymmetric structures. At the same time, it can be seen that
the dimer approximation is not satisfactory in order to reproduce these experimental data with
the desired high accuracy. Thus, other extended theoretical calculation where also solvent
effects and larger cluster sizes are taken into account would be absolutely necessary. In
addition, other spectroscopic data, like vibrational absorption intensities calculated via atomic
polar tensor [84] and comparing them with the measured vibrational intensities would be also
useful in order to explain the unusual behavior of urea in gas or solid phase.
3.3. Guanine-Cytosine DNA Base Pair
The guanine-cytosine (GC) base pair's intermolecular interaction can be considered as a

contribution of two very important HBs: a number of two C=OH-N and one PNH-N
bonds. Due to the biological manifoldness of DNA base pair conformations (dry-DNA, wet-
DNA, double helix, super-double helix, etc.) their theoretical characterization is much
diversified. A given theoretical model should take into account the backbone and
environment effects as well as the influence of the DNA-protein interactions. In virtue of this
fact, choosing the correct theoretical method is essential in the investigation of DNA base
pairs. In the last five years the substantial computer advance gave for molecular modeling
scientists the opportunity to include accurate electron correlation effects in their calculations.
poner et al. [85] and Podolyan et al. [86] used the well-known MP2 method with different
basis sets (mostly including the polarization effects) and they give a very detailed description
of the interaction energies and geometry structures of the adenine-thymine and guanine-
cytosine base pairs. At the same time the normal mode analysis of molecular vibration could
give us supplementary information about the efficiency of different methods. In connection
with this, several vibrational frequency calculations and experimental measurements were
performed [9, 86, 87, 88, 89] in order to study different interaction effects in normal mode
vibrations of base pairs (mostly for guanine-cytosine dimer). For instance, the intermolecular
interactions could significantly influence the intramolecular normal mode vibrations such as
red-shift or improper blue-shifting [90, 91] of the vibrational frequencies. Furthermore, the
intermolecular normal mode vibrations depend very much on the applied method or basis
sets, and last but not least on the BSSE effects [3, 74, 92, 93]. The different Watson-Crick and
Hoogsteen G-C geometries, harmonic frequencies and their anharmonic corrections [79, 80]
were calculated at DFT level of theory considering the PBE exchange-correlation functional
implemented in Gaussian03 [69] program package and using the 6-31G basis set. The
harmonic frequency values were scaled using the 0.986 factor corresponding to PBE/6-31G
type calculations.
In Figures 4 and 5 two different conformation (4: Watson-Crick [94] and 5: Hoogsteen
[95]) of G-C base pair are presented. Beside of the well-known Watson-Crick base pair
configuration the Hoogsteen base pairs have been known for more than 40 years. In
Hoogsteen base pairs the N face of guanine is hydrogen bonded to cytosine N side by an H+
proton. Such interactions were postulated in U(AU) triple helices [96] and it was also found
in chemically modified nucleic acids [97, 98]. Isolated Hoogsteen base pairs have been
reported in some protein/DNA complexes [99] and occasionally in RNA [100]. Its crystal
structure is presented in [101].
Figure 4. The Watson-Crick conformation of Guanine-Cytosine base pair.
Figure 5. The Hoogsteen conformation of Guanine-Cytosine base pair.

178 Attila Bende
The geometry of the DNA base pair was the subject of many scientific works, among
which the theoretical investigation performed by Guerra at al. [102] and van der Wijst [103]
are the most detailed ones. They present a systematic comparison of different DFT exchange-
correlation functionals and basis sets as well as they also compare the intermolecular
interaction energy values and H-bond distances with the experimental results. The best
agreement was obtained for the BP86 and PW91 exchange-correlation functionals, while the
widely used B3LYP functional consistently underestimates hydrogen-bond strengths and
overestimates hydrogen-bond distances. Nearly same good results can be obtained also with
the PBE functional as it found in case of BP86 and PW91 ones. Considering the above
mentioned method and basis set, for the intermolecular distances were obtained the following
values: a) Watson-Crick: d1(OH-N) = 2.80 , d2(NH-N) = 2.93 and d3(OH-N) = 2.92
, b) Hoogsteen: d1(NH+-N) = 2.66 , d2(OH-N) = 3.08 .
The guanine-cytosine binary system in its Watson-Crick configuration has a number of

29 atoms and presents a number of 81 normal mode vibrations from which 6 have
intermolecular character. In Figure 6 the IR absorption spectra for two characteristic spectral
regions of 500 2000 cm-1 and 2750 3750 cm-1, respectively, are presented.
Figure 6. The IR absorption spectra for Watson-Crick configuration of guanine-cytosine DNA base pair
at harmonic and anharmonic approximation.
The black vertical line shows the normal mode vibrational frequencies in harmonic
approximation, while the red lines are frequencies where the anharmonic approximation was
also taken into account. The values show a considerable frequency shift due to the
anharmonic approximation. These shifts are very pronounced in case of 2750 3750 cm-1
spectral region, where the C-H and N-H covalent stretching vibration are located.
Figure 7. The IR absorption spectra for Hoogsteen configuration of guanine-cytosine DNA base pair at
harmonic and anharmonic approximation.
Figure 8. The IR absorption spectra for Watson-Crick and Hoogsteen configuration of guanine-cytosine
DNA base pair at harmonic approximation.
The guanine-cytosine binary system in its Hoogsteen configuration has a number of 30

atoms and presents a number of 84 normal mode vibrations from which 6 have intermolecular
character. In Figure 5 can be observed that the NH+-N intermolecular bond is stabilized
with the help of the H+ proton. The H+-N is not a real covalent bond and therefore its
stretching vibration is also different from the usual H-N stretching vibrations. In case of
Watson-Crick configuration there are three characteristic stretching vibrations: the first one is
a pure H4-N4 vibration (5 = 3292.9 cm-1) of O6H4-N4 intermolecular donor-acceptor
complex, while the second and third ones are a combined N1-H1 and N2-H2 symmetric (9 =
3085.8 cm-1) and asymmetric (10 = 3027.8 cm-1) stretching vibrations of N1-H1N3 and N2-
H2O2 intermolecular donor-acceptor complexes. In case of Hoogsteen configuration there
are only two characteristic vibrations which belong to the intermolecular interaction region:
180 Attila Bende
the first is an N-H stretching vibration (10 = 3014.4 cm-1) of N-HO donor-acceptor
complex, while the second one is also an N-H stretching vibration (11 = 2053.2 cm-1) but as a
component of the NH+-N unusual intermolecular donor-acceptor complex. If one considers
the anharmonic corrections, the similar behavior can be observed as it was found in case of
formamide and urea systems. There are large anharmonic shifts for all three 5, 9 and 10
stretching vibrations of Watson-Crick configuration: a5 = 263.1 cm-1, a9 = 294.8 cm-1 and a10
= 362.4 cm-1. In case of Hoogsteen conformation the anharmonic shifts are: a10 = 187.6 cm-1
and a11 = 958.0 cm-1. The a11 anharmonic shift is very large compared with the harmonic
frequency values. This can be explained with the unusual nature of NH+-N intermolecular
donor-acceptor complex.
Two different type intermolecular normal mode vibrations can be found both in case of
Watson-Crick and Hoogsteen configurations. In one of them the vibration motion occurs in
the plane defined by the monomer molecules (here we have a number of three normal modes),
while in the second case the intermolecular vibrational motions are out-of-plane vibrations.
Since the characterization of the out-of-plane vibrations is quite difficult, this will not
constitute the subject of our further investigation. Accordingly, the three intermolecular
normal mode (in-plane) frequencies are: I = 101.2 cm-1, II = 125.5 cm-1 and III = 131.0 cm-1
for Watson-Crick conformation and I = 88.9 cm-1, II = 109.4 cm-1 and III = 170.6 cm-1, for
Hoogsteen conformation, respectively.
Similar to the previous urea case presented in section 3.2, there are also significant inter-
and intramolecular normal mode couplings. In case of Watson-Crick system the
intramolecular 9 and 10 stretching vibrations are relatively strong coupled (about 5-6 cm-1)
with all three I, II and III intermolecular normal modes. For Hoogsteen configuration these
couplings are stronger: 17.0-21.0 cm-1.
3.4. Adenine-Thymine DNA Base Pair
The adenine-thymine binary system (Watson-Crick configuration) has a number of 30

atoms and presents a number of 84 normal mode vibrations from which 6 have intermolecular
character. For its geometry structure see Figure 9.
Since we are interested in the stretching vibrations (4 and 11) of those intramolecular
covalent bonds where H atoms are involved, as well as in those intermolecular vibrations of
which motion is situated mostly in the molecular plane (78, 80 and 82), we present only
these specific normal mode vibrations. At the same time, one can identify another group of
seven normal modes (41, 42, 54, 60, 61, 64, and 69) specific for purine and pyrimidine ring
vibrational deformation which can significantly disturb the H-bond vibrations. All these
normal mode frequency values in harmonic, BSSE corrected harmonic, and anharmonic
approximations are presented in Table 7. Considering the BSSE correction, the most affected
normal modes are the 4 and 11 N-H stretching vibrations. In these two cases we found 76.6
cm-1 and 429.5 cm-1 frequency increasing, respectively. Similar findings can be obtained in
case of I and II intermolecular normal modes, where in spite of the fact that BSSE effects
not show large frequency shifts, they could represent significant corrections compared with
the uncorrected frequency values. Regard to anharmonic corrections, one can observe that
large frequency shifts are obtained in the case of N-H covalent-bond stretching vibrations (-
281.1 cm-1 for 4 and -160.4 cm-1 for 11). Considering the ring deformation normal mode
vibrations (41, 42, 54, 60, 61, 64, and 69), the anharmonic correction is more important
than BSSE effects, but even so, their frequency shifts are less than 20 cm-1. As it was
concluded in the previous case of urea dimers, the anharmonic and BSSE corrections could be
considered in a very good approximation as additive effects. According to this fact, we
present in the fifth column of Table 7 the integral correction (int) of the anharmonic and
BSSE effects. The results show that in some frequency cases we have an opposite
contribution of frequency shifts, while in some other cases the anharmonic and BSSE
collective corrections increase the magnitude of the frequency shift. Analyzing the
anharmonic coupling matrix one observes strong vibrational coupling between 11 intra- and
78 intermolecular normal modes (x11,I = 8.2 cm-1) as well as between 11 intra- and II
intermolecular normal modes (x11,II = 10.4 cm-1). The case of this strong coupling could be
explained by the same fact that in the case of cyclic urea dimer namely, by the presence of the
same molecular plane for both normal modes and the same vibrational direction for 11 and I
modes. In other cases there is no significant coupling between the intra- and intermolecular
normal modes.
Table 7. The harmonic () and anharmonic (a) frequencies (in cm-1) of some selected
intramolecular and intermolecular normal modes in adenine-thymine DNA base pair,
obtained at B3LYP level of theory and using D95V basis set (The int is the predicted
frequency value, considering, together, the BSSE and anharmonic corrections)
NCP dim dim

Nr. dim
CP a NCP int
4 3329.3 3405.9 3048.2 3124.8

11 2546.7 2976.2 2386.3 2815.8
41 1035.2 1035.7 1018.5 1019.0
42 1031.4 1024.2 1014.2 1007.0
54 742.4 745.9 726.9 730.4
60 637.7 630.3 632.8 625.4
61 607.4 611.1 601.2 604.9
64 550.2 550.4 542.0 542.2
69 397.2 404.1 388.8 395.7
I 119.9 108.2 115.4 103.7
II 114.6 101.6 110.3 97.3
III 66.8 60.3 58.3 51.8
Krishnan et al [104] show that to compare the experimentally observed IR spectra of

adenine-thymine base pair with the calculated frequencies is not a simple task. First of all
because the Watson-Crick configuration of A-T base pair is not the most stable isomer
conformation [105]. Making a detailed theoretical anharmonic frequency analysis they were
able to assign the IR-UV double resonance spectra [106] also to a particular isomer which is
not the Watson-Crick structure. A direct experimental assignment of N-H stretching
vibrations in A-T oligomers in condense phase is very difficult because the N-H stretching
182 Attila Bende
vibration spectral region overlap with the waters O-H stretching spectral region. Reducing
the water content of the A-T oligomers does not solve the problem because they do not adopt
a well define structure at extremely low water concentration. In order to identify and to
characterize the N-H stretching vibrations of A-T base pair oligomers in DNA Heyne et al
[107] use the two-color IR pump-probe technique to overcome the above mentioned
experimental problem. They found that the adenine (NH2) absorbs at 3215 cm-1 and has
pronounced anharmonic couplings to the (C=O) mode of the thymine and (NH2) mode of
the adenine.
Figure 9. The adenine-thymine DNA base pair.
4. Conclusion
In this Chapter a detailed investigation, including geometry structure, harmonic and
anharmonic frequency calculations, on cyclic conformation of formamide and urea dimers, as
well as on the guanine-cytosine and adenine-thymine DNA base pairs were presented.
Considering the results some general conclusions can be drawn. First of all, in order to
describe accurately the geometry structures of the molecules one needs to consider proper ab
initio methods, which are able to describe correctly the different intermolecular interaction
effects (electrostatic, polarization, induction, dispersion and three- or four-body terms).
Including all this effects in our calculation, high level electron correlation methods like
perturbation or coupled-cluster methods as well as basis sets which contain successively
larger shells of polarization (correlating) functions (d, f, g, etc.) are required. For these
calculations one need a huge amount of computer capacity and therefore we can only limit to
a small size molecular systems (up to 15-20 atoms). Recently introduced local and density-
fitting approximations are very promising tools, they can reduce very much the calculation
efforts and in this way the molecular size limit could be extended. These methods are also
free from the mathematical artifact called basis set superposition error or BSSE.
In order to obtain accurate description for the infrared absorption spectra, the harmonic
approximation is not good enough and therefore the anharmonic approximation is also should
be included. Including these effects, some normal mode vibrations, like X-H (X=C or N),
C=O and N-H+ stretching vibrations, need more detailed investigation. For the N-H and C=O
covalent-bond stretching vibrations the anharmonic frequency correction is significant. In
case of Hoogsteen conformation of guanine-cytosine base pair the anharmonic approximation
is comparable with the harmonic frequency value. For the same N-H and C=O covalent-bond
stretching vibrations the BSSE corrections are also significant, but only in the case when the
normal mode vibrations are in the intermolecular region. Normal mode vibrations which are
located in the intermolecular region, the influence of the adjoining molecule (dimer effect) on
the vibrational frequency is comparable with the magnitude of the BSSE and anharmonic
corrections. Analyzing the magnitude of the anharmonic and BSSE corrections, it was found
that their contributions in the harmonic frequency shift could be considered in a very good
approximation as an additive effect. The anharmonic coupling between intra- and
intermolecular normal modes is significant only when the motion of normal mode vibrations
occur in the same molecular plane (the plane defined by those atoms which move during the
vibration) and along of the same vibrational direction. Using the classical DFT functionals
and applying double-zeta quality basis sets, like 6-31G or D95V, one could obtain a good
qualitative description of the anharmonic corrections, but further investigations considering
the recently developed DFT or perturbation methods and triple-zeta quality basis sets are
needed in order to obtain also a good quantitative description for them.
The strong coupling between different intra- and intermolecular normal modes can be
considered as an important and biologically relevant effect. In this way the vibrational
relaxation processes can take place very easily and some strongly excited localized vibrations
can wither away as thermal vibrations.
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Chapter 9
E MERGENT P ROPERTIES IN B OHMIAN C HEMISTRY

Jan C.A. Boeyens
Unit for Advanced Study, University of Pretoria, South Africa
Abstract
Bohmian mechanics developed from the hydrodynamic interpretation of quantum

events. By this interpretation all dynamic variables retain their classical meaning in
quantum systems. It is of special significance in chemistry as a discipline which is
traditionally based on the point electrons of quantum field theory. It could be more
informative to assume a non-dispersive electronic spinor, or wave packet, with diver-
gent and convergent spherical wave components, and with many properties resembling
those of a point particle.
Complex chemical matter is endowed with three attributes: cohesion, conforma-
tion and affinity, which can be reduced to the three fundamental electronic properties
of charge, angular momentum and quantum potential, known from the wave struc-
ture. The chemical effects of these respective scalar, vector and temporal principles,
all manifest as extremum phenomena. The optimal distribution of electronic charge in
space appears as Paulis exclusion principle. Minimization of orbital angular momen-
tum becomes the generator of molecular conformation. Equilization of electronegativ-
ity, the quantum potential of the valence state, dictates chemical affinity. The chemical
environment is said to generate three emergent properties: the exclusion principle,
molecular structure and the second law of thermodynamics. These concepts cannot be
predicted from first fundamental principles.
Only by recognition of the emergent properties of chemistry is it possible to simu-
late chemical behaviour. The exclusion principle controls all forms of chemical cohe-
sion, atomic structure and periodicity; molecular structure underpins vector properties
such as conformational rigidity, optical activity, photochemistry and other stereochem-
ical phenomena; while transport properties and chemical reactivity depend on the sec-
ond law.
Simulation of these chemical concepts by constructionist procedures, starting from
basic physics, is impossible. The ultimate reason is that complex chemical properties
are not represented by quantum-mechanical operators in the same sense as energy and
momentum. The Bohmian interpretation, which enables the introduction of simplify-
ing emergent parameters, in analogy with classical procedures, allows the calculation
of molecular properties by generalized Heitler-London methods, point-charge simula-
tion and molecular mechanics.
192 Jan C.A. Boeyens
1. Introduction
The editorial challenge to address the quantum frontiers of atoms and molecules in
chemistry cuts far deeper than a survey of current activity in quantum chemistry, which for
all practical purposes means ab-initio computational chemistry.
There is no quantum theory of chemistry: Quantum mechanics originated as a theory
to understand radiation and its interaction with sub-atomic matter. It gave birth to the mod-
ern science of spectroscopy, in which form it stimulated the development of sophisticated
observational techniques that revolutionized physics, chemistry and biology. However, the
early promise of a quantum theory of matter in general has not come to fruition. A theory
that fails to elucidate the nature of electrons, atoms and molecules can never lead to an un-
derstanding of chemistry. It may enable computations of unrivalled complexity, but without
a conceptual framework the results have no meaning.
As a theory of spectroscopy, quantum mechanics serves to relate measured quantities,
such as frequency and wavelength to the dynamic concepts of energy and angular momen-
tum, by means of differential operators e.g.:
i~/t E, i~/ L.
Although chemically more useful information on molecular structure and electronegativity

is also embedded in the state functions, there are no known operators whereby to extract
this information directly. The current computational alternative fails for the same reason.
Minimization of the scalar quantity, energy, can never generate three-dimensional structure,
which is a vector concept.
The failure to rationalize chemical behaviour is not a failure of quantum theory, but
rather, a failure of the traditional interpretation of the theory. The ruling interpretation of
quantum theory, known as the Copenhagen interpretation, incorporates a number of fea-
tures totally at variance with chemistry. It defines quantum objects, including photons,
electrons, atoms and molecules, as structureless point particles without extension. It re-
duces a continuously varying density, such as the electronic charge distribution in atoms,
molecules and crystals to a probabilistic function. It offers no rationale for the occurrence
of stationary states, apart from a postulate. Non-local effects are forbidden and the doctrine
teaches more about measurement problems and quantum uncertainty than about chemical
interaction.
The unfortunate reality is that Schrodingers description of elementary matter as wave
structures, which could not be reconciled with the Copenhagen orthodoxy, was ruled un-
acceptable and re-interpreted in terms of the quantum jumps and probability density of the
particle model. This compromise resulted in the awkward concept of wave-particle duality,
familiar to all modern chemists, but understood by none.
The challenge that we are facing here is to retrace our steps to the point where the
time-honoured concepts of classical chemistry merge in a natural way with the ideas of
wave mechanics and start rebuilding a theory that stimulate(s) the mutual understanding
of the various branches of chemistry and its neighbouring sciences , realizing that the main
stumbling block for the development of a theory of large and complex molecular systems
is not computational but conceptual [1].
Emergent Properties in Bohmian Chemistry 193
I propose to start with an outline of the essential concepts of cohesion, conformation

and affinity; show how these relate to the more fundamental concepts of space, matter and
number; and the derived concepts of interaction, waves and periodicity. Next we examine
the Schrodinger formalism, the Bohmian interpretation and the application of wave me-
chanics, supported by higher-level emergent properties. The photoelectric effect, probably
the most effective argument to have established the particle nature of photons is shown to
be explained more convincingly by the transactional-wave model of electromagnetic inter-
action.
2. The Fundamental Concepts

Any object or event observed in Nature can always be considered as the product of
more primitive events or the interaction between more primitive entities. It is quite natural,
in this reductionist spirit, to ascribe the actions and features of a living organism to some
lower-level activity of biological cells, which in turn is driven by intracellular chemical
interactions. The molecular building blocks of biological cells are assumed to consist of
atoms, held together by electromagnetic forces, while the sub-atomic nucleons interact with
strong interaction, and so on, ad infinitum. Not really. The reduction has to stop somewhere.
As progressively smaller entities are implicated at the more primitive levels, it is reasonable
to conclude that the cascade ends in a void, traditionally assumed to be the same as space,
or the vacuum.
At this point it is easy to get distracted by the interminable philosophical dispute about
the possible existence or non-existence of a void. As a practical alternative I prefer to define
space in geometrical terms and the vacuum as a physical entity.
2.1. Space
The simplest way of looking at space is as a coordinate system that serves to describe
the relative positions of observable objects. The intuitively most obvious is a cartesian sys-
tem on three orthogonal axes. However, this may not necessarily be the most convenient
coordinate system. Although it works well in a laboratory environment, it is well known to
be inappropriate in geographical context, which is simplified by using spherical trigonom-
etry. By the same argument cartesian coordinates may not be the most convenient to map
the relative positions of astronomical objects. To first approximation the planets and most
of their moons have been assumed to move in a single plane, called the ecliptic, around the
sun. Individual elliptic orbits of planets and moons have a simple description in terms of
Keplers laws in a plane, but most of these planes are known to make non-zero angles with
the ecliptic.
Moving into interstellar, or even intergalactic, space the situation becomes more com-
plicated when dealing with cosmological distances, times and velocities, which demands
relativistic rather than Galilean kinematics. Special relativity is conveniently formulated in
four-dimensional Minkowski space and general relativity requires non-Euclidean geometry,
i.e. curved space.
In general relativity the geometry of space is described by a curvature tensor, which
is linearly related to a stress tensor that describes the distribution of matter in the cosmos.
This reciprocal relationship shows that an empty universe has zero curvature and that curved
space generates matter. The mechanism whereby curvature generates matter is visualized in
the process of covering a curved surface with an inflexible sheet. The higher the curvature,
the poorer the fit and the more the wrinkles in the cover that cannot be smoothed away. Such
wrinkles in space are interpreted as matter and energy the content of the stress tensor.
2.1.1. Number
Figure 1. Spiral structure of a fossilized nautilus shell.
Not only the topology of space-time, but also the physical content of the universe, re-
sembles the natural number system in remarkable detail [2]. This explains the unreasonable
effectiveness of mathematics as a scientific tool and the success of number theory to predict
natural phenomena as a manifestation of cosmic symmetry [2, 3]. The physical world, as
an image of the natural numbers, can never be known in more detail than the number sys-
tem. Concepts such as infinity and singularity, poorly understood mathematically, therefore
make no physical sense. On the other hand, the concept of high-dimensional space, readily
manipulated mathematically, and, although physically difficult to visualize, has a legitimate
place in scientific discourse.
To deal with the ubiquitous, but bothersome, infinities of physics, the infinity concept of
projective geometry can be used to define both the number system and the physical cosmos
as closed. Realizing that any closed system is periodic, by definition, a wave structure of
the vacuum and periodicity of matter are inferred.
The implied cosmic symmetry is referred to as self-similarity. The chambered structure
of a nautilus shell, shown in Figure 1, is one of the best-known examples of this symme-
try type. All the chambers have the same shape and only differ in size, which increases
regularly along a golden logarithmic spiral. The same pattern occurs in the arrangement of
growing seed buds in a sunflower head and in the image of a spiral galaxy. Recognition of
the same growth features [2, 4] in atomic nuclei, atoms, covalent molecules and the solar
system, reveals self-similarity on a much wider scale. The number theory of self-similarity
shows that all of these structures are based on the Fibonacci number sequence, which con-
verges to the golden ratio.
2.2. Vacuum
The fabric of space is a matter of conjecture. However, if tangible matter occurs on
curving flat space, flat space is not void. A useful analogy is to picture the vacuum as a
regular undulating expanse filled by waves of constant wavelength. When curved, interfer-
ence of the primary waves produces persistent wave packets, earlier identified as wrinkles.
In local space such a wave packet is conveniently described as the superposition of three-
dimensional spherical waves, converging to and diverging from a centre of mass. These
waves are the retarded and advanced solutions of the general wave equation, which implies
motion, either forward or backward in time.
2.2.1. Wave Packets

A typical wave packet generated by such a superposition of waves is shown in Figure
2. The tangent curve follows the amplitude of the 1/r Coulomb potential, which reflects
the actual charge density, except when r 0. The secondary waves propagate with the
group velocity vg of the system and the primary waves have phase velocity v , such that

vg v = c2 , where c = 1/ 0 0 , is the velocity of light in the vacuum. Such a wave
packet [4]:
it cos kr sin kr
= Ae or (1)
kr kr
has been shown [5] to describe elementary waves, equivalent to the postulated elementary
distortions of space, i.e. the elementary particles of atomic physics. Interpreted as an
electron, the distance between nodal points represents dB = h/me vg , the de Broglie
wavelength of a free electron and C = 2/k = h/me c, the Compton wavelength. The
amplitude of the standing wave is proportional to the electronic charge.
0 = A, in eqn.(1), represents a wave packet with charge proportional to 0 or A.
Electrons and protons, despite their difference in mass have charges of e. The neutron
is neutral. The field intensity = A2 (sin kr/kr)2 = C/r2 defines the force between
charges, in line with Coulombs law, except when r 0. The breakdown of Coulombs
law, which occurs naturally for charged wave structures is equivalent to the special renor-
malization postulate in quantum field theory.
2.2.2. Electron and Atom

A particle image, as shown in Figure 3, is obtained by rotating the diagram of Figure
2 about two axes perpendicular to x. The charge density can either contract or expand,
Figure 2. One-dimensional section through a spherical wave packet with components con-
verging on and diverging from x0 .
depending on environmental pressure. The minimum radius that can be reached on com-
pression depends on the rest mass of the object. For an electron r0 = e2 /m0 c2 .
Figure 3. Wave structure of a free electron with de Broglie wavelength dB = h/me vg .
Given the inferred flexible structure of an electron as a continuous indivisible charge,

the self-similarity of atoms and the solar system is not obvious. The pioneering work on
the planetary model of atomic structure was firmly based on Keplers model of elliptic
orbits. Two crucial parameters that define a Kepler ellipse are the semimajor axis and
the eccentricity, which characterize the size and shape of an orbit. By Newtons laws these
respective parameters are related to the energy and angular momentum of the orbital motion.
In retrospect Keplers laws are seen to embody the general conservation principles for
energy and angular momentum in celestial mechanics. The efforts of Bohr and Sommer-
feld to explain electronic motion in atoms by the same model were spectacularly successful,
despite a few subtle, but fatal, defects. Whereas Keplers model is valid in a gravitational
field, it needs modification in an electromagnetic field as an accelerated charge radiates en-
ergy and an accelerated point charge therefore cannot maintain a stable orbit. Conservation
of angular momentum in a central electrostatic field should rather be interpreted as conser-

vation of the spherical shape of a continuous charge. Polar deformation under an external
influence is described by the three-dimensional surface harmonics, or eigenfunctions, of the
circulation Laplacian, with discrete eigenvalues:
L2 Ylml = l(l + 1)k 2 Ylml ,

Lz Ylml = ml kYlml .
This classical result acquires quantum-mechanical meaning by equating the arbitrary con-
stant k with ~, the elementary unit of angular momentum [6].
Figure 4. Phase-locked cavity with perfectly reflecting walls, filled with radiation in the
form of standing waves.
The difference between atomic and planetary systems goes a long way towards un-
derstanding of cosmic self-similarity. Although electrons in an atom are spread in three
dimensions and planets orbit the sun in an approximately two-dimensional plane, both ar-
rangements depend parametrically on the golden ratio. In the same way sunflower seeds
of varying size are closely packed in a plane, compared to the three-dimensional stacking
of nucleons; both styles conditioned by the golden ratio. The only common factor in all
cases is the general curvature of space. Evidently, the curvature of cosmic space must be a
function of the golden ratio, from the sub-atomic to supergalactic scales.
2.2.3. Mass
Not only the charge, but also the characteristic mass and spin of sub-atomic species are
accounted for by their wave structure. Jennison and Drinkwater [7] demonstrated that mi-
crowave radiation trapped in a phase-locked cavity, as in Figure 4, generates an interaction
pattern which is mathematically equivalent to a system with inertial mass.
Disturbing the equilibrium by a pulse that moves a cavity wall at velocity v for a pe-
riod t, which is matched to the wave propagation across the cavity, modifies the internal
pressure by Doppler shifting of the waves and sets the entire system into motion with veloc-
ity 2v. The radiation pressure on the walls is balanced by an electromagnetic field, which
keeps the system in static equilibrium. In the real vacuum the analogue of the phase-locked
cavity is a standing wave, filled with radiation of Compton wavelength, internal energy E,
in equilibrium with the external radiation (wave) field. Simple calculation [7] shows that
the inertial mass of the wave packet obeys Newtons law, F = ma, on identifying E/c2
with the rest mass.
2.2.4. Spin
The standing-wave description of an electron defines it as an integral part of the vac-

uum, not obviously free to move without impediment. Linear motion of an electron must
then clearly lead to continuous drag and deformation of both electron and its immediate
environment, culminating in rupture of the vacuum and creation of a turbulent state. An
electron that rotates in the vacuum, although more symmetrical, winds up the connecting
medium until it shears and develops a discontinuity along a cylindrical surface. The only
motion that occurs without distortion of the spherical wave packet or mechanical entangle-
ment of the environment is rotation around a point. Unlike axial rotation this mode is more
like a continuous wobble that returns to the original situation after two complete revolu-
tions. The three dimensions of space participate equally in the motion without the transfer
of rotational energy from the spinning object to the connecting medium. The strain that
builds up during the first part of the rotational cycle relaxes during the second part. Apart
from half-frequency cyclic disturbance in the connecting medium, the electron is free to
move through the vacuum without permanent entanglement.
An object, which performs this type of spherical rotation, is described mathematically
by a spinor, or a quantity that reverses sign on rotation through an odd multiple of 2
radians.
3. Quantum Theory
Quantum theory started with the discovery of line spectra and Balmers observation that
the spectral lines of atomic hydrogen obey a digital formula, later generalized to:

1 1
= Rc 2 2 , n2 > n1 = 1, 2, 3 . . . (2)
n1 n2
The first sensible explanation of the formula was proposed in 1904 by Nagaoka who used
the planet Saturn with its system of rings as the basis of an atomic model, with electrons at
energy levels (rings) in simple numerical order, orbiting a heavy positively charged nucleus.
Experimental confirmation of such an arrangement was found by Rutherford in 1910 and
a dynamic model, based on Plancks quantum condition, E = h, was proposed in 1914
by Bohr. Where Nagaoka argued that electrodynamically stable orbits required a standing
electron wave of length = 2r/n at an average distance r from the nucleus, Bohr postu-
lated quantum stability for an orbiting electron with angular momentum p = nh/2 n~.
With electrostatic and mechanical forces in balance, (using electrostatic units, 40 = 1):
e2 p2 e2 e2 e2
= , E =T +V = = ,
r2 mr 2r r 2r
the postulate leads to the Balmer formula
2 2 me4

1 1
h = E = , (3)
h2 n21 n22
2 2 me4 n2 h2
En = , rn = 2 2 . (4)
n2 h2 4 me
The rest is history. When de Broglie rediscovered the Nagaoka condition in 1924 by pos-
tulating that all matter has an associated wavelength of = h/mv, only the mathematical
framework for defining a general wave formalism of electronic behaviour, was lacking.
3.1. Wave Mechanics

The mechanical behaviour of a Newtonian particle is described correctly by three quan-
tities energy, momentum and angular momentum, which describe the motion as a func-
tion of either time, displacement or rotation. In wave formalism each of these parameters is
specified as a periodic function [8] with respect to time ( ), translation () or rotation ():
= 2/, k = 2/, ml = 2/,

E = ~, p = ~k, Lz = ~ml .
The carrier of the electromagnetic field is described by the differential wave equation:
2 1 2
2 = 2
= 2 2. (5)
t c t
To remain consistent with the previous relationships the dynamic variables need to be spec-
ified as differential operators:
E ~i/t, p ~i, Lz ~i/,
which can be checked by direct substitution. To allow for the first-order temporal depen-
dence of the energy, the equation for matter waves is restricted to processes which only
depend on time through a factor exp(2it), leading to the final form:
2
~ 2
+ V = ~i (6)
2m t
which formally resembles the classical Hamiltonian definition of total energy, as
p2
H =T +V = + V = E. (7)
2m
By defining a density function = and a current density
~
j= ( ) (8)
2mi
there follows a continuity equation as in classical hydrodynamics

+ divj = 0. (9)
t
A general expression for a one-electron wave function over all available states
X
= ck k e2it (10)
k
may be used to calculate the current density over two states k and l:
~e X
j= ck cl (l k k l ) e2i(k l )t . (11)
mi
k,l
If only a single eigenvibration is excited, the current disappears and the distribution of
electron density remains constant. Otherwise an electron flows from one state to another in
an exchange that involves a photon to keep the energy in balance.
This flow of electricity can hardly be described as a quantum jump. More realistically
the vibrations of the two affected states (emitter and acceptor) are seen to interact and
generate a beat (wave packet) that moves to the state of lower energy. The virtual photon
that links two equilibrium states turn into a real photon that carries the excess energy, either
into or away from the system.
In chemical applications Schrodingers equation is best known in its amplitude form,
which is obtained by substituting = exp(2it), followed by elimination of the time
parameter to give:
2m
2 + 2 (E V ) = 0. (12)
~
In spherical polar coordinates this equation, for the hydrogen problem, separates into inde-
pendent radial and angular equations:
d2 R 2 dR
l(l + 1)
2m
+ + E V (r) R = 0, (13)
dr2 r dr ~2 r2

1 Y 1 Y
sin + + l(l + 1)Y = 0, (14)
sin sin2 2
with separation constant = l(l + 1), integer l. The angular part is further separable into:
d2
+ m2l = 0 (ml = l . . . l), (15)
d2
m2l

1 d d
sin + l(l + 1) = 0. (16)
sin d d sin2
An electron associated with a stationary proton (V = e2 /r) defines the only problem of
some chemical significance for which the radial equation has been solved. Since the proton
is here regarded as a point particle, the system does not represent a wave-mechanical model
of a hydrogen atom, despite contrary claims in all chemistry texts. Like the Bohr model, it
defines a set of quantized energy levels to match most spectroscopic measurements, apart
from the Lamb shift, fairly well.
The angular equations are valid for central-field problems and produce quantized values
of the orbital angular momentum. These eigenvalues should not be confused with the angu-
lar momenta of an orbiting particle. They are, more appropriately, considered as symmetry
parameters, such that ml = 0 defines a spherically symmetrical charge distribution. For

given l there is always an odd number of 2l + 1 sub-levels with different quantum
P numbers
ml , which, for many-electron systems, can be chosen in such a way that l ml = 0, in
all cases. The choice reflects the electrostatic property of the charge distribution to assume
spherical symmetry. A hydrogen atom, by this model, has ml 6= 0 only for excited states,
which spontaneously relax to the ml = 0 spherically symmetrical ground state.
3.1.1. Electron Spin
Schrodingers equation appears incomplete in the sense of lacking an operator for spin,
only because its eigenfunction solutions are traditionally considered complex variables. The
wave function, interpreted as a column vector, operated on by square matrices, such that
ei(tkx) 1 ei(tkx)

0 1
= .
0 ei(tkx) 2 2 ei(tkx)
1 e+

abbreviated to , represents a spinor that moves in the x-direction. By forming the
2 e
derivatives:
1 e+

= i ,
t 2 e
2 1 e+

= k2 ,
x2 2 e
it follows that (in three dimensions):

i = 2 2 .
t k
This is Schrodingers equation, providing (~k)2 = 2m~, i.e.
~ 2
i = , as in (6):V = 0
t 2m
which shows ~ = E = p2 /2m, k = 2/, p = h/. This result is interpreted [4]

to show that a region of the continuum, which rotates in spherical mode, interacts with
its environment by generating a wave-like disturbance at half the angular frequency of the
core. The angular momentum on the surface of a unit sphere is L = m. At = 2,
k = 1, the spin angular momentum follows as L = ~/2, with intrinsic magnetic moment
= ~e/2mc.
3.2. Bohmian Mechanics

The connection between wave mechanics and hydrodynamics, expressed by equations
(7) and (8), was developed in more detail by Madelung, writing the time dependence of
as an action function, = e2it ReiS/~, which seperates (5) into a coupled pair that
resembles the field equations of hydrodynamics:
S (S)2 ~2 2 R
+ + V = 0, (17)
t 2m 2mR
R2 R2 S

+ = 0, (18)
t m
which describe the irrotational flow of a compressible fluid, assuming R2 to represent the
density (x) of a continuous fluid with stream velocity v = S/m. It was shown that both
density and flux vary periodically with the same periodicity as ik = (Ei Ek )/h, that
results from superposition of states i and k. This means that radiation is not due to quantum
jumps, but rather happens by slow transition in a non-stationary state.
An attractive feature of the hydrodynamic model is that it obviates the statistical inter-
pretation of quantum theory, by eliminating the need of a point particle. It is worth noting
that the assumption of a point electron derives from the observation that it responds as a
unit to an electromagnetic signal, which must therefore propagate instantaneously through
the interior of the electron, at variance with the theory of relativity. However, by now it
is known from experiment that non-local (instantaneous) response is possible in quantum
systems and the initial reservation against Madelungs proposal and Lorentzs definition of
an electron as a flexible sphere should fall away.
On reinterpretation it was pointed out by David Bohm that equation (17) differed from
the classical Hamilton-Jacobi equation only in the term
~ 2 2 R
Vq = . (19)
2mR
The quantity Vq , called quantum potential vanishes for classical systems as h/m 0. A
gradual transition from classical to quantum behaviour is inferred to occur for systems of
low mass, such as sub-atomic species. All dynamic properties of classical systems should
therefore be defined equally well for quantum systems, although the relevant parameters
are hidden [10].
3.2.1. Quantum Potential

As for the classical potential, the gradient of quantum potential energy defines a quan-
..
tum force. A quantum object therefore has an equation of motion, m x= V Vq .
For an object in uniform motion (constant potential) the quantum force must vanish, which
requires Vq = 0 or a constant, k say. Vq = 0 defines a classical particle; alternatively1
(V + Vq ) = T , the kinetic energy of the system. Hence ~2 2 R/2mR = E, which
rearranges into
2mE
2 R + 2 R = 0
~
Schrodingers equation for a free particle.
1
It is a common misconception that Vq = T for a free electron compare [11]. Stationary states do not
occur for Vq = 0, but when Vq = V .
The quantum potential concept is vitally important for understanding the structure of
an electron and of quantum systems in general. The fact that the amplitude function (R)
appears in both the numerator and denominator of Vq implies that the effect of the wave
field does not necessarily decay with distance and that remote features of the environment
can affect the behaviour of a quantum object.
The quantum potential for a many-body system:
n
~2 2i R
X
Vq =
2mR mi
i=1
depends on the quantum state of the entire system. The potential energy between a pair
of entities, Vq (xi , xj ) is not uniquely defined by the coordinates, but depends on the wave
function of the entire system, . This condition defines a holistic system in that the whole
is more than a sum of the parts. The instantaneous motion of one part depends on the coor-
dinates of all other parts at the same time. That defines a non-local interaction of the type
assumed to exist within an indivisible electron, and now inferred to occur in all quantum
systems, including molecules. If the system is distorted locally, the entire system responds
instantaneously. As the quantum potential is not a function of distance, the behaviour of
a composite system depends non-locally on the configuration of all constituents, no mat-
ter how far apart. In a chemical context the properties, structure and rearrangement of
molecules must depend intimately on the quantum potential. It is necessary to give up the
notion that molecular rearrangement involves the breaking and making of bonds and rather
consider it as a modification of the intramolecular electronic wave interference pattern.
However, all systems are not correlated equally well. Whenever a wave function can be
written as a product
(r1 , r2 , t) = A (r1 , t)B (r2 , t)
the quantum potential becomes the sum of two terms:
Vq (r1 , r2 , t) = VqA (r1 , t) + VqB (r2 , t).
The two sub-systems evidently behave largely independently. That is a good description
of a molecular crystal, or liquid, with relatively weak interaction between molecular units.
Systems like these are better described as partially holistic.
The contentious issue of quantum-particle trajectories is put into perspective by the
Bohmian model. One interpretation is that the quantum electron has an unspecified diffuse
structure, which contracts into a classical point-like object when confined under external
influences. The observed trajectory, as in a cloud chamber, may be considered to follow the
centre of gravity.
In a two-slit experiment an electron wave passes through both slits to recombine, with
interference, but without rupture. The interference pattern disappears on closure of one slit
or when the slits are too far apart, compared to the de Broglie wavelength. It now behaves
exactly like a classical particle, when forced through a single slit2 [12].
2
The de-Broglie Bohm formulation of particle plus pilot wave is considered an unnecessary complication
by this author. Instead, may be thought of as a state of vibration of empty space.
3.2.2. Stationary States

Writing the wave equation in two equivalent forms:
(x, t) = 0 eiEt/~,
(x, t) = R(x, t)eiS(x,t)/~,
and noting that R(x, 0) = R0 (x); S(x, 0) = S0 (x); 0 = R0 eiS0 /~, it follows that:
S(x, t) = S0 (x) Et, (20)

R(x, t) = R0 .
The unexpected conclusion is that a real wave function, 0 = , implies S0 (x) = 0 and
hence the momentum S = p = 0 and E = V + Vq . Those states with ml = 0 all have
real wave functions, which therefore means that such electrons have zero kinetic energy and
are therefore at rest. The classical (electrostatic) and quantum forces on electrons in such
stationary states are therefore balanced and so stabilize the position of the electron with
respect to the nucleus.
For the hydrogen atom in the ground state, R(r) = N er/a0 and hence,
d2 R N
2
= 2 er/a0 ,
dr a0
such that, from (19), Vq = ~2 /2ma20 . In general
~2
Vq = , (21)
2mr2
and the quantum force on the electron:
Vq ~2
Fq = = 3
r mr
whereas the electrostatic force F = e2 /r2 . These forces are in balance when
~2 e2 ~2
= ; r= = a0 ,
mr3 r me2
the Bohr radius. This means that V = Vq at r = a0 /2, halfway between proton and
electron.
3.2.3. Orbital Angular Momentum

Orbital angular momentum is perhaps the most awkward concept to visualize as the
property of a quantum-mechanical point electron, but is readily understood in hydrody-
namic analogy. Like tidal motion, atomic orbital motion in a continuous spherical charge
cloud consists of the propagation of a wave disturbance, without matter circulation, as
first proposed by Nagaoka and described by the quantized spherical surface harmonics,
Ylml = N Plml eiml , in terms of Legendre polynomials, P .
In Bohmian formalism angular momentum is described by rotation of the phase func-

tion:
S(x, t) = S0 (x) Et
= ml ~ Et.
The wavefronts S=constant are planes parallel to and rotating about the z-axis, with angular
velocity /t = E/ml ~.
Single-valuedness of = R exp(iS/~) requires that (S) = (S + 2n~) = (S +
nh). This is interpreted to mean that n = |ml | wave crests occur during each cycle. Positive
and negative values of ml represent anticlockwise and clockwise rotations respectively.
This interpretation of orbital angular momentum has a formal resemblance to the semi-
classical model of Bohr and Sommerfeld, but there is no physical rotation of charge. Two
electrons with magnetic quantum numbers of ml have wave structures that rotate, in
phase, in opposite directions, with resultant distortion of zero. Quenching of orbital an-
gular momentum during chemical interaction between neighbouring atoms happens by the
same principle. The wave pattern in the case where l 6= 0 and ml = 0 is to be interpreted
as the three-dimensional analogue of the circular modes of a vibrating drumhead. There is
no axial component to the disturbance. The wave motion is more like spherical vibration,
compared to spherical rotation that causes electron spin and which can be oriented in the
polar direction of a magnetic field.
4. Chemical Change
In the same sense that biological activity is more than chemical change, chemical effects
depend on a number of emergent properties unknown to physics. The concepts of chemical
affinity, cohesion and structure were discovered experimentally and not anticipated from
first principles. Although chemical events can therefore not be inferred from the laws of
physics, the Bohmian interpretation of quantum mechanics provides an attractive frame-
work for their understanding. The fundamental reason for this emergence is the chemical
environment. The interaction between chemical species, partially characterized in isolation,
is as hard to predict as the behaviour of an individual in a crowd. Not being acquainted with
the concepts molecule, phase transition and free energy, there is no possibility of deriving
the laws of chemical affinity, reactivity and composition from the quantum numbers that
quantify the energy and angular momentum of electrons in isolated atoms. The problem is
approached here by examining the possible modes of interaction between charges and the
response of atoms to close confinement.
4.1. Interaction Theory

Interaction at a distance is interpreted in modern theories as a field phenomenon. The
electromagnetic field, described by Maxwells equations as waves, propagate through the
vacuum, with a constant velocity that depends on the permittivity and permeability of free

space, c = 1/ 0 0 . The wave equation (4) has solutions (t) and (t), known as
retarded and advanced waves, respectively. The transmission of electromagnetic energy
between an emitter and a distant receptor is assumed to be negotiated by a pair of retarded

and advanced waves. As a spherical wave signal from the emitter reaches an acceptor, it
responds with an advanced return signal that reaches the emitter at the exact moment of first
emission, to establish a standing wave, known as a photon.
Further interaction depends on the potential energy difference between emitter and re-
ceptor. Transfer of excess energy occurs by relaxation of the standing wave, which is exper-
imentally observed as photon emission. Alternatively the standing wave, known as a virtual
photon, that exists between interacting sites, becomes balanced against external factors, at
a distance that defines the electrostatic force of interaction between the charges as:
q1 q2
F = .
40 r2
All chemical interactions are of this type [4].
In Bohmian formalism the theory predicts the stability of atomic matter as a function of
the fine-structure constant.
Sommerfeld [13] (p.107) introduced the fine-structure constant as = v1 /c =
e2 /40 c~ (= 2e2 /ch, in esu), where v1 is the velocity of an electron in the first Bohr
orbit. More generally, the parameter = v/c for a freely moving electron with de Broglie
wavength dB = h/mv and Compton wavelength C = h/mc is defined, more appropri-
ately as = C /dB . An electron in a hydrogenic stationary state has ndB = 2n2 a0 ,
hence:
e2
n = .
n~c
In the Bohmian interpretation an atomic stationary state occurs when the potential energy
of the electron, at rest, is balanced by the quantum potential.
The relativistic mass of an electron at the position of the nucleus, with respect to the
rest mass mo in the ns state, would be
mo mo
m= p =
2
1 v /c 2 1 2
i.e.,
m2 m2o 4 2 e4 En
2 = = = ,
m2 n2 h2 c2 mc2
Hence En = m c2 , where m = m m2o /m m mo .
This is interpreted here to show that an electron in a stationary state has its mass reduced,
with respect to the nucleus, by an amount m , which reappears as the binding energy
En . The same argument explains nuclear binding energy as a mass defect.
Transition of an electron with n > 1 to a lower unoccupied energy level by emission
of a photon with energy h and spin ~, is anticipated. However, in the 1s state with quan-
tum number l = 0, there is no orbital angular momentum to transfer in promoting photon
emission and the ground state remains stable. The calculation does not imply different ve-
locities for the electron at different energy levels only a quantized change in de Broglie
wavelength. The mass-energy difference amounts to exchange of a (virtual) photon in the
form of a standing wave between the charge centres.
With the classical radius of the electron defined as r0 = e2 /mc2 it is noted that
2
me4 e2

r0
= = = 2 ,
a0 m~2 c2 ~c
where a0 is the Bohr radius. This result follows from the two relationships:
2e2
C = = 2r0 ,
mc2
C 2~2
= = 2a0 = dB .
me2
Now define Z = 2r0 . Whereas the wavelength dB = C / represents a wavepacket
with group velocity vg < c, the phase velocity v > c is associated with the Zitterbewegung
of wavelength Z = C ; vg v = c2 [15].
This argument relates to two problematic parameters: and the classical electron ra-
dius r0 which still awaits quantum-mechanical definition. The fine-structure constant ap-
pears firmly associated with the wave nature of an electron, seen as a standing wave that
results from the superposition of diverging and converging spherical components. The inter-
nal wave structure of the electron is observed as high-frequency Zitterbewegung while the
macroscopic effects in an electromagnetic field are fixed by the spread of the wavepacket,
conveniently defined as a de Broglie wavelength. Trapped in the field of a proton the de
Broglie wavelength is quantized to avoid self-destruction, such that
C e2
= n = .
dB n~c
For an effective charge separation of rn , the ratio n may be considered the ratio of two
energies:
e2
2
e 1
=
n~c rn h
an electrostatic and a quantum-mechanical factor. The constant c = / = describes the
virtual photon that occurs as a standing wave (n = 2r) between the charge centres. The
balance between the classical coulombic attraction and the quantum-mechanical repulsion
(the quantum potential) defines the fine-structure constant with a value, fixed by the de
Broglie wavelength of the virtual photon.
In a strong field the size of an electronic wavepacket may be compressed below the
Compton radius to an absolute minimum of Z , which describes the minimum size to which
an electron may be compressed, measuring r0 = Z /2, for an electron defined as an
electric charge e distributed over a sphere of radius r0 . The potential energy E = e2 /r0
corresponds to r0 = e2 /mo c2 , as measured classically.
4.2. Environmental Effects

Schrodingers solution for the hydrogen electron serves as the starting point for the qual-
itative discussion of all chemical effects in quantum formalism. It is routinely forgotten that
the simple hydrogen solution ignores all interactions that the electron would experience in
a chemical environment. Even the use of hydrogen energy levels to rationalize the structure
of the periodic table is of limited value.
A useful approach to simulate environmental effects was pioneered by Sommerfeld on
solving Schrodingers equation under modified boundary conditions. Non-zero environ-
mental pressure was introduced by assuming that (r) 0 as r approaches some finite
value rc , rather than infinity. All energy levels move to higher values with decreasing rc ,
until the ground level reaches the ionization limit at rc = r0 , the ionization radius.
It is noted that on reaching the ionization limit by uniform compression the electron
that becomes decoupled from the nucleus finds itself confined to a spherical cavity at zero
potential and kinetic energy. However, the non-zero energy of a free electron in a hollow
sphere, must therefore be interpreted as quantum potential energy. The Helmholtz equation
for such an electron:
2 + k 2 = 0 , k = 2mE/~2
p
p
has the radial solutions, R = 2kr/ kl (kr). At the first zero of the spherical Bessel
function 0 = sin(kr)/(kr), kr0 = , and hence (compare 21)
h2
E0 = = Vq . (22)
8mr02
The Fourier transform of 0 is the box function

2/2r0 if |r| < r0 ,
f (r) = (23)
0 if |r| > r0 .
It follows that the decoupled (valence) electron of the hydrogen atom, compressed to r0 is
uniformly spread across the ionization sphere.
4.3. Emergent Properties

Chemical theory requires insight into more than atomic stability. One-electron quantum
theory provides no guidance beyond the hydrogen atomic ground state and the structure of
many-electron atoms must be inferred from the empirically known periodic table of the
elements. However, the superficial correspondence between the calculated quantum states
of hydrogen and the observed elemental periods strongly suggests a functional relationship
between the two sets. To better appreciate the relationship it is noted that both sets can be
generated by convergent sequences of Fibonacci or Lucas fractions as shown below.
4.3.1. Periodicity

h1 h2
A modular pair of rational fractions k1 , k2 has the property:

h1 h2
k1 k2 = 1.

Such a pair is geometrically represented by two Ford circles with radii and y-coordinates
of 1/2k 2 at x-coordinates of h/k. A series of rational fractions with all neighbouring terms
in unimodular relationship is represented by a set of tangent Ford circles [4]. Examples of
such modular series are the Farey sequences, Fn and the converging Fibonacci and Lucas
fractions on the segment ( 12 35 32 ) of F5 :
Despite a number of uncertain half-lives, a reasonable estimate of 264 divides the sta-
ble (non-radioactive) nuclides into 11 periods of 24. Plotting the ratio of protons:neutrons
(Z/N ) for all isotopes as a function of atomic number, the hem lines that separate the pe-
riods of 24, intersect a reference line, at Z = , in Z-coordinates which correspond to
well-known ordinal numbers that define the periodic table of the elements [2, 3]. Remark-
ably, the same hem lines intersect a reference line at Z/N = 0.58 in atomic numbers that
correspond to the closure of the calculated wave-mechanical energy levels for hydrogen.
Noting that the radii of unimodular Ford circles are inversely proportional to the number
(2k2 ) of atoms in elemental periods, we look for converging circles that match the two
forms of periodicity. The primary circle
at x = 0 or 1, rF = 21 , is flanked by two tangent circles at x = 0.5 and 1.5 0.5,

rF = 81 ; further converging pairs are at x = 23 , rF = 18
1
and x = 34 , rF = 32
1
. This
arrangement mimics the periodic table:
What is probably the aesthetically most pleasing form of the periodic table is obtained
by rearrangement in circular array, as shown in Figure 5 for the hundred naturally occurring
cosmic elements.
Interpreted in terms of electronic distribution it implies twelve 8-fold and three 2-fold
energy levels, with all closed-shell elements grouped together. These are not hydrogen-like
energy levels, but they agree with the valence levels, calculated for compressed atoms in
Hartree-Fock-Slater approximation [14].
The hypothetical arrangement based on the hydrogen solution is recognized in the
nested set of Ford circles at x = 1, predicting consecutive periods of 2n2 , n = 1, 2, . . . ,
arranged as follows:
If n is interpreted as Schrodingers principal quantum number, periods of the correct

length (2n2 ) are predicted. Each of the periods consists of n subshells for subsidiary quan-
tum numbers 0 l < n. The number of elements per subset equals 2(2l + 1), l ml l.
This result provides the basis of Paulis exclusion postulate, which defines an emergent
property, not of quantum-mechanical origin.
The hypothetical and observed versions of the periodic table are in agreement for el-
ements 1 to 18. The superficial agreement (e.g. for elements 28, 46 and 78; and 2936)
beyond that point is purely accidental. We conclude that the wave-mechanical hydrogen
model fails to account for elemental periodicity mainly because it ignores all interactions
apart from the central-field unitary electrostatic attraction. The common thesis of chem-
istry textbooks that Schrodingers equation, with due allowance for interelectronic effects,
accounts for the periodic table, fails on two important counts. It predicts transition series of
ten elements, compared to the observed eight. The guiding principle, known as the Aufbau
procedure, is valid only for the alkaline-s and p blocks. Less than two-thirds of the nominal
transition elements obey an Aufbau rule. The correct periodic system occurs in an environ-
Figure 5. The Periodic Table of the elements in circular form.
ment that requires the convergence of stable nuclear composition, Z/N to the golden ratio,
, and subject to an emergent exclusion principle.
Further new properties are expected to emerge in the analysis of chemical affinity, co-
hesion and conformation, at a higher hierarchical level.
4.3.2. Electronegativity
Chemical affinity is the intuitive qualitative concept that guided experimental chemistry
for centuries. The first quantitative measure of affinity was discovered by Lothar Meyer
as the atomic volume of an element his basis of periodicity. It served to differentiate
between electropositive and electronegative elements, with a natural affinity between them.
The concept was generalized by Pauling, Mulliken and others, by placing all elements on
Figure 6. Electronegativity as quantum potential of the valence state
a single empirical electronegativity scale. By demonstrating the equivalence of electroneg-

ativity and the quantum potential of the valence state [16] it was finally recognized as an
emergent atomic property, readily reduced to fundamental quantum theory.
Like hydrogen, an atom is said to be in its valence state when ionized by environmen-
tal pressure. The energy of the electron, decoupled from the nucleus but confined to the
ionization sphere, is given by (22). Characteristic ionization radii, r0 , are obtained by nu-
merical Hartree-Fock-Slater calculation [14] with boundary conditions modified as for H.
Redefined on this basis, electronegativity, , is calculated as
h2
2 = ,
8mr02
expressed in eV, such that relates to Pauling

electronegativities on a linear scale and 2
to the Mulliken scale. A plot of = E0 reveals the same periodicity as Figure 5 and
as Lothar Meyer atomic volumes. The uniform electron density of the valence state, from
(23):
1
= 2 (r), (r) = (/V0 ) 2 exp {(r/r0 )p } , p >> 1. (24)
The scale factor, , which compensates for an inaccessible core, is proportional to r0 and
varies inversely with the number of nodes as defined by an effective principal quantum
number n. Hence, = cr0 /n. The wave function

1
exp {(r/r0 )p }
p
(r) = 3c/4n (25)
r0
describes the interaction of an atom with its chemical environment.
4.3.3. Covalence
Chemical cohesion has for many years been the main topic of theoretical chemistry,
conducted as an exercise in computational quantum physics, described by one practitioner
[17] as if repeatedly ...validating Schrodingers equation! . There is a curious conviction
that the Born-Oppenheimer scheme enables molecular structure to be computed ab initio.
An initially assumed structure is treated only as a device to kickstart the calculation. Once
the electronic density has been obtained, the nuclear framework is computed theoretically,
without assumption. It always comes out miraculously close to the assumed structure.
To the uninitiated the procedure appears to be circular and unlikely to produce anything
of physical significance beyond the assumed molecular structure. An obvious alternative
is to model the electron exchange that constitutes atomic pairwise interactions, known as
covalent bonds, before assembly into a three-dimensional structure is attempted.
The computational details for this procedure, which requires atomic wave functions,
have been documented as the well-known Heitler-London method. Appropriate wave func-
tions (25) are obtained from empirically adjusted ionization radii that compensate for steric
factors [4]. HL calculations predict both dissociation energy and equilibrium interatomic
distance for any first-order covalent interaction. High-order interaction results from the
valence-level screening of the internuclear repulsion.
Figure 7. Covalent binding energy curve for homonuclear diatomics in dimensionless units.
The same set of characteristic atomic radii (r) can be used to model covalent electron
exchange by point-charge simulation, as a function of interatomic separation (d) only. It
is found that with the ratio d/r and binding energy E, expressed in dimensionless units,
all homonuclear diatomic interactions are described by a single interaction curve, shown in
Figure 7.
The curve turns where d/r = and E = 2 , at the point where exactly two electron
waves are concentrated in the interatomic region. The condition is seen to reflect the ex-
clusion principle for fermions. Its relationship to the golden ratio defines the origin of the
exclusion principle as the curvature of space-time. Without this emergent property there is
no understanding of covalent interaction.
4.3.4. Molecular Shape

The inability to derive molecular structures from fundamental quantum theory identifies
molecular shape as another emergent property. Although it cannot be inferred from basic
theory it is readily reduced to the conservation of orbital angular momentum.
Conventional computational schemes, designed to minimize energy, with total neglect
of orbital angular momentum, must, by definition converge to a spherically symmetrical ar-
rangement. To prevent this from happening a potential field of lower symmetry is imposed
by assuming a fixed nuclear framework. Instead of imposing an experimentally determined
structure, conservation of orbital angular momentum provides a theoretically more satisfy-
ing algorithm to generate such a structure from first principles.
Polarization of mutually approaching reactants resolve local angular-momentum vec-
tors, just like an applied magnetic field. During the formation of a molecule, the alignment
of reactants that minimizes angular momentum in the local polar direction is favoured.
In many reaction systems there is sufficient symmetry for the orbital angular momentum in
the polar direction to become quenched completely. Where the quenching in low-symmetry
(chiral) systems is incomplete, the residual angular momentum will couple to the magnetic
field of polarized light, causing optical activity. Should quenching be possible only for a
specific angular alignment of neighbouring fragments, a rigid system, which resists tor-
sional deformation, is obtained. So-called double bonds and aromatic systems are common
examples.
The empirical stereochemical rules, pioneered by Kekule, vant Hoff and others, are
consistent with the principles outlined here and these have been generalized into empirical
computational schemes, collectively known as molecular mechanics. There is no more
fundamental procedure to predict molecular structure.
References
[1] H. Primas, Chemistry, Quantum Mechanics and Reductionism, 2nd ed., Springer-
Verlag, Berlin, 1983.
[2] J. C. A. Boeyens and D.C. Levendis, Number Theory and the Periodicity of Matter,
Springer.com, 2008.
[3] J. C. A. Boeyens, Periodicity of the stable isotopes, J. Radioanal. Nucl. Chem., 2003
(257) 3341.
[4] J. C. A. Boeyens, Chemistry from First Principles, Springer.com, 2008.
[5] M. Wolff, Beyond the Point Particle A Wave Structure for the Electron, Galilean
Electrodynamics, 1995 (6) 8391.
[6] J. C. A. Boeyens, Angular Momentum in Chemistry, Z. Naturforsch. 2007 (62b) 373

385.
[7] R. C. Jennison and A. J. Drinkwater, An approach to the understanding of inertia from

the physics of the experimental method, J. Phys. A, 1977 (10) 167179.
[8] J. C. A. Boeyens, Quantum theory of molecular conformation, C.R. Chimie, 8 (2005)

1527 1534.
[9] E. Schrodinger, Collected Papers on Wave Mechanics, (Translated from the second
German edition), 2nd ed., Chelsea, NY, 1978.
[10] D. Bohm, A Suggested Interpretation of the Quantum Theory in Terms of Hidden

Variables, Phys. Rev., 1952 (85) 166179, 180193.
[11] D. W. Belousek, Einsteins 1927 Unpublished Hidden-Variable Theory: Its Back-

ground, Context and Significance, Stud. Hist. Phil. Mod. Phys., 1996 (27) 437461.
[12] P. R. Holland, The Quantum Theory of Motion, University Press, Cambridge, 1993.
[13] A. Sommerfeld, Atombau und Spektrallinien, 4th ed., Vieweg, Braunschweig, 1924.
[14] J. C. A. Boeyens, Ionization radii of compressed atoms, J. Chem. Soc. Faraday Trans.,
1994 (90) 33773381.
[15] J. C. A. Boeyens, New Theories for Chemistry, Elsevier, Amsterdam, 2005.
[16] J. C. A. Boeyens, The Periodic Electronegativity Table, Z. Naturforsch., 2008 (63b)

199209.
[17] N. C. Handy, in: R. Broer, P.T.C. Aerts and P.S. Bagus, New Challenges in Computa-
tional Chemistry, University of Groningen, 1994.
Chapter 10
THE ALGEBRAIC CHEMISTRY OF MOLECULES

AND REACTIONS
Cynthia Kolb Whitney*

Galilean Electrodynamics, 141 Rhinecliff Street,
Arlington, MA 02476-7331, USA
Abstract
A new line of research generally characterized as Algebraic Chemistry is here applied to the
problem of modeling energies involved in molecule formation and in chemical reactions. The
approach is based on algebraic scaling laws that allow one to estimate energies of interest by
evaluating simple algebraic expressions, without recourse to computer calculations based on
detailed quantum mechanical formulations and phase-space integrations, such as found in
traditional Quantum Chemistry. The simplicity of the algebraic approach means that it can
address molecules and reactions involving more atoms than the ones that are presently
convenient for traditional Quantum Chemistry. In fact, there is no complexity-related limit on
the atom count amenable to molecule or reaction analysis with the algebraic method.
Algebraic Chemistry is a simple tool always suitable for hand calculations. In the cases of
many real molecules and reactions, data is available to test the algebraic approach, and thus
build some confidence about it. This is important because the scaling laws used come from
new, and not yet broadly known, theoretical extensions to the traditional quantum mechanics
of atoms, and even to special relativity theory and classical electromagnetic theory. These
extensions of traditional theory are briefly summarized in Appendices and detailed further in
the References.
Keywords: Algebraic Chemistry, Quantum Chemistry, heat of molecule formation, heat of

chemical reaction.
*
E-mail address: Galilean_Electrodynamics@comcast.net
218 Cynthia Kolb Whitney
1. Introduction
The present work develops a technique for quantitative analysis of molecules and
reactions of arbitrary complexity. The approach is called Algebraic Chemistry, because it is
based on simple multiplicative scaling laws. The present work extends the development of
Algebraic Chemistry [1-4] from the discussion of individual elements to the discussion of
complete molecules and reactions. The objective is to make Algebraic Chemistry more ready
for full adoption into Chemistry, and less likely to remain a disruptive stepchild within
Physics.
Much of the earlier work in the development of Algebraic Chemistry concerned
ionization potentials of atoms. It showed that all the information necessary to specify
ionization potentials of arbitrary order for all the elements is embodied in first-order
ionization potentials for all the elements, and that, in fact, all the information necessary to
specify the first-order ionization potentials for all the elements is embodied in the first-order
ionization potential of Hydrogen, and that, in fact, this number is predictable from theory.
Here the idea of scaling laws is used to extend the known information about ionization
potentials of neutral atoms to estimate ionization potentials for already-ionized atoms. This
new information is not to be confused with higher-order ionization potentials. The higher-
order ionization potentials of neutral atoms, apparently [1], describe multiple ionizations that
occur simultaneously, whereas the ionization potentials of already-ionized atoms describe
single ionization events that occur sequentially. The one-at-time physical process is gentler
than the all-at-once physical process, and is more typical of events that actually occur
throughout most of normal Chemistry.
Like the previously known information about the higher-order ionization potentials of
neutral atoms, the new information about ionization potentials of already-ionized atoms is
entirely derivable from first-order ionization potentials of all the elements. Section 2 shows
exactly what the scaling laws have to be, given the algebraic model under consideration. The
new information is then used in subsequent Sections to estimate energies involved in
molecule formation and chemical reactions.
2. Scaling Laws
The basis for having scaling laws at all lies in imagining atoms to consist of a nucleus
and an electron cluster sufficiently well defined that the atom as a whole is similar to a two-
body system. Being imagined as similar to a two-body system, all atoms are then similar to
Hydrogen, and scaling laws based on Hydrogen follow. This idea is developed in [1], and
then applied and extended in [2-4], and is summarized for the present applications in
Appendix 3. The key results are as follows:
The magnitude of the potential energy for the one electron in the Hydrogen atom is:
e2 (re + rp ) = 3c 2 me2 25 mp (1)

The Algebraic Chemistry of Molecules and Reactions 219
where e is electron charge, r is orbit radius, c is light speed, m is mass, and subscripts e
and p distinguish electron from proton.
Suppose we want to model the system potential energy, not for Hydrogen per se, but for
its isotopes, Deuterium and/or Tritium. The proton mp and rp then need to be replaced with
a more generic nuclear mass M and its orbit radius rM . The magnitude of potential energy
for this more massive atom is:
e2 (re + rM ) = 3c 2 me2 25 M . (2)
Next, suppose we want to deal with a neutral atom with nuclear charge number Z , as
well as the generic nuclear mass M . Then we have Z electrons as well. For the more
charged system, the magnitude of the potential energy becomes:
Z 2e2 (re + rM ) = Z 2 3c 2 me2 25 M . (3)
This scaled-up expression represents the magnitude of the total potential energy of the
system involving Z electrons. What is then comparable to the ionization potential for
removing a single electron is:
( ) (
Z e2 (re + rM ) = Z 3c 2 me2 25 M (Z / M ) 3c 2 me2 25 ) (4)
Thus we see that Z / M scaling that is predicted for measured ionization potentials. This
is cancelled out by M / Z scaling to produce the IP s collected in Appendix 1 and used in
following Sections.
More generally, if the atom is in an ionized state, we have a distinct electron count Ze
and proton count Z p . For the baseline nuclear-orbit part, we have for the total system:
( )(
Z p Ze e2 (re + rM ) = Z p Ze M 3c 2 me2 25 ) (5)
What is then generally comparable to the nuclear-orbit part of the ionization potential for
removing a single electron? Appendix 3 shows that it is as if all factors of e changed to
Z p Ze e . What is then comparable to the ionization potential for removing a single electron
is:
Z p Ze e2 (re + rM ) = (Z Z p e )(
M 3c 2 me2 25 ) (6)
In the present work, all scaling laws are based on first-order ionization potentials of
neutral elements. Removing the Z / M scaling by multiplying raw ionization data by the
inverse, M / Z , produces IP s that are all comparable to the IP of Hydrogen. In this
paper, the symbol IP always means M / Z -scaled ionization potential to compare with
that of Hydrogen. Let the M / Z -scaled first-order ionization potential for Hydrogen be
represented by IP1,1 . The first subscript 1 means first ionization potential, and the second
subscript 1 means first element; i.e. Hydrogen. The M / Z scaled first-order IP for the
element Z is then represented by IP1,Z .
In the earlier work [1], the problem addressed was modeling IP s of all orders higher
than unity for all elements - the all-at-once problem. The results showed that we could enlist
information from one element to develop information about an ion of another element. That
idea is exploited here to infer the first-order IP s of already-ionized atoms the one-at-a-
time problem.
The IP1,Z for removing an electron separates into a baseline, nuclear-orbit part, IP1,1 ,
and a deviation, electron-cluster part, IP1,Z = IP1,Z IP1,1 . The baseline part is
independent of Z , but the deviation part is a complicated function of Z . The present paper
takes the deviation part as input data. But there exists a basis for future deeper analysis and
modeling of the deviation part. The development of an Expanded SRT, detailed in [1] or [2],
allows for superluminal speeds, which in turn allows for same-charge systems. Rings of
multiple charges rotating at superluminal speeds are analyzed in [3], and such rings stacked
like little magnets are used to model the electron populations in atoms.
The deviation IP1,Z can be positive or negative, depending on where the element is in
the Periodic Table. The deviation generally tends to zero at mid period, between noble gasses.
It is maximally positive at a noble gas, and maximally negative just after a noble gas. For
example, [see Appendix 1] the deviation term for Helium is
IP1,2 = IP1,2 IP1,1 = 49.875 14.250 = 35.625 ,
whereas the deviation term for Lithium is
IP1,3 = IP1,3 IP1,1 =12.469 14.250 = 1.781 .
+
Let symbols like IP1,Z and IP1,Z represent first-order IP s for already-ionized atoms.
The superscript + means positively charged due to previous electron removal, and multiple
+s would mean multiple electrons removed. Superscript means negatively charged due to
previous electron addition, and multiple s would mean multiple electrons added. The
Z n Ze M scaling maps the IP1,1 baseline part of the IP1,Z for the neutral element into
+
the baseline part of the IP1, Z or IP1, Z or whatever. The increment part is different; it
depends only on the number of electrons involved in the charge cluster, so the scaling that
applies to it is just Ze / M , and what it applies to is the deviation term for the element
whose Z matches the Ze needed.
The IP1,1 and the IP1,Z are the basic data used below to describe first-order IP s like
IP1,+Z and IP1,Z for already-ionized atoms.
3. Example Atoms
In Physics, it is traditional to begin any discussion about atoms with the simplest possible
atom, Hydorgen 1 H . I am going to depart from this tradition: I am starting this discussion
with Carbon 6 C . Hydrogen is just too simple; with Hydrogen too many important parts of
the ionization problem disappear as invisible zeros. Carbon has no such degeneracies, and
yet it is still a lot like Hydrogen; after Hydrogen, it is the next keystone element [see
Appendix 4]. Like all keystone elements, it is just as willing to give as to take electrons, until
the number reaches a noble-gas number: 2 or 10 for Carbon (as compared to 0 or 2 for
Hydrogen).
For Carbon 6 C , IP1,6 = IP1,1 + IP1,6 times Z / M = 6 / M 6 represents the work
that must be supplied to take one electron off the neutral Carbon atom. That exercise produces
+
a positively charged ion 6 C . The transition also returns some heat, because after the
ionization, the electron cluster is different: 5 electrons instead of 6, and all resting at a
different energy. I call it heat, not work, because it is uncontrollable; Nature simple does
this. The heat returned is evidently (IP1,6 6 IP1,5 5) / M 6 . Observe how the 5 for
5 B information enters here.

+ +
The ionization potential of the singly ionized 6 C , IP1,6 , times 6 / M 6 represents the
work that must be supplied to remove another electron from the already singly ionized
(
Carbon atom. It is IP1,1 6 5 + IP1,5 5 )M 6 . Observe how the 6 5 due to the
+
previous ionization enters here. It means that IP1,6 is certainly not the same thing as the so-
called second ionization potential of the neutral Carbon atom, IP2,6 . As before, heat is also
returned as the electron cluster readjusts. This time, the amount of heat returned is
(IP1,5 5 IP1,4 4) M6 . Observe how the 4 for 4 Be information enters here.

Proceeding to the next step, the work for removing another electron from the now doubly
++ ++
(
ionized 6 C , IP1,6 , times 6 / M 6 is IP1,1 6 4 + IP1,4 4 M 6 . The heat )
(
returned this time is IP1,4 4 IP1,3 3 ) M6 . The now triply ionized 6 C+++ takes
+++
work IP1,6 6 / M 6 = (IP1,1 6 3 + IP1,3 3 )M 6 to remove another electron.
(
The M / Z -scaled heat returned is IP1,3 3 IP1,2 2 ) M6 . This turns out to be a
+++ ++++
negative number. This means that getting from 6 C to 6 C cools the local
++++
environment. And the now quadruply ionized 6C would take work
++++
IP1,6 (
6 / M 6 = IP1,1 6 2 + IP1,2 2 )M 6 . Because IP1,2 is a large
number, this last ionization is not very likely to happen. That is, like the 2 He atom, the
++++
6C ion is quite stable.
With all this information, one can construct an energy tally for all the electron removal
+ ++ +++
scenarios that Carbon invites: 6 C 6 C , 6 C 6 C , 6 C 6 C , and
++++
6C 6C :
+
6C 6C takes IP1,1 6 / M 6 and (IP1,6 6 IP1,5 5) / M 6 ;
6C 6C
++
( 6 5 ) M and (IP
takes IP1,1 6 + 6 1,6 6 IP1,4 4) / M 6 ;
takes IP (6 + 6 5 + 6 4 ) M
+++
6C 6C 1,1 6
and (IP1,6 6 IP1,3 3) / M 6 ;
6C 6C
++++
(
takes IP1,1 6 + 65+ 64 + 63 )M 6
and (IP1,6 6 IP1,2 2) / M 6 .
Carbon also allows the addition of electrons, producing negatively charged ions. To

quantify these, let use the pattern for electron removal, which means we start with 6 C .

The work to remove an electron must be IP1,6 6 / M6 =
(IP1,1 6 10 + IP1,10 10 )M 6 . Like IP1,2 , IP1,10 is a large number, meaning


that, like 10 Ne , 6 C is quite stable. The heat returned in this de-ionization is
(IP1,10 10 IP1,9 9) M6 . The next ion down, 6C

, takes work

IP1,6 6 / M6 = (IP1,1 6 9 + IP1,9 9 )M 6 to remove the next electron. The
heat returned in this de-ionization is (IP1,9 9 IP1,8 8) M6 . Then the next ion
down, 6 C

, takes work IP1,6 6 / M 6 = (IP 1,1 6 8 + IP1,8 8 )M 6 for
another electron removal, and this de-ionization returns heat
(IP1,8 8 IP1,7 7 ) M6 . And 6C

takes work

IP1,6 6 / M 6 =
(IP1,1 6 7 + IP1,7 7 )M 6 for the last electron removal, and this final de-
(
ionization then returns heat IP1,7 7 IP1,6 6 ) M6 .
The process of adding electrons to an atom is just opposite to the process of removing
electrons. So the energy tally for all the electron addition scenarios is:

6C 6C takes IP1,1 6 7 M 6 and (IP1,7 7 IP1,6 6) / M 6 ;
6C 6C

takes IP1,1 ( 68 + 67 )M 6
and (IP1,8 8 IP1,6 6) / M 6 ;
6C 6C

takes IP1,1 ( 69 + 68 + 67 )M 6
and (IP1,9 9 IP1,6 6) / M 6 ;
6C 6C

takes IP1,1 ( 6 10 + 69 + 68 + 67 )M 6
and (IP1,10 10 IP1,6 6) / M 6 .
With Carbon now well in tow, we are ready to look back to Hydrogen. The transition
+
1 H H takes IP1,1 / M1 and (IP1,1 IP1,0 ) / M1 , but the latter two IP data items

are zero, so the pattern being followed isnt well revealed by them. The transition 1 H H
takes IP1,1 1 2 M1 and (IP1,2 2 + IP1,1 1) / M1 , but IP1,1 is zero, and so

doesnt fully reveal the pattern. That is why it was better to violate tradition and start with
Carbon.
Since hydrocarbons are so important in the discipline of Chemistry, it will also be useful
to have at hand the corresponding results for Oxygen. Being so close to 10 Ne , 8 O is
+
probably characterized thoroughly enough by just four transitions: 8 O 8 O ,
++
8O 8O and 8 O 8 O , 8 O 8 O .
+
8 O 8 O takes IP1,1 8 / M 8 and (IP1,8 8 IP1,7 7) / M8 ,
8O 8O
++
(
takes IP1,1 8 + 8 7 )M 8 and (IP1,8 8 IP1,6 6) / M 8 ;

8O 8O takes IP1,1 8 9 M8 and (IP1,9 9 IP1,8 8) / M 8 ,
8O 8O

takes IP1,1 ( 8 10 + 89 )M 8 and
(IP1,10 10 IP1,8 8) / M8 .
4. Application to Analysis of Molecules

The basic idea exploited in this work is that a molecule consists of ionized atoms, some
positively ionized and some negatively ionized, exerting Coulomb attraction for each other. It
is therefore possible to learn something about a molecule by determining what its constituent
ions are, and modeling the energy requirements for creating those ions from the neutral atoms
involved. The first part of that question was addressed in Ref. [1], which gave the following
two mirror-image propositions:
Proposition 1: Molecules that are relatively stable have total electron counts such that
every atom present can be assigned an electron count equal to that of a noble gas, or else zero.
Proposition 2: Molecules that are highly reactive have total electron counts such that not
every atom present can be assigned an electron count equal to that of a noble gas, or else zero.
Proposition 1 is very often fulfilled, and was illustrated by molecules from small
( NH 3 , NaOH ) to larger ( CH 3CO 2C10 H17 , (CH 3CO2 )2 Pb 3H 2O ,
(C17 H 35CO2 )2 Ca ). Proposition 2 was illustrated with some common atmospheric gasses
( O 2 , O3 , or NO ).
So the Propositions are probably true, but we really need to know much more. We need
not just a binary division into stable / reactive; we need numerical rankings within those
categories. That would mean modeling the energy requirements for creating the ions
involved. Furthermore, it is often true that a stable molecule admits more than one possible
set of noble-gas electron assignments, or that a reactive molecule admits more than one
possible set of not-quite noble-gas electron assignments. When multiple assignments are
possible, which one is the one Nature picks? Again, we need numerical rankings.
The present work is aimed at developing such quantitative rankings, based on the
algebraic modeling concepts developed in the previous Section. There are several preliminary
remarks to be made: 1) In all of the following examples, the IP data used come from the
algebraic model developed in [1] and summarized in Appendix 1 and Appendix 2. Occasional
IP data points differ detectably from M / Z -corrected raw data. So be it. I wish to test the
concept of algebraic modeling over all, and if errors that are manifest in molecule modeling
actually arise from errors in atom modeling, they are nevertheless errors, and I want them to
be seen; 2) The calculations reported carry several more digits than can be justified as
significant. This level of numerical detail is provided only to make the calculations easier to
follow and to reproduce, and not to imply an amazing level of precision; 3) Comparison to
reported data is generally desired, but not always possible, for reasons discussed below.
One problem is that the energies calculated here are just for the formation of the ions in a
single molecule. Some of this energy will be consumed in actually forming the molecule; i.e.
giving the ions enough energy to stay at some stand-off distance from each other. Some more
energy will be consumed in getting to the state of matter for which data are reported. That
means many molecules, in bulk matter a mole endowed with collective attributes. Molar
heats of formation are generally reported for standard conditions, i.e. temperature (typically
25o C), pressure (for gasses, one atmosphere), dilution (for solutions, infinite dilution), etc. A
single molecule can hardly be said to possess such properties. Indeed, not even the state of
matter solid, liquid, or gas seems meaningful for a single molecule. So it is clear that the
energy calculated here for forming the ions in a single molecule in isolation cannot be said to
correspond directly to reported data on the heat of formation for a molecule as a constituent of
bulk matter. The energies calculated here are generally are generally less than reported heats
of formation. Why less? Because, for molecules that actually form spontaneously, thus
releasing heat, the reported heats of formation are by convention negative. That means the
energies for forming the ions in molecules should also come out negative, and indeed more
negative than the heats of formation reported for bulk matter. Less is more, the saying goes!
Another problem, all too pervasive throughout Chemistry, is the need for conversion
among many different systems of units. That is why the edition of Langs Handbook that
provided most of the data in this paper has some 42 pages devoted to specifying conversion
factors. And even at that generous page count, it does not have the particular conversion
factor needed here. Heats of formation are quoted there in kilogram-calories per mole (here
abbreviated as Kg-cals), whereas ionization potentials are quoted in electron volts per
atom (here abbreviated as eVs). Our energy-tally results are reported in electron volts per
molecule, and with molecule being just a generalization on atom, those units too are
abbreviated as eVs. So for almost everything in this paper, we need the conversion from
Kg-cals to eVs. The meaning of kilogram-calories seems somewhat ambiguous, but the
relevant conversion information provided appears to be: kilogram-calories to joules: 4186;
7 12 23
joules to ergs: 10 ; eVs to ergs: 1.602 10 ; gm-mole to molecules: 6.0228 10 .
The needed conversion factor is then probably
Kilogram-calories to joules joules to ergs 4186 107

= 0.043
eV's to ergs gm mole to molecules 1.602 1012 6.0228 1023
This interpretation can be checked by successful use with enough example molecules.
Many examples will be presented the following Sections.
5. Analyses of Some Small Molecules

A Molecule with Two Atoms
H 2 . Reported heat of formation: 0 Kg-cals, times conversion faction 0.043 yields 0

eVs out (meaning no energy is released in forming this molecule). Probable electron
assignments: one 1 H atom, 0 electrons; the other 1 H atom, 2 electrons.
Relevant Model Data about 1 H :

+
The transition 1 H 1 H takes work IP1,1 / M1 = 14.250 / 1.008 = 14.137 eVs.

The transition 1 H H takes negative work for the extra electron falling into nuclear
orbit: IP1,1 1 2 M1 = 14.25 1.414 / 1.008 = 19.990 eVs, and takes negative
heat for the formation of an electron cluster: IP1,2 2 / M1 , where
IP1,2 = IP1,2 IP1,1 = 49.875 14.250 = 35.625 , so that IP1,2 2 / M1 =

35.625 2 / 1.008 = 70.685 eVs. The sum of energies taken is
19.990 70.685 = 90.675 eVs. Observe that this 2-electron negative state, H , is
+
very much favored over the neutral state, 1 H , or the zero-electron state positive state, 1 H .
Thus the formation of the ions in the H2 molecule takes

14.137 90.675 = 76.538 eVs, the minus meaning that heat is released in forming this
molecule. So there is a lot of energy available, which can allow H 2 molecules to form, and
H 2 bulk matter to vaporize; i.e., become a gas.
Another Molecule with Two Atoms
O 2 . Reported heat of formation: 0 Kg-cal, times conversion factor 0.043 is 0 eVs.

Probable electron assignments: 8 O , 6; 8 O , 10. Note: it is not possible for both 8 O atoms
to get a Noble gas electron count.
Relevant model data about 8 O :
The transition 8 O 8 O
++
(
takes IP1,1 8 + 8 7 )M 8 , or
( ) ( )
14.250 8 + 8 7 15.999 = 14.250 8 + 7.483 15.999 = 13.791 eVs, and
(IP1,8 8 IP1,6 6) M8 , or
(13.031 8 7.320 6) 15.999 = (104.248 43.920) 15.999 = 3.771eVs.
++
So the transition 8 O 8 O takes altogether 13.791 + 3.771 = 17.562 eVs.
The transition 8 O 8 O

(
takes IP1,1 8 10 + 8 9 M8 , or )
( )
14.250 8.944 + 8.485 15.999 = 15.524 eVs,
(
and IP1,10 10 IP1,8 8 ) M8 , or
( ) (
29.391 10 13.031 8 15.999 = 293.910 104.248 15.999 = )
11.855 eVs.

So the transition 8 O 8 O takes altogether 15.524 11.855 = 27.379 eVs.
++
Interpretation concerning O 2 : Transforming the neutral 8 O atom to the positive 8 O

ion takes 17.103 eVs, and transforming 8 O to the negative 8 O ion takes
27.379 eVs, so forming the ions in the O2 molecule takes

17.562 27.379 = 9.817 eVs. This molecule readily forms, and there is excess energy
available to vaporize the bulk matter formed.
A Third Molecule with Two Atoms
CO . Reported heat of formation: 26.42 Kg-cal as a gas, multiplied by conversion

factor 0.043 yields 1.136 eVs. Probable electron assignments: 6 C , 4; 8 O , 10. Note: it is
not possible for both atoms to get a Noble gas electron count.
Relevant model data about 6 C :
The transition 6 C 6 C
++
takes IP1,1 6 + ( 65 )M 6 , or
( ) (
14.250 6 + 5.477 12.011 = 13.617 eVs, and IP1,6 6 IP1,4 4 ) M6 ,
or
(7.320 6 9.077 4) 12.011 = (43.920 36.308) 12.011 = 0.6338 eVs.
Interpretation concerning 6 C : Transforming a neutral 6 C atom to a positive 6 C++ ion
takes 13.617 + 0.6338 = 12.983 eVs.
Relevant model data about 8 O (part of the information given for O 2 ):

The transition 8 O 8 O takes 27.379 eVs.
Interpretation concerning CO : Forming the ions in the CO molecule takes
12.983 27.379 = 40.362 eVs. This molecule readily forms, and as bulk matter it
readily becomes a gas. Indeed, it looks even more favorable than CO 2 , analyzed next. This
may explain why CO is a frequent, though unwelcome, product of combustion.
A Molecule with Three Atoms
CO 2 . Reported heat of formation: 94.05 Kg-cal as gas, or 98.69 Kg.cal as aqueous

solution (either way meaning energy is released in forming this molecule) multiplied by the
conversion factor 0.043 yields 4.044 -eVs for gas or 4.244 eVs for solution. Probable
electron assignments: 6 C , 2; 8 O s, 10 each.
Relevant Model Data about 6 C :
The transition 6 C 6 C
++++
(
takes IP1,1 6 + 65+ 64 + 63 )M 6 , or
( )
14.250 6 + 5.477 + 4.899 + 4.243 12.011 = 24.463 eVs,
and ( IP1,6 6 IP1,2 2) / M 6 , or
(7.320 6 35.625 2) / 12.011 = (43.920 71.250) / 12.011 = 2.275 eVs.
++++
So the transition 6 C 6 C takes altogether 24.463 2.275 = 22.188 eVs.
Relevant model data about 8 O : (same as for CO above);

Interpretation concerning CO 2 : Forming the ions in the CO2 molecule takes

22.188 2 27.379 = 32.570 eVs; that is, this molecule easily forms, and there is
plenty of energy to make the bulk matter into a gas. Observe that just looking at eVs for ion
formation, without the complications embedded in Kg-cals for getting to the gaseous state at
prescribed conditions, shows CO 2 at 32.570 eVs to be less favorable than CO at
40.362 eVs. The 26.42 Kg-cals for CO as a gas, vs. 94.05 Kg-cals or 98.69 Kg-
cals for CO 2 as gas or aqueous solution, obscures this situation.
Another Molecule with Three Atoms
H 2O . Reported heat of formation 57.80 Kg-cals as gas, 68.32 Kg-cals for liquid,
multiplied by the conversion factor 0.043 yields 2.485 eVs as gas, 2.938 eVs for
liquid. Probable electron assignments: 8 O , 10, 1 H , both zero.
Relevant Model Data about 1 H (part of the Information given for H 2 above):
+
The transition 1 H 1 H takes 14.137 eVs.
Relevant model data about 8 O (same as for CO 2 above):

Interpretation concerning H 2O : The formation of the ions in the H 2O molecule takes

2 14.137 27.379 = 0.895 eVs. This is very near zero, but it is positive, and so seems
puzzling: it suggests that water takes some net energy to form, rather than yielding some
+
energy. But one more phenomenon can occur with water. The two H ions are really naked
protons, extremely tiny, and so able to form a positive binary charge cluster similar to the

negative binary charge cluster that two electrons form in an H ion. If the two naked protons
indeed do that, the process yields some energy. That energy would be related to, the
70.685 eVs that the two electrons in the H ion take [see H 2 ].
We do not at this time have a scaling law to express the relation between clusters of
electrons and clusters of protons. What we do have is the comparable data for heavy water
(made with deuterons): 59.56 Kg-cal for gas, 70.41 Kg-cal for liquid. These results are
not so different from those for regular water. So the yet-to-be-articulated scaling from
electrons to protons, and to deuterons, does not strongly involve the mass of protons vs.
deuterons. So perhaps it does not strongly involve the mass of either one vs. the mass of
electrons. If that is so, the resulting heat could be very similar to, possibly even equal to, the
70.685 eVs for the two electrons in the H ion. Taking this value as an estimate, the
proton clustering would easily make the energy tally for making the ions in the water
molecule appropriately negative, at 0.895 70.685 = 69.790 eVs. This energy yield
would allow water to both form its molecule and then melt into a liquid.
Note too that proton clustering would also make a water molecule polarized which
indeed it definitely is. As a result of this polarization, a lot of other molecules dissolve in
water, meaning they dissociate into positive and negative ions. This dissolution behavior
7
includes even the pure water itself: at any given moment in time, about one out of 10 of the
+
molecules in a sample of pure water is dissociated into H and OH ions. Hence we have
the phenomenon of pH with neutral set at 7.
A Molecule with Four Atoms
Co3C . (Like H 2 , the Co3C molecule involves only atoms of keystone elements [see
Appendix 4]. Unlike the other molecules treated so far, Co3C is a crystalline solid at
standard conditions, so no part of the heat released in forming its constituent ions is used in
getting to liquid or gas state.) Reported heat of formation +9.5 Kg-cals (the + meaning
heat is consumed in making this molecule) times conversion factor 0.043 yields
+0.4085 eVs. Probable electron assignments: 27 Co , one 25, two 30s; 6 C , 2.
Relevant model data about 27 Co :
The transition 27 Co 27 Co
++
(
takes IP1,1 27 + 27 26 )M 27 , or
( )
14.250 27 + 26.495 58.933 = 12.935 eVs, and
(IP1,27 27 IP1,25 25) M 27 , or

(1.980 27 1.289 25) 58.693 = (53.460 32.225) 58.693 = 0.362 eVs.
++
So the transition 27 Co 27 Co takes altogether 12.935 + 0.362 = 12.573 eVs.

The transition 27 Co 27 Co takes
IP1,1 ( 30 27 + 29 27 + 28 27 )M 27 , or
( )
14.25 28.460 + 27.982 + 27.495 58.933 = 20.296 eVs, and
(
IP1,30 30 IP1,27 27 ) M 27 , or
( ) (
4.242 30 1.980 27 58.933 = 127.260 53.460 58.933 = )
1.252 eVs.

So the transition 27 Co 27 Co takes altogether 20.296 1.252 =
21.548 eVs.
++
Interpretation concerning 27 Co : Transforming 3 neutral 27 Co into one 27 Co ion

and two 27 Co ions takes 12.573 + 2 (21.548) = 30.524 eVs.
Relevant model data about 6 C : (same as in CO 2 ):

++++
The transition 6 C 6 C takes altogether 22.188 eVs.
Interpretation concerning Co3C : Making the ions in the Co3C molecule takes
30.524 + 22.188 = 8.336 eVs. Evidently, all this energy, and a slight bit more, is
consumed in forming the molecule and its bulk-matter crystal structure.
It is encouraging that the calculation here produces a result that is reasonably
interpretable. It is cautioning that the calculation involves some rather small differences
between rather large numbers. This circumstance may be even worse for some molecules. If
so, related numerical problems would probably occur with traditional Quantum Chemistry as
well. Nature is a challenge for us all!
A Molecule with Five Atoms
CH 4 (Methane; another keystone-only molecule, like H 2 and Co3C ) Reported heat

of formation: 17.89 Kg-cals, times conversion factor 0.043 yields 0.769 eVs. Probable
electron assignments: 6 C , 10; 1 H , all zero.

Relevant model data concerning 6 C : The transition 6 C 6 C takes
IP1,1 ( 6 10 + 69 + 68 + 67 )M 6 , or
( )
14.250 7.746 + 7.348 + 6.928 + 6.481 12.011 = 14.250 28.503 / 12.011 =
(
33.816 , and IP1,10 10 IP1,6 6 ) M6 , or
( ) (
29.391 10 7.320 6 12.011 = 293.91 43.920 12.011 = )
20.813 eVs.

Interpretation concerning 6 C : The transition 6 C 6 C takes
33.816 20.813 = 54.629 eVs.
+
Relevant model data concerning 1 H (from Sect. 5): The transition 1 H 1 H takes
14.137 eVs.
+
Interpretation concerning 1 H : Turning 4 neutral 1 H atoms into 4 positive 1 H ions
takes 4 14.137 = 56.548 eVs. These four ions are really four naked protons. Recall the
case of two naked protons in the H 2O : they apparently formed a positive binary charge
cluster. So consider that the four naked protons in CH 4 could form two binary clusters, or
one four-fold cluster. The two-binaries configuration seems favored on energetic grounds,
and it seems to be confirmed on polarization grounds. Observe that the four-fold
configuration would produce a polarized molecule, maybe four times as strongly polarized as
H 2O , whereas the two-binary configuration allows the two binaries to seek opposite sides of

the central C ion, and so produce no net polarization of the CH 4 molecule. And note
that CH 4 is indeed not a polarized molecule.

The energy taken to make two binary proton clusters is related to, and probably very
similar to, twice the 70.685 eVs estimated for making the one binary proton cluster in
H 2 O ; i.e. 141.320 eVs.
Interpretation concerning CH 4 : Forming the ions in the CH 4 molecule takes
something like 54.629 + 56.548 141.320 = 139.401 eVs. This molecule readily
forms, and as bulk matter becomes a gas.
A Molecule with Six Atoms
CH 4O (Methyl alcohol). Reported heat of formation 48.10 Kg-cals for gas, times
conversion factor 0.043 yields 2.0683 eVs. Probable electron assignments: 6 C , 2; 1 H ,
one at 0, three at 2; 8 O , 10.
Relevant Model Data about 6 C (same as in CO 2 ):

++++
The transition 6 C 6 C takes altogether 22.188 eVs.
Relevant model data about 1 H (same as in H 2 ):

+
The transition 1 H 1 H takes 14.137 eVs and the transition 1 H 1 H takes
90.675 eVs.
Relevant model data about 8 O (part of the information given for O 2 ):

Interpretation concerning CH 4O : Forming the ions in the CH 4O molecule takes

17.040 + 14.137 + 3 (90.675) 27.379 = 268.227 eVs. This molecule readily
forms, and as bulk matter becomes a gas.
6. Analysis of a Much Larger Molecule

With Algebraic Chemistry, there is no real impediment to analyzing large molecules.
This can be demonstrated here with some suitably larger molecule. A socially significant one
is sucrose; C12 H 22O11 ; we do eat a lot of that one! It has 45 atoms and 182 electrons. That
qualifies it as much larger, I do believe. The probable electron assignments are: C s, 6 at
2 , 6 at 10 ; H s, all 0 s; O s, all 10 s. The relevant model data all comes from Sect. 5:
++++
Concerning 6 C : From CO 2 , the transition 6 C 6 C takes 22.188 eVs; from
CH 4 , the transition 6 C 6 C takes 54.629 eVs.

+
Concerning 1 H : From H 2 , the transition 1 H 1 H takes 14.137 eVs.

Concerning 8 O : From O 2 The transition 8 O 8 O takes 27.379 eVs.
Interpretation concerning 6 C : Transforming 6 neutral 6 C atoms into 6 positive

++++
6C ions takes 6 22.188 = 133.128 eVs, and transforming 6 neutral 6 C atoms to

6 negative 6 C ions takes 6 (54.629) = 327.774 eVs.
Interpretation concerning 1 H : Transforming 22 neutral 1 H atoms into 22 positive

+
1H ions takes 22 14.137 = 311.014 eVs. [Do these then form binary clusters?
Probably not; where would they go?]
Interpretation concerning 8 O : Transforming 11 neutral 8 O atoms into 11 negative

8O ions takes 11 (27.379) = 301.169 eVs.
Interpretation concerning C12 H 22O11 : Forming the ions in the C12 H 22O11 molecule
takes
133.128 327.774 + 311.014 301.169 = 184.801 eVs .
I wanted to compare the total heat of ion formation modeled here and the heat of bulk
matter formation reported in Langs Handbook of Chemistry. However, the latter information
was not available in the rather old edition that had provided all the other heat data used in this
paper. The modern-day web revealed reason for the omission: the presumed direct synthesis
reaction for sucrose,
1
12C(s) + 11H 2 (g) + 5 O2 (g) C12 H 22O11(s) + heat ,
2
was never accomplished in the lab. Note that all species on the left side were reported to have
zero heat of formation, and that sucrose did form naturally, and would have been expected to
have a negative heat of formation. The assumed condition for the reaction to work would
likely have been that the heats of formation be less negative on the left than on the right, so
the reaction would have looked feasible. So its actual non-feasibility would have been a big
surprise.
Algebraic Chemistry reveals the reason for the failure. The prerequisite for the reaction to
work is really about the energy taken to form ions. From Sect. 5, forming all the ions in all
the species on the left side of the sucrose synthesis reaction takes
12 0 + 11 (76.538) + 5.5 (9.817) = 841.918 53.994 = 895.912 eVs.
This is more negative than the estimated 184.801 eVs to form the ions in the sucrose
molecule on the right. This situation indicates that the presumed direct synthesis reaction for
sucrose does not go to the right, as it is depicted.
The web also provided a sucrose heat of formation instead inferred from its combustion
reaction,
C12 H 22O11(s) + 12O 2 (g) 12CO 2 (g) + 11H 2O + heat
Since this reaction definitely works, Algebraic Chemistry should be able to confirm that
fact. Forming the ions on the left side of the reaction is estimated to take
184.801 + 12 (9.817) = 302.605 eVs, whereas forming the ions on the right side is
estimated to take 12 (32.570) + 11 (70.685) = 390.840 779.535 =
1168.375 eVs, which is indeed more negative. This says the sucrose combustion reaction
does indeed run to the right as depicted.
But the reported heat of formation inferred from the sucrose combustion reaction is not
reported in the Kg-cal/mole units that the heats of formation for the other molecules quoted
earlier were; it is instead reported in Kjoules/mole (here abbreviated Kjs). So the needed
conversion factor changes,
from
Kilogram-calories to joules joules to ergs 4186 107

= 0.043
to
Kjoules to joules joules to ergs 103 107
= 0.0104
The reported 2226.1 Kjs is 23.25 eVs. This is much less in magnitude than the
184.801 eVs here calculated to form the ions in sucrose. This means that a very large
portion of the energy generated making the ions in sucrose is then tied up in making the
molecule and its crystal structure. Being so energy-packed, it is no wonder that sucrose
crystals dissolve so easily in water!
7. Analyses of Current Benchmark Reactions

The history of the sucrose problem highlights the importance of studying not only
molecules, but also reactions. There was recently a status report on efforts in Quantum
Chemistry in the form of a collection of papers collectively titled Challenges in Theoretical
Chemistry [Science Magazine, October 2008]. Among the papers included was one entitled
Quantum Dynamics of Chemical Reactions, by D.C. Clary [5].
A Reaction Involving Four Atoms
In [5] Clary set as a benchmark a reaction involving four atoms:

OH + H 2 H 2O + H . He cited extensive calculations on this reaction using the wave
packet method [6,7]. We can also analyze this same reaction from the viewpoint of Algebraic
Chemistry, as follows:
Analysis of the Left Side of the Reaction, OH + H 2 :
Analysis of OH : Probable electron assignments: 8 O , 9; 1 H , zero.

From Sect. 2, the transition 8 O 8 O takes IP1,1 8 9 M8 , or
14.250 8.485 / 15.999 = 7.558 eVs, and (IP1,9 9 IP1,8 8) / M8 , or

(20.254 9 13.031 8) / 15.999 = (182.286 104.248) / 15.999 =
4.878 eVs.
+
From Sect. 5, H 2 , the transition 1 H 1 H takes 14.137 eVs. So forming the ions
in the OH radical takes 7.558 4.878 + 14.137 = 1.701 eVs.
Analysis of H 2 : From Sect. 5, the formation of the ions in the H 2 molecule takes
76.538 eVs.
Forming all of the ions involved in the left side of the reaction, OH + H 2 , takes
1.701 76.538 = 74.837 eVs.
Analysis of the Right Side of the Reaction, H 2O + H :
Analysis of H 2O . From Sect. 5, the formation of the ions in the H 2O molecule is

estimated to take 69.790 eVs.
Analysis of H : None required.
So formation of the ions involved in the H 2O + H right side of the reaction is estimated
to take 69.790 eVs. This is less negative than the 74.837 eVs on the left side. So this
reaction does not run to the right, as it is depicted, and so is not a realistic target for analysis
by Quantum Chemistry.
But note: The OH on the left side of the reaction, OH + H 2 , is not usually seen that

way, as a neutral species; it is usually seen as a negative ion, OH . So perhaps we should
look at some variations on the stated reaction OH + H 2 H 2O + H . For example,

consider OH + H 2 H 2O + H + e .
Analysis of the New Left Side of the Reaction, OH + H 2 :

Analysis of OH : Probable electron assignments: 8 O , 10; 1 H , zero. From Sect. 5,
O 2 , the transition 8 O 8 O takes 27.379 eVs. From Sect. 5, H 2 , the transition

+
1H 1H takes 14.137 eVs. So forming the ions in the OH radical takes
27.379 + 14.137 = 13.242 eVs.
76.538 eVs.

So formation of the ions involved in the left side of the reaction, OH + H 2 , takes
13.242 76.538 = 89.780 eVs. This is even worse than the 74.837 eVs for the
original left side, OH + H 2 .
But note: the H on the right side of either OH + H 2 H 2O + H or the alternative
OH + H 2 H 2O + H + e is not usually seen like that, as a neutral atom; it is more

+
often seen as H or H . So perhaps we should also look at two further variant reactions:
OH + H 2 H 2O + H + + 2e and OH + H 2 H 2O + H .
Analysis of the Common Left Side of these two Teactions, OH + H 2
From above, formation of the ions involved takes 89.780 eVs.
Analysis of the Two Right Sides of the Two Reactions, H 2O + H + + 2e and
H 2O + H
Analysis of H 2O . From Sect. 5, the formation of the ions in the H 2O molecule is

estimated to take 69.790 eVs.
+ +
Analysis of H and H : From Sect. 5, H 2 , the transition 1 H 1 H takes
14.137 eVs, and the transition 1 H 1 H takes 90.675 eVs.

Analysis of 2e : None required.
+
So in the first case, the right side of the reaction H 2O + H + 2e is estimated to take
69.790 + 14.137 = 55.653 eVs, whereas in the second case, the right side of the

reaction H 2O + H is estimated to take 69.790 90.675 = 160.465 . The first case
still does not run to the right as depicted, but the second case does, and very strongly so. So
only this one last variant form of the reaction involving these four atoms appears to be a
realistic target for analysis by Quantum Chemistry.
A Reaction Involving Six Atoms
In [5], Clary also cited a six-atom reaction, printed as H + CH 4 CH 3 + H , but
probably really meaning H + CH 4 CH 3 + H 2 , for which the wave-packet calculations

require significant approximations [8], but for which some recent progress has been achieved
by exploiting permutations of identical atoms [9]. We can also look at this reaction from the
viewpoint of Algebraic Chemistry.
Analysis of the Left Side of the Reaction, H + CH 4 :
Analysis of H : None required.

Analysis of CH 4 : From Sect. 5, forming the ions in the CH 4 molecule takes
something like 139.401 eVs.
So forming the ions involved in the left side of the reaction, H + CH 4 , takes something
like 139.401 eVs.
Analysis of the Right Side of the Reaction, CH 3 + H 2 :
Analysis of CH 3 : Probable electron assignments: 6 C , 9; 1 H , all zero.

Relevant model data on 6 C : From Sect. 2, the transition 6 C 6 C takes
IP1,1 ( 69 + 68 + 67 )M 6 or
( )
14.250 7.348 + 6.928 + 6.481 12.011 = 24.626 eVs,
(
and IP1,9 9 IP1,6 6 ) M6 , or (20.254 9 7.320 6) 12.011 =
( )
182.286 43.92 12.011 = 11.520 eVs.
+
Relevant model data on 1 H : From Sect. 5, H 2 , the transition H H takes
14.137 eVs, so creating 3 H + ions takes 3 14.137 = 42.411 eVs.

Interpretation concerning CH 3 : Forming the ions in the CH 3 molecule takes
24.626 11.520 + 42.411 = 6.265 eVs. Observe that this is significantly positive,
meaning this molecule is not easy to make.
14.137 90.677 = 76.538 eVs.
So forming the ions involved in the right side of the reaction, CH 3 + H , takes
6.265 76.538 = 70.273 eVs. This is less negative than the 139.401 eVs for forming
the ions on the left side of the reaction, H + CH 4 , so the reaction
H + CH 4 CH 3 + H 2 does not run to the right as it is depicted.

But again, some aspects of the reaction H + CH 4 CH 3 + H 2 are not realistic: the
H seen on the left is usually seen as H + or H , and the CH 3 seen on the right is usually

seen as (CH 3 ) . Since making a reaction that can run to the right requires less negative on
the left and/or more negative on the right, the best candidate reaction appears to be:
H + + CH 4 + 2e (CH 3 ) + H 2 .
+
Change on the left side: From Sect. 5, H 2 , the transition H H takes
14.137 eVs. So forming all the ions on the left side of the reaction now takes
14.137 139.401 = 125.264 eVs.

Change on the right side: Analysis of (CH 3 ) ; Probable electron assignments: 6 C ,
10; 1 H , all zero. Relevant model data on 6 C : From Sect. 5, CH 4 , the transition

6C 6C takes 54.629 eVs. So forming all the ions on the right side of the
reaction now takes 54.629 + 42.629 76.538 = 88.538 eVs.
This is not enough change to make a reaction that runs to the right as depicted. So this
family of reactions appears not very promising for study with the techniques of Quantum
Chemistry.

At the present time, many of our most talented people, armed with our most powerful
computing capabilities, are committed to applying of traditional Quantum Mechanics to the
problems of interest for Quantum Chemistry. In this book, you are likely to see many current
accomplishments reported, along with future agendas laid out. So Quantum Chemistry is
today a work in progress.
The exercises documented in the present paper demonstrate that while the work in
Quantum Chemistry continues to develop, we can at the same time accomplish some
preliminary analyses by applying the techniques of Algebraic Chemistry. Such exercises can
be useful, for example, in planning computational and experimental investigations. We can
calculate the amount of heat that the formation of an atomic ion in a molecule will consume
(negative heat for natural formation). We can predict if a hypothetical chemical reaction may
fail to transpire naturally (ion-formation heat more negative on the left side of the reaction
than on the right side).
Extensions of the present work are also possible. One that is important, although beyond
the scope of the present paper, is the calculation of energies for lots more ions, in lots more
molecules, involved in lots more reactions. Another extension is less obvious, but just as
necessary: the calculation of energies, not just for formation of the ions in molecules, but also
for the settlement of ions into molecules, and the organization of molecules into the particular
states of matter for which their data are quoted: solid state, liquid state, or gas state. And
sometimes data might be quoted for even more specifically described states, such as: solid
crystal, amorphous solid, super-conducting, polymer, plastic, pure liquid,
aqueous solution, super fluid,, molecular beam, plasma,etc. So there is a lot of
scope for future development in the line of work reported here.
Appendix 1. Essential Data about First-Order Ionization

Potentials
The following Tables capture the input data that one needs to conduct analyses of the
type introduced in this paper.
Table 1. Periods 1, 2 and 3
Charge Mass Ionization IP = Ionization Model Model

Element Z M Potential Potential M / Z IP IP
H 1 1.008 13.610 13.718 14.250 0
He 2 4.003 24.606 49.244 49.875 35.625
Li 3 6.941 5.394 12.480 12.469 1.781

Be 4 9.012 9.326 21.011 23.327 9.077
B 5 10.811 8.309 17.966 17.055 2.805
C 6 12.011 11.266 22.551 21.570 7.320
N 7 14.007 14.544 29.101 27.281 13.031
O 8 15.999 13.631 27.260 27.281 13.031
F 9 18.998 17.438 36.810 34.504 20.254
Ne 10 20.180 21.587 43.562 43.641 29.391
Na 11 22.990 5.145 10.753 10.910 3.340

Mg 12 24.305 7.656 15.506 16.565 2.315
Al 13 26.982 5.996 12.444 14.923 0.673
Si 14 28.086 8.154 16.357 18.874 4.624
P 15 30.974 10.498 21.677 23.871 9.621
S 16 32.066 10.373 20.790 23.871 9.621
Cl 17 35.453 12.977 27.063 30.192 15.942
Ar 18 39.948 15.778 35.017 38.186 23.936
The data are separated into blocks corresponding to the periods in the Periodic Table. A
few useful comments are interleaved with the blocks to complete the display.
The IP Model to which the Tables refer is detailed in Appendix 2.
Observe the M / Z scaling that is introduced to convert the raw ionization-potential data
into the IP data to be modeled mathematically. The reason for the M / Z scaling emerges
from the physical model in Appendix 3. Basically, the physical model shows that the
measurable ionization potentials of elements do, to first approximation, scale with Z / M .
So raw ionization-potential data is very element specific, and in fact it is very isotope
specific. To create information that is not so element/isotope specific, we remove that Z / M
scaling by applying its inverse M / Z .
Observe finally that these Tables refer only to neutral atoms. The scaling to similar
information for ions is worked out in Appendix 3.
Table 2. Period 4

K 19 39.098 4.346 8.944 9.546 4.704
Ca 20 40.078 6.120 12.265 13.057 1.193
Sc 21 44.956 6.546 14.013 13.057 1.193
Ti 22 47.867 6.826 14.851 13.638 0.612
V 23 50.942 6.743 14.934 14.244 0.006
Cr 24 51.996 6.774 14.676 14.877 0.627
Mn 25 54.938 7.438 16.345 15.539 1.289
Fe 26 55.845 7.873 16.911 15.539 1.289
Co 27 58.933 7.863 17.163 16.229 1.980
Ni 28 58.693 7.645 16.026 16.951 2.701
Cu 29 63.546 7.728 16.934 17.705 3.455
Zn 30 65.390 9.398 20.485 18.492 4.242
Ga 31 69.723 6.006 13.509 14.494 0.244
Ge 32 72.610 7.905 17.936 17.860 3.610
As 33 74.922 9.824 22.303 22.007 7.757
Se 34 78.960 9.761 22.669 22.007 7.757
Br 35 79.904 11.826 26.998 27.116 12.866
Kr 36 83.800 14.015 32.623 33.412 19.162
One key to the task of modeling ions is to separate the IP s into two parts: one being a
baseline amount corresponding to the Hydrogen IP , IP1, Z 14.250 , and the other being
the increment from the Hydrogen IP ; i.e., IP1, Z = IP1, Z IP1,1 = IP1, Z 14.250 eVs.
For neutral atoms, the two parts both scale with Z . For ions, the Z -scaling generalizes
differently for the two parts. The baseline 14.250 eVs scales with Ze Z M , where Ze is
the electron count and Z M is the nuclear charge. (Appendix 3). The IP just scales with
Ze .
The way all these data are used to work out information for ions is to sum up the
information for the desired number of single-electron removals. In the case of the baseline
14.250 eV contributions, that results in a sum of various square roots. In the case of the IP
contributions, a lot of cancellations occur, leaving just two terms, one from the beginning
state and one from the end state.
Observe that the Periods differ in length, and the remaining ones will be much longer
than these first three.
The periods also differ in dips from the end of one period to the start of the next period.
The dips go: 1 / 4 , 1 / 4 , 1 / 4 , and then 2 / 7 (the inverse of the 7 / 2 ) thereafter. That is,
Period 2 is 7 / 2 1 / 4 = 7 / 8 below Period 1, Period 3 is 7 / 8 below Period 2, and Period
4 is 7 / 8 below Period 3. All the rest of the periods will start, and end, just where Period 4
did.
The result of the dips is that the elements mid period generally have IP s that are very
similar to that of Hydrogen. There are other functional similarities as well, so that the whole
list of elements that are exactly mid period is called out and featured by the terminology
keystone elements (Appendix 4).
Table 3. Period 5

Rb 37 87.620 5.695 9.657 9.546 4.704
Sr 38 88.906 6.390 13.132 13.057 1.193
Y 39 91.224 6.846 14.567 13.057 1.193
Zr 40 92.906 6.888 15.614 13.638 0.612
Nb 41 92.906 6.888 15.608 14.244 0.006
Mo 42 95.940 7.106 16.232 14.877 0.627
Tc 43 98.000 7.282 16.597 15.539 1.289
Ru 44 101.070 7.376 16.942 15.539 1.289
Rh 45 102.906 7.469 17.080 16.230 1.980
Pd 46 106.420 8.351 19.319 16.951 2.701
Ag 47 107.868 7.583 17.403 17.705 3.455
Cd 48 112.411 9.004 21.087 18.492 4.242
In 49 114.818 5.788 13.563 14.494 0.244
Sn 50 118.710 7.355 17.462 17.860 3.610
Sb 51 121.760 8.651 20.655 22.007 7.757
Te 52 127.600 9.015 22.120 22.007 7.757
I 53 126.904 10.456 25.037 27.116 12.866
Xe 54 131.290 12.137 29.508 33.412 19.162
Table 4. Period 6

Cs 55 132.905 3.900 9.425 9.546 4.704
Ba 56 137.327 5.218 12.796 13.057 1.192
La 57 138.906 5.581 13.600 12.393 1.857
Ce 58 140.116 5.477 13.232 12.583 1.667
Pr 59 140.908 5.425 12.957 12.776 1.474
Nd 60 144.240 5.498 13.217 12.972 1.278
Pm 61 145.000 5.550 13.192 13.171 1.079
Sm 62 150.360 5.633 13.660 13.374 0.876
Eu 63 151.964 5.674 13.687 13.579 0.671
Gd 64 157.250 6.141 15.089 13.579 0.671
Tb 65 158.925 5.851 14.305 13.787 0.463
Dy 66 162.500 5.934 14.609 13.999 0.251
Ho 67 164.930 6.027 14.836 14.213 0.037
Er 68 167.260 6.110 15.029 14.431 0.181
Tm 69 168.934 6.183 15.137 14.653 0.403
Yb 70 170.040 6.255 15.463 14.878 0.627
Lu 71 174.967 5.436 13.395 17.860 3.610
Hf 72 178.490 7.054 17.487 18.755 4.505
Ta 73 180.948 7.894 19.568 19.696 5.446
W 74 183.840 7.988 19.844 20.684 6.434
Re 75 186.207 7.884 19.574 21.721 7.471
Os 76 190.230 8.714 21.811 21.721 7.471
Ir 77 192.217 9.129 22.788 22.811 8.560
Pt 78 195.076 9.025 22.571 23.955 9.705
Au 79 196.967 9.232 23.019 25.156 10.906
Hg 80 200.530 10.446 26.184 26.418 12.168
Tl 81 204.383 6.110 15.417 16.515 2.265
Pb 82 207.200 7.427 18.768 19.696 5.446
Bi 83 208.980 7.293 18.361 23.490 9.240
Po 84 209.000 8.423 20.958 23.490 9.240
At 85 210.000 28.015 13.765
Rn 86 222.000 10.757 27.769 33.412 19.164
There are many tantalizing facts modeled but not yet understood:
Observe that the IP Model rise on all periods is 7 / 2 . The meaning of the
universal factor 7 / 2 is not yet known; it is at present just a fact of Nature.
Observe that, except for Period 1, the IP always start negative at the beginning of
a period, and ends positive at the end of the period. And the positive increments are
larger than the negative ones. The reason is that all this data falls into a simple
pattern when plotted on a log scale, as shown in Appendix 2. On the log scale, the
increments up and down are similar in magnitude.
Observe too that within each period, there are sub periods. These correspond to runs
of nominal single-electron quantum states being filled. On the log scale, the sub
periods form straight-line segments. That means they follow power laws. And the
slopes are simple functions of the quantum numbers of the nominal single-electron
states being filled. The physical meaning of these functions is not yet known.
Table 5. Period 7

Fr 87 223.000 9.546 4.704
Ra 88 226.000 5.280 13.560 13.057 1.193
Ac 89 227.000 6.950 17.727 12.393 1.857
Th 90 232.038 6.089 15.699 12.583 1.667
Pa 91 231.036 5.892 14.959 12.776 1.474
U 92 238.029 6.203 16.050 12.972 1.277
Np 93 237.000 6.276 15.994 13.171 1.079
Pu 94 244.000 6.068 15.752 13.374 0.876
Am 95 243.000 5.996 15.337 13.579 0.671
Cm 96 247.000 6.027 15.507 13.579 0.671
Bk 97 247.000 6.234 15.875 13.787 0.463
Cf 98 251.000 6.307 16.154 13.999 0.251
Es 99 252.000 6.421 16.345 14.213 0.037
Fm 100 257.000 6.504 16.716 14.431 0.181
Md 101 258.000 6.587 16.827 14.653 0.403
No 102 259.000 6.660 16.911 14.877 0.627
Lf 103 17.859 3.610
Rf 104 18.755 4.505
Db 105 19.696 5.446
Sg 106 20.684 6.434
Bh 107 21.721 7.471
Hs 108 21.721 7.471
Mt 109 22.811 8.561
Uun 110 23.955 9.705
Uuu 111 25.156 10.906
Uub 112 26.418 12.168
??? 113 16.515 2.265
??? 114 17.019 2.769
??? 115 23.490 9.240
??? 116 23.490 9.240
??? 117 28.015 13.765
??? 118 33.412 19.162
There are two more periods remaining, and their Tables have some blank spaces where
this author did not find raw data available. Predictions, however, are no problem to provide,
and are listed in anticipation that the real data will eventually emerge for comparison.
Appendix 2. The Algebraic Model for Ionization Potentials
10000
1000
100
10
1
0 10 20 30 40 50 60 70 80 90 100 110 120
Figure A2.1. Ionization potentials, scaled by M/Z and modeled algebraically.
Figure A2.1 depicts the behavior of IP s for all elements (nuclear charge Z = 1 to
Z = 120 shown). Element Z actually allows Z ionization potentials, but for larger Z ,
many IP s are not so easy to measure. Readily available data go only to seventh order, so
that is how many orders are shown here.
The points on Figure A2.1 are measured IP eVs, scaled for comparison with each other
as indicated by the new theory summarized in the next Appendix. The scale factor M / Z ,
where M is nuclear mass number and Z is nuclear charge, is in no way indicated by
traditional QM.
The lines on Figure A2.1 represent the algebraic model for IP s, rendered in its current
best state of development. The model is capable of producing plausible estimates for all
M / Z -scaled IP s for all IO s, even beyond those measured, and all Z s, even beyond
those known to exist.
The model-development approach is an example data mining. Figure A2.1 has less than
400 out of approximately 5000 desired data points. But that is enough data points to reveal a
pattern. The work involved is a good example of continuing positive feedback between theory
and experiment. Theory shows what to look for; experiment shows what to try to understand.
The first step in model development was fundamentally observational: for IO = 1 , with
M / Z scaling, there are consistent rises on periods, and consistent mid-period similarity to
Hydrogen ( Z = 1 ). For IO > 1 , there is consistent scaling with IO . There are several ways
that the scaling can be described, and the simplest way found so far is summarized as follows:
1) First-order IP s contain ALL the information necessary to predict ALL higher-order
IP s via scaling; 2) Every ionization potential IP of any order IO can be expressed as a
function of at most two first-order IP s; 3) For a given ionization order IO > 1 , the
ionization potentials for all elements start at element Z = IO , and follow a pattern similar to
the IP s for IO = 1 , except for a shift to the right and a moderation of excursions. Details
are given in [1].
Figure A2.2. First-order IP s: map of main highways through the periods.

Only the first-order IP s are needed in the present work. They follow a definite pattern,
detailed below. For every period, the rise is 7 / 2 , and the drops from one period to the next
start at 7 / 8 and go to unity. Figure A2.2 shows the data used and the pattern inferred
concerning periods.
Within each period, there are internal rises keyed to the nominal quantum numbers of
single-electron states being successively filled. Eqs. (A2-1a-1b) and Figure A2-3 give this
level of detail.
incremental rise = total rise fraction (A2-1a)

fraction = (2l + 1) / N 2 ( N l) / l (A2-1b)

N l fraction l fraction l fraction l fraction

1 0 1
2 0 1/2 1 3/4
2 0 1/3 1 3/4
3 0 1/4 2 5/18 1 2/3
3 0 1/4 2 5/18 1 2/3
4 0 1/4 3 7/48 2 5 / 16 1 9 / 16
4 0 1/4 3 7/48 2 5 / 16 1 9 / 16
Figure A2.3. First-order IP s: map of local roads through the periods.

The pattern described above has been inferred from the data. Let us be quite clear:
knowledge about the pattern is presently wholly ontic (about what the observable facts are);
we also need knowledge that is epistemic (about why the facts are that way). We definitely
do not have this yet.
Appendix 3. Hydrogen, the Basis for all Scaling Laws

The work reported in this paper derives from a sequence of earlier works [1-4] that are
reviewed very briefly in this Appendix. The story really goes all the way back to Maxwell [4].
The differential equations that he bequeathed us admit a large diversity of particular solutions.
In any application, the trick lies in choosing the right particular solution to fit the problem. An
imperfect choice was made around the turn of the twentieth century. The problem was to
describe an electromagnetic signal as the basis for developing special relativity theory (SRT).
Einstein imagined a signal pulse, presumably of finite energy, that would propagate like a
wave, infinite in extent and infinite in energy, forever undistorted at speed c = 1 0 0 ,
where 0 and 0 are electric permittivity and magnetic permeability of free space. Actually,
that scenario isnt possible. We were given a warning in the well-known phenomenon of
diffraction: when limited in directions transverse to the nominal propagation direction,
electromagnetic waves always develop a spread in propagation directions. We should have
wondered what would happen if the electromagnetic wave were also confined in the
longitudinal direction as it would have to be, to make a wave packet of finite energy. Would
some kind of spread result? Indeed, wouldnt there have to be some kind of longitudinal
spread in order for the concept of wavelength to ever to become applicable? Well yes, it
turns out that, following emission from a source, a pulse expands in the longitudinal direction,
and preceding absorption into a receiver, the spread-out energy distribution contracts to pulse
again.
Redeveloping SRT to use the more realistic model for an electromagnetic signal leads to
a new theory that is expanded with respect to the original one. I call it Expanded SRT. It
includes all the symbols and formulae that the original SRT contains. But it also includes an
additional symbol, and additional formulae, and more precise interpretations of the old ones.
The additional symbol is V for old-fashioned Galilean speed, distinguished from Einsteinian
speed v , which is limited to light speed c . Galilean speed is not limited.
With SRT thus extended, it is appropriate to review decisions that were based on the
earlier ideas. One of these concerned the applicability of Maxwells electromagnetic theory
(EMT) to problems at the small scale of atoms. Traditional QM was developed on the
presumption that Maxwell theory could not apply. The reasoning was that an electron orbiting
around a nucleus should produce radiation, which would rob the orbit of energy, causing
collapse of the atomic system. But the Expanded SRT shows that the system also has a
second physical process going on; namely, internal torquing. This one provides an energy
gain mechanism. So it is possible to have the atomic system persist with a balance between
the two physical processes.
The new internal torquing mechanism is characterized by an energy gain rate
PT = (e4 / mp ) c(re + rp )3 . (A3-1)
The more familiar radiation mechanism is characterized by an energy loss rate
PR = (25 e6 / me2 ) 3c3(re + rp )4 . (A3-2)
4
This is enhanced by a factor of 2 over the totally familiar Larmor dipole formula. The
enhancement is caused by Thomas rotation of the atomic system, which is in turn caused by
non-central forces, which were absent from Newtonian physics, and were not originally
noticed in Maxwellian physics.
The balance between the two mechanisms occurs when PT = PR . At the balance point
for the Hydrogen system, we have Eq. (1) in the main text; i.e.,
e2 (re + rp ) = 3c 2 me2 25 mp . (A3-3)
for the magnitude of the potential energy of the one electron in the Hydrogen atom.
Eq. (A3-3) provides the basis from which to build. The extension to Deuterium and/or
Tritium requires that the proton mass mp be replaced with a more generic nuclear mass M
and that rp be replaced by rM . Then we have Eq. (2) in the main text; i.e.,
e2 (re + rM ) = 3c 2 me2 25 M . (A3-4)

for the magnitude of the potential energy of this more massive system.
The extension for a neutral atom with nuclear charge number Z , involves Z electrons
as well. To develop an opinion on this question, we must return to Eqs. (A3-1) and (A3-2).
2 2 2 2 2 2
All the factors of e change to Z e , and the factor of me changes to Z me . PT = PR
4 6 2 4
becomes Z PT = ( Z / Z ) PR = Z PR . So nothing happens to the equality (A3-4). But
for the more charged system, the magnitude of the potential energy becomes Eq. (3) in the
main text; i.e.,
Z 2e2 (re + rp ) = Z 2 3c 2 me2 25 M . (A3-5)
This scaled-up expression represents the magnitude of the total potential energy of the
system involving Z protons and Z electrons. What is then comparable to the ionization
potential for removing a single electron is Eq. (4) in the main text; i.e.,
( ) (
Z e2 (re + rM ) = Z 3c 2 me2 25 M (Z / M ) 3c 2 me2 25 ) . (A3-6)
Thus we see the Z / M scaling that is predicted for raw-data ionization potentials, and
so is cancelled out by M / Z scaling to produce the IP s documented in Appendix 1 and
used in Appendix 2.
More generally, if the atom is in an ionized state, we have a distinct electron count Ze
and proton count Z p . For the baseline nuclear-orbit part, we have for the total system Eq. (5)
in the main text; i.e.,
( )(
Z p Ze e2 (re + rM ) = Z p Ze M 3c 2 me2 25 ) . (A3-7)
What is then generally comparable to the nuclear-orbit part of the ionization potential for
removing a single electron? To develop an opinion on this question, we must return again to
2 2
Eqs. (A3-1) and (A3-2). Clearly, all of the factors of e change to Z p Ze e . It is as if all
factors of e changed to Z p Ze e . Removal of one electron is then like removal of one
Z p Ze e charge. What is comparable to the ionization potential for removing a single

electron is then Eq. (6) in the main text; i.e.,
Z p Ze e2 (re + rM ) = (Z Z p e )(
M 3c 2 me2 25 ) . (A3-8)
Appendix 4. The Periodic Arch

Figure A4.1 shows a new and convenient presentation of the Periodic Table from [1]. It is
called the Periodic Arch (PA).
Figure A4.1. The Periodic Arch (PA).
The keystone elements referred to in the main text are the ones that fall at the keystone
positions of the successive layers of the PA. They are important as facilitators of molecule
formation because they can give or take electrons in equal numbers. The terminology
keystone element is appropriate for many other reasons as well. Hydrogen 1 H is certainly
the keystone for all of present-day physical analysis of atoms. Carbon 6 C is certainly the
keystone for all of organic chemistry and biological life. Silicon 14 Si is certainly the
keystone for present-day technological life. Cobalt 27 Co is not so famous, but it lies
between Iron 26 Fe and Nickel 28 Ni , and is functionally better than either of them: harder,
more corrosion resistant, and more heat resistant. And, like Iron, it is much strengthened by
the addition of a trace of Carbon that other keystone element. We humans are currently
more than three millennia into our Iron Age, which, with the help of Carbon and other trace
additives, has morphed into our Steel Age. Had Cobalt been more plentiful on this planet,
this might have been our Cobalt/Steel Age. Rhodium 45 Rh is also not so famous, mainly
because it is not so plentiful, but it is good for plating and alloying. The remaining keystone
elements, Ytterbium 70Yb , and Nobelium 102 No , remain to be exploited very much.
Acknowledgments
A number of individuals have played important roles in fostering the development of this
whole line of research. I am especially grateful to Michael C. Duffy, Ruggero M. Santilli, and
Mihai V. Putz.
References and Notes

[1] Whitney, C.K. Closing in on Chemical Bonds by Opening up Relativity Theory. Int. J.
Mol. Sci. 2008, 9, 272-298.
[2] Whitney, C.K. Single-Electron State Filling Order Across the Elements. Int. J. Chem.
Model. 2008, 1, 105-135.
[3] Whitney, C.K. Visualizing Electron Populations in Atoms. Int. J. Chem. Model. 2008,
1, 245-297.
[4] Whitney, C.K. Recent Progress in Algebraic Chemistry. Computational Chemistry:
New Research, Frank Columbus, Ed., Nova Science Publishers, in press.
[5] Clary, D.C. Quantum Dynamics of Chemical Reactions. Science 2008, 321, 789-791.
[6] Zhang, D.H., Zhang, J.Z.H., J. Chem. Phys. 1994, 101, 1146.
[7] Zhang, D.H., J. Chem. Phys. 2006, 125, 133102.
[8] Yang, M.H.; Zhang, D.H., Lee, S.Y., J. Chem. Phys. 2002, 117, 9539.
[9] Zhang, X., Braams, B., Bowman, J.M., J. Chem. Phys. 2006, 124, 021104.
Chapter 11
QUANTUM AND ELECTRODYNAMIC VERSATILITY

OF ELECTRONEGATIVITY AND CHEMICAL HARDNESS
Mihai V. Putz*
Abstract
Aiming to affirm specific physical-chemical quantities of electronegativity and hardness as
the major electronic indicators of structure and reactivity, their systematic density functional,
as well their quantum and electrodynamic field formulations are presented; it may serve for
analytical studies of chemical bonding, reactivity, aromaticity, up to the biological activity
modeling of atoms in molecules and in nanostructures.
1. Introduction
In the last years, the first rate scientific research was mainly focused on the synergistic
approaches of the structure and properties of the natural complex systems at the quantum
chemical level [1-7].
Yet, while the pure physics still struggles on the great unification paradigm through the
fundamental forces in nature, being in the last decades subject to a continuous reform, a
similar attitude is now emerging in chemistry, at the quantum level of representation, related
with the existing natural chemical bonds: the ionic, covalent, metallic, hydrogenic and the van
der Walls (as driven, induction and diffusion) ones. Because the types of chemical bonds
coexist in various degrees and combination through the matter organization, only a unitary
quantum treatment, based on the first physical-chemical principles, can release an estimation
of the structure-properties correlations across the complex natural nano-systems: metals,
clusters, fullerenes, liquid crystals, polymers, ceramics, biomaterials, metaloenzymes. As a
*
E-mail addresess: mvputz@cbg.uvt.ro, mv_putz@yahoo.com. Tel: +40-256-592633; Fax. +40-256-592620,
252 Mihai V. Putz
synergistic field of research, the nanosystems have received many connotations. When the
spatiality of the chemical bond is studied, e.g., when the atomic systems condensate into a
smaller volume than of the isolated components, the arising composite nanosystems display
exceptional properties of coherences, used afterwards in processing, storing and
communication of the quantum information [8-10]. On the other hand, when dealing with the
chemical concentration of elements, it has already been proven that the range of nano-molar
better reflects the complex bio organic and inorganic combinations, especially when
focusing on the doze zones of responses for an essential element, with a role in selection or
inhibition of a certain biological function in organisms, with effects on the growth and
reproduction of cells and living organisms [11].
This way, a unitary picture to link and flexibly adapt the quantum mechanical formalisms
at the chemical bonding level was intensively searched [12]. In such studies, it was recently
established that for an adequate treatment in the quantum space of the polyatomic
combinations stays the electronic density (r ) rather than the already historical wave
function (r1 ,...rN ) as the main variable for a system with N electrons. This because, on the
contrary to the wave function, the electronic density is an experimentally detectable quantity,
is defined in the real three-dimensional space, and not within a 3N Hilbert abstract one, being
also directly related with the total number of electrons in the concerned system through the
functional relation [13-20]:
(r)dr = N (1)
Therefore, the electronic density receives the central role within the newest quantum
paradigm of matter, the Density Functional Theory (having Walter Kohn as its father, Nobel
laureate in Chemistry for this theory in 1998) [15].
On the other hand, the reactivity indices studies are essential for indicating the
propensity of a multielectronic system to participate in a chemical reaction. At the molecular
level, these indices are defined in order to quantitatively measure the chemical reactivity,
while at the biomolecular level they are associated with the biological activity. Thus, as the
reactivity indices are informationally placed at the interface between the electronic systems
stability and their tendency to transform and combine, they are mathematically introduced as
the integral functions of the electronic density function, releasing the so-called electronic
density functionals as the efficient tool for the global prediction of the electronic properties of
the investigated nanosystems [21].
Although the Density Functional Theory offers concepts, e.g., the density functionals, the
reactivity indices or the localization functions, with an exact formal character, still the
computational effort to evaluate the electronic densities for the polyatomic systems is often
immense and not without being susceptible to errors from the numerical recipes used. Also,
many times, the chemical intuition is totally hidden within the routines and the basis sets
chosen for implementations [12].
Faced with such programmatic problems, a closed form solution is searched, with a
proper phenomenological impact relative to the qualitative-quantitative predictive character
of the chemical reactivity and the biological activity when characterizing the complex natural
nanosystems.
Quantum and Electrodynamic Versatility of Electronegativity 253
However, there was recently realized a suitable revisited point of view that we should
recall the basic atomic structure, and from that only treating the valence shell as the main
ingredient of the chemical interactions.
Then, it was searched for an intermediate concept and quantity between the single- and
polyatomic systems such that an iterative construction, that adequately describe the
hierarchy of matter organization, to be possible in reflecting the specific structure and
interaction. In this context, it was recently established that the complete description of a
polyatomic system both at equilibrium and in interaction may be realized through a minimal
set of quantum observables, containing an electronic density functional derived from energy
functional expansion [22,23]:
E 1 2E
E[ N + N ] = E0 [ N ] + N + (N )2 + ...
2
(2)
N V 2 N V
When restrained to the second order, as the most common perturbative approach, eq. (2)
provides the variation of energy relationship with the charge variation
E = N + (N )
2
(3)
by means of the chemical electronegativity [24-28]
E
= (4)
N V
and chemical hardness [29-37]
1 2E 1
= 2 = (5)
2 N V 2 N V
indices, in the field of external applied potential V.

It appears that this simple energy-charge correlation furnishes the basics of the chemical-
physical phenomenology either in isolate and reactive state [38-44], as well in bonding
modeling [45-52] up to the most recent reactive biological activity (ReBiAc) principles [53].
In this context, the present work likes to review few of the most intriguing forms of
electronegativity and chemical hardness emphasizing the versatility of these reactivity indices
in reflecting various energetic (energy) density functionals, of the second quantized or
electrodynamical fields.
2. Density Functionals of Electronegativity and Hardness

2.1. Absolute Electronegativity and Hardness
Aiming to elaborate the implications of eqs. (3)-(5), if one likes to model the energy
consumed in forming the AB bonding through the gauge equilibrium reactions [54,55]:
254 Mihai V. Putz
A + B + AB A + + B (6)
may equivalently write
E = E NA0 1 + E NB0 +1 E NA0 +1 E NB0 1
( ) ( ) ( ) (
= E NA0 1 E NA0 + E NA0 E NA0 +1 E NB0 1 E NB0 E NB0 E NB0 +1 )
= IP A + EA A ( IP B + EA B )
= 2( A B ) (7)
thus establishing two important facts:
The so called Mulliken electronegativity considered in (7) in terms of ionization

potential (IP) and electronic affinity (EA) [56]
IP + EA
M (8)
2
may be viewed as the (chemical) finite difference approximation of the differential

electronegativity (4)
IP + EA ( E N 0 1 E N 0 ) + ( E N 0 E N 0 +1 ) E
M = N , (9)
2 2 N V
while furnishing as well the more general form of absolute electronegativity by means of the
integral [57,58]:
N +1
1 0
A = dE N (10)
2 N 0 1
Eq. (7) prescribes that in order to proper describe the reactive propensity of the
chemical systems the change in electronegativity d P has to be also considered,
eventually averaged against the interval (N0-1, N0+1)
1 1
= N 0 +1
(11)
2
dN
N 0 1
in accordance with above (5) introductory definition, towards the so called absolute hardness:
N +1
1 0
A = d (12)
2 N 0 1
that unfortunately cannot give particular information as far (N) remains unknown.
However, worth noting that when considering the eq. (11) as the factor for eq. (12) one
accounts for the average of the acidic (electron accepting, N0 N N0+1) and basic (electron
donating, N01 N N0) behaviors, being therefore an inherent part of the hardness
definition, although equal arguments for skipping it may be as well considered; this is at the
end only a scaling factor and remains to be chosen as per whish for the given problem at hand
(and somehow depending on the taste of the investigator) [59-61].
Now, unlike the differential expressions (4) and (5), the absolute electronegativity and
hardness take the symmetrical forms of (10) and (12) in terms of their potential (i.e. their
cause), the (total for ground state or valence for excited states) energy and (differential)
electronegativity, respectively. Moreover, eqs. (10) and (12) highly advocates the energy and
electronegativity total differentials as furnishing the main thermodynamical (quantum)
equation for achievement a systematic development of chemical reactivity in terms of
changing charges and applied potential, N and V(r), respectively. Nevertheless, this
electronegativity-hardness symmetric formulation produces an elegant unification of the -
theories and the hard-and-soft-acids-and-bases (HSAB) rules beyond the ionization potentials
and electronic affinities [43,44].
2.2. Systematic Electronegativity and Hardness
Since the established absolute electronegativity and hardness dependence on energy and
differential electronegativity with the forms (10) and (12), for an N-electronic system, being
under the external potential influence V(r), their respective functionals E = E[ N ,V (r )] and
= [ N ,V (r)] may be next employed either as total differential equation or as perturbative
expansions in order to systematically obtain electronegativity and chemical hardness density
functionals.
For total differential equation of energy and electronegativity one has the working forms:
E E
dE = dN + V (r)dr = dN + (r )V (r )dr , (13)
N V V (r ) N

d = dN + V (r ) dr = 2dN + f (r )V (r )dr (14)
N V V (r ) N
being the last relation introducing the Fukui index [45-50]

256 Mihai V. Putz
(r ) (15)
= = f (r )
V (r ) N N V
based on the Cauchy property of the total differentiable quantities of eq. (13), playing the role
in locally revealing the reactivity nature of the system being a descriptor which measures how
sensitive a systems electronegativity is to an external perturbation at a particular space point.
These equations may be now employed to furnish various systematic realizations of
electronegativity and hardness, either under chemical or absolute forms.
For instance, refereeing to the energy equation (13), while considering as the change in
electrons restricted to the valence shell, it can be appropriately integrated:
{ }
Nv Nv
E ( N v ) E ( N v ) = dN + (r) [V (r)] dr =
Nv
Nv dN +
Nv
Nv (r )V N v (r )dr (16)
to give the electronic affinity and ionization potential working expressions
N v +1
EA = dN + C A , (17)
Nv
N v 1
IP = dN + C A (18)
Nv
assuming the variation of electronic charge to be unity ( = 1 ) around the number of concerned
valence electrons, Nv; note the appearance of the so called chemical action [18, 62-64]
C A = N v (r )V N v (r )dr (19)
with a major role in chemical bonding and reactivity, see [52] and Chapter 1 of this edited
monograph. Further on, the ionization potential and electron affinity of eqs. (17) and (18)
may be combined amomg them so that when replaced into the finite difference
approximations of derivative forms of electronegativity and hardness of eqs. (4) and (5) to
produce their chemical forms
N +1
IP + EA 1 v
C = dN , (20)
2 N v1
=
2
N v +1
IP EA
C = C dN + C A (21)
2 Nv
which may be regarded as working forms of the absolute definitions (10) and (12),
respectively.
Table 1. Different electronegativity (left column) and hardness (right column) in the
absolute (first two rows) and chemical (last two rows) formulations relating the local
and global softness contributions [18]

Nv
1 1 1
= dN s ( x)V ( x)dx =
0 S S 2 N V
1
S =
2S
N +1
1 v 1
C = dN C = C
2 Nv1 2 N V
N v +1
CCA = C dN + C A
Nv
This step, however, succeed in expressing both the chemical electronegativity and
hardness as uniformly depending on single kernel electronegativity, which can be, instead,
expressed from employing the above electronegativity total differential equation (14). To this
end, one makes use of the so called local softness definition [33,36]
(r ) (22)
s (r ) =
V ( r )
which through integrating to the global softness
N 1
S = s (r ) dr = = (23)
D V ( r ) 2
allows for rewriting of eq. (14) as
1 s (r )
d = dN dV (r )dr (24)
S S
followed by the formal integration:
Nv
s (r ) V (r ) 1 1
Nv
1
=
S
dN
S 0
dV dr =
S
dN s (r )V (r )dr
S
(25)
0 0
From practical implementation point of view, one can identify the form (25) as the
realization of the absolute electronegativity (10) to be inserted in the chemical forms of
258 Mihai V. Putz
electronegativity and hardness as prescribed by eqs. (20) and (21), with the analytical
advantage that now the dependence was moved on the knowledge of local softness rather than
on the total energy. To summarize, all working absolute and chemical levels of
electronegativity and hardness are collected in the Table 1.
The final step in this algorithm regards the way in which the softness influence is
considered. For that one consider the complete softness hierarchy from the global to local to
kernel contributions
1
S = s (r )dr = s (r , r ' )drdr ' (26)
2
and to asses for local and non-local effects the specific density related terms; as such under
three quantum mechanical constraints, namely the translational invariance condition, the
Hellmann-Feynman theorem, and the normalization of the linear response function, it leaves
with the approximate formulathere was derived the approximate formula [16]:
s(r, r ' ) = L(r) (r r ' ) + (r ) (r' ) (27)
with the local response function
(r) [ V (r )] (28)
L(r ) =
[ V (r)]2
being (r r ' ) the delta-Dirac function. Therefore, going back by performing the
successive integrations of (27) one gets for the local and global softness the respective results:
s (r ) = L(r ) + N (r ) , (29)
S = a+ N2 (30)
where the short-hand notation:
a L(r )dr (31)
was considered.
Now, while supplementing the reactivity softness related index (31) by the associate one
which appears as the last term in integration (25),
b L(r )V (r )dr (32)
the various explicit density functional of absolute and chemical electronegativity and
hardness are obtained, within various approximation levels of charge and applied potential
order, as systematized in Table 2 [54].
Table 2. The absolute electronegativity and hardness density functionals as results from electronegativity and total energy expansions
within different combination between the first and second order of charge and first order of external potential variations, respectively.
The notations a, b, and CA corresponds to integrals of eqs. (31), (32), and (19), respectively [54]
Electronegativity Hardness
Sources Absolute (Softness) Absolute (Energy) Absolute
d dE Nv N +1
1 v
N +1
1 v
2 Nv 1
= d = dE [1]
A = d
0 2 N v 1
Nv 1
(Nv 1) arctan
1 a Nv +1
1 1 N arctan
dN dN arctan v 1 a (N +1)arctan Nv +1 1 a
S a a v
2 a 2 a N 1
1 a + (N +1)2 arctan v
a
+ ln v

2 a + (Nv 1)2
1
dN
S
a + (Nv +1)2
1 1 N 4Nv + 3aln Nv 2 N + 2
a + (Nv 1)
dNdN dN arctan v
2
arctan + arctan v
a a
N S a a
1 3 Nv 1 N
( )
1 Nv 1
1 dNdN Nv a arctanNv / a ( Nv 1)arctan arctan + arctan v
= dN 2 N V + 16a
a 4 a
2
a a
a + N2 2a + 6 a
N +1 N +1
(Nv +1)arctan v
arctan v
N a
+ dNdN a
(a + N2)2
Table 2. Continued
Electronegativity Hardness
Sources Absolute (Softness) Absolute (Energy) Absolute
Nv 1 [
2 CA (1 + a Nv2 ) 2bNv ]
(b + Nv 1)arctan 4
(1 + a) + 2(a 1)Nv + Nv
2 2
1 1 N 1 a
dN dN arctan v
S a a 1 a Nv +1 1 Nv +1
(b + Nv +1)arctan arctan
s (r )
V (r )dr
+ (r )V (r )dr b + NvCA 2 a 2 1 a
+
a N 1
S a + N v2 C 1 a + (N 1)2
+ A ln v
2
arctan v
2 a + (Nv +1) a

1
dN dN
1 N
arctan v
[ (A v)
4 C 1+ a N 2 2bN
v]

S 4Nv (1+ a) + 2(a 1)Nv + Nv
2 2 4
a a
1
( )

1 dNdN (2b + 3Nv 3)arctan Nv 1 Nv 2
dNdN N v a arctan N v / a 3 a arctan
2 N V + = + 2 a 1 1 a
N S 2a 16a N + 1

+
(2b + 3Nv + 3)arctan v 4 a N + 2
s(r) + (r)V (r)dr b + NvC A
a

+ arctan v

V(r)dr a
a + ( Nv 1)2
S a + N v2 + a(2CA 3) ln 2 Nv 1
a + ( Nv + 1) arctan
2 a
a Nv Nv +1
+ arctan arctan
a a
By analyzing the Table 2 there is remarked that the chemical electronegativity of eq. (20)
is obtained as a special case of the absolute one of eq. (10) when the total or valence energy is
restrained itself as to the first order variation in charge, i.e. the fourth row of Table 2, while
the total differential equation of electronegativity and energy corresponds to the sixth row of
Table 2, providing a reasonable complex electronegativity and hardness density functionals to
be further used in modeling chemical bonding and reactivity [55].
Yet, although with such variety of quantum formulations for electronegativity and
hardness, depending of the chemical reactivity framework, appears the fundamental question
whether the basic definitions (4) and (5), which opened all the above exposed analytical
phenomenology, are of intrinsic quantum nature to be then implicitly subsisting in any other
related formulation. This matter will be in next addressed.
3. Electronegativity and Chemical Hardness by Second

Quantization
3.1. Affinity and Ionization Fields by Second Quantization
Starting from the bi-dimensional unitary operator on the Fock electronic space F{ 0 ,1 }
1 = 0 0 + 1 1 = aa + + a + a = {a,a + } (33)
one may easily introduce the annihilation and creation operators respectively as:
a = 0 1 , (34a)
a + = 1 0 (34b)
noting their fundamental actions
a + 0 = 1 0 0 = 1 , (35a)
a 1 = 0 1 1 = 0 (35b)
throughout fulfilling the fundamental ortho-normal rules
0 1 = 1 0 = 0, (36a)
0 0 = 1 1 =1 (36b)
for the vacuum and single electronic states, respectively.

262 Mihai V. Putz
Going now to treat the electronegativity and hardness by means of the second
quantization, one will consider the valence state reality as characterized by the unperturbed
stationary state 0 with associated eigen-energy E0 :
H 0 = E 0 0 (37)
Yet, the normalization constrain for the valence wave-function allows the unitary
operator decomposition on the vacuum and uni-particle occupancies as:
1 = 0 0 = 0 1 0 = 0 (aa + + a + a ) 0 = 0 aa + 0 + 0 a + a 0
2 2
= 00 + 10 = (1 0 ) + 0 , 0 [0,1] (38)
and for further identifying the wave function projections:
0 0 = 0 0 = 1 0 , (39a)
1 0 = 0 1 = 0 (39b)
In these conditions, the valence wave-function may be modified such that the affinity and
ionization chemical states are written as corrections or perturbations added towards the
occupancy or vacuum quantum states, respectively as:
( )
A = 1 + a + a 0 = 0 + 1 0 0 1 0 = 0 + 0 1 , (40a)
I = (1 + aa + ) 0 = 0 + 0 1 1 0 0 = 0 + 1 0 0 (40b)
These quantum chemical affinity and ionization electronic states are to be used to closely
characterize the electronegativity and hardness fields in a way to resolve the question of their
observable character.
3.2. Observability of Electronegativity and Hardness
Aiming to evaluate the electronegativity and hardness response to the affinity and
ionization perturbations of eqs. (40) one employs their basic definitions (4) such that to
include the perturbative effect [65,66]:
E E
= = , (41a)

1 E 1 E E
2
= =
+
(41b)
2 2 2
by iteratively employing the chain-derivation rule

= (42)

From expressions (41) appears that the main components of electronegativity and
hardness are the density and energy derivatives respecting the perturbation factor .
Therefore they both will be unfolded respecting the affinity and ionization chemical states
(40) in a special way so that to record their reciprocal transition (no matter in which temporal
order), while normalized at their scalar product for limiting occupancy 0 << 0 1 (since
they are not necessary orthogonal while related), written respectively as [65]:
I A
I a + a A
= , (43)
I A
0 << 0 1
I H A
E IA = (44)
I A 0<< 0 1
Starting with computing the perturbed occupancy, we get successively:
=
( ) ( )
0 1 + aa + a + a 1 + a + a 0
0 (1 + aa )(1 + a a )
+ +
0 0<< 1
0
=
(
0 a + a + a + aa + a + aa + a + a + 2 aa + a + aa + a 0)
( + +
0 1 + a a + aa + aa a a 0
2 + +
) 0<< 0 1
1+
= 0 (45)
1 + 0
since the chemical fields evaluations:
0 aa + a + a 0 = 0 0 1 1 0 1 0 0 1 0 = 0 (46a)
264 Mihai V. Putz
0 a + aa + a 0 = 0 1 0 0 1 1 0 0 1 0 = 0 (46b)
0 aa + a + aa + a 0 = 0 0 1 1 0 1 0 0 1 1 0 0 1 0 = 0 (46c)
based on the above (34), (36), and (39) rules. From expression (45) the perturbation factor is
firstly yield
0
= (47)
0 (1 )
that provide the density involved derivatives appearing on eqs. (41):

=
(1 + 0 ) 2
, (48a)
0 (1 0 )
1 + 0
= 2 (48b)
1 0
Then, going to the energy calculation based on ansatz (44) the chemical affinity and
ionization field produce the results:
0 (1 + aa + )H (1 + a + a ) 0
E =
0 (1 + aa + )(1 + a + a ) 0 0<< 0 1
0 H 0 + 0 H a + a 0 + 0 a a + H 0 + 2 0 a a + H a + a 0
=
1 + 0
1+
= E0 (49 )
1 + 0
since the eigen-equation of the non-perturbed valence state (37) are employed by means of
the creation-annihilation quantum rules:
0 H a + a 0 = 0 H 1 0 0 1 0 = E 0 0 1 1 0 = E 0 0 , (50a)
0 a a + H 0 = 0 0 1 1 0 H 0 = 0 0 0 0 E0 = E0 (1 0 ) , (50b)
while the term

0 aa + H a + a 0 = 0 0 1 1 0 H 1 0 0 1 0 (51)
send to zero within the usual second quantization Hamiltonian expansion over its one and two
particle terms with the corresponding integrals hpq and gpqts over the p, q, t, and s orbitals,
respectively:
1
H = h pq a +p a q + g pq,ts a +p a t+ a q a s (52)
pq 2 pqts
noticing that
0 H 1 ~ 0 a +p ... 1 = 0 1 0 ... 1 = 0 (53)
With the help of eq. (49) there is immediate to obtain the first and second energy
involved derivatives in (41) Finally, from eq. (20), respectively as:
E 1 0
= E0 , (54a)
(1 + 0 )2
E 1 0
= 2 E0 0 (54b)

(1 + 0 )3
Finally, through combining expressions (48) and (54) into (41) the second quantization
based electronegativity and hardness are shaped as [65,66]:
E0 , 0 0 ( E0 < 0)
= = 0 = (55a)
0 E 0 = 0 H 0 , 0 1
0, 0 ( 0,1)
1 + 0
= 0 E0 = 0 = ?, 0 0 (55b)
0 (1 0 )
0 = ?, 0 1
Once again there is clear that electronegativity behaves quite differently by its hardness
companion in eq. (3). In other words, while electronegativity plainly behaves as a quantum
observable through recovering the finite chemical potential definition in (55a), the hardness in
(55b) remains as hidden variable for the vacuum and single occupancy while being absent
for observation for factionary occupied quantum chemical states. This last remark cuts
however the question of factionary occupancy in chemical reactivity phenomena, largely
dominated and controlled by the hardness principles [13,17,18]. On the other side, the
266 Mihai V. Putz
electronegativity reveals its correctness in manifesting as the power with which one system
attracts electrons in fulfilling its vacuum states, the upper branch in (55a).
Overall, the second quantization treatment of electronegativity and hardness enlighten on
versatility with which the reactivity indices drives the chemical states in bonding and
reactivity; yet, from the second quantization results appears that the reactivity/bonding
scenario according which the electronegativity acts as the first influence by means of the
equalization of the chemical potential involved, followed by the hardness second stage and
(energetically) order refining the electronic chemical states between vacuum and full
occupancies with no fractional allowed states in bonding. This is an important result that
overcomes the conceptual difficulties eventually raised by the quantum chemical
computations of the fractional electronic populations at equilibrium [12,13,26,39].
4. Electronegativity and Hardness Electrodynamical Counterpart

Being already convinced of the huge role electronegativity plays in isolated or reactive
electronic systems, there is just one step until the correspondence between the
electronegativity and electrodynamics equations to arise, since both are originating in
electronic source or movements.
As such, if one rewrites eq. (15) as mirroring the charge conservation (the continuity) law
of electrodynamics [67]
(r )
+ = 0 , (56a)
N V V (r ) N
G G
+ j = 0 (56b)
t
one get the following physico-chemical correspondences:

, (57a)
t N
G
, (57b)
V (r )
G
j (58)
thus providing both the space-time chemical counterpart derivatives as well as identifying
electronegativity with the electronic charge current field, as a non-trivial, however not un-
realistically reactivity physical picture. This result may be further employed since recalling
the other definition for charge current in terms of electrodynamical magnetic field intensity,
namely
G G G
j = H (59)
which being equated with electronegativity (4) as prescribed by (58)
E G G
= H (60)
N V
adds more electromagnetic field- chemical reactivity correspondences:
G
, (57c)
N
G
H E[N ] , (61a)
1 (62a)
Next, the electrodynamical contact with hardness may use the fact the last is zero when
factionary occupied states are involved, according with upper branch of eq. (55b) while
having to fulfill the derivative relationship with electronegativity as conditioned by eqs. (4)
and (5); therefore the magnetic induction may be assigned for electronegativity and hardness
in the way that
G 1
B , (61b)
2
G
B
(63)
t
thus combined into the consecrated relationship:
G 1 1
B = (64)
t N 2 2 N
Now, we are going to combine these main ingredients of the chemical electrodynamical
picture for completing the physical field- chemical reactivity correspondences. This way, the
specialization of the Biot-Savart law
G G G
B = 0 j (65a)
in the light ob above one-to-one substitutions reduces to the equation

268 Mihai V. Putz
1
= 0 (65b)
2 N
from where the magnetic susceptibility 0 is eventually associated as follows:
1
0 (62b)
2N
thus taking a non fixed parametric value but rather a variable one being in inverse relation
with the electrons number in a given system.
In the same line, the Faraday-Lenz law
G
G G B
j = (66a)
t
rewrites as

1 = (66b)
N
from where the electric conductance takes the fixed value as
= 2 (62c)
Yet, the last determination has two important consequences. One is derived by combining
it with the electric current- field intensity formula:
G G
j = E (67)
leaving with another electronegativity connection with one electrodynamical field component,
here the electric field intensity:
G 1
E (61c)
2
noting, remarkably, an unification with the magnetic field induction (61b). The second
consequence is provided by reshaping the Gauss law
G G
0 j = (68a)
within the above chemical reactivity quantities and eq. (56a)


2 = 0 = 0 (68b)
V N
to yield for the electric susceptibility the correspondence form
0 2N (62d)
recording the inverse value with that provided by the magnetic companion of eq. (62b), with
obvious meaningfully inside.
Finally, worth introducing the electrodynamical field equivalence for the chemical action
of eq. (19) and to explore the implications. Looking to the structure of the chemical action as
the convolution of the electronic density with applied potential, there appears as the natural
identification of it with the polarization field [67]
G
CA P (69)
With this addition to the list of electrodynamical field chemical reactivity

correspondences the polarization law provides the electric field induction transformation
G G G
D = 0 j + P N + C A (70)

Yet, besides the above correspondences the present formalism allow for determination of
a new chemical (dynamical) reactivity equation, since reconsidering the previous Biot-Savart
law (65a) in its extended form with polarization
G
G G G D
H = j + (71a)
t
that due to the present chemical reactivity counterparts successively becomes:

1 E[ N ] = + ( N + C A )
N N
E N C A
= N +
N N N
C A
= 2 N + (71b)
N
which may be considered as new achievement in the panoply of the chemical reactivity
indices theory; in fact eq. (71b) establishes the intimate relationship between the chemical
270 Mihai V. Putz
action, electronegativity and hardness involving only the electronic number; in other terms it
may be considered as a generalization of the electronegativity- hardness reciprocal
relationship by the contribution of the chemical action variation over the exchanged electronic
charge with environment or within bonding. Relations like this may be most useful derived
when obtained from consecrated electromagnetic fields transformations since including the
field to wave- to quantum information in an undulatory non-separated (entangled)
manner.
This may ultimately contribute in formulating a consistent quantum-relativistic
formulation of the chemical field and reactivity (see also the Chapter 1 of this volume), beside
the precious connection the Chemistry will achieve with information theory and quantum
theory of hidden variables.
Overall, worth observing that only one quantity remains untouched or transformed when
passing from electromagnetic field to chemical reactivity sides, namely the electronic density;
it constitutes the invariant of the present approach, therefore, while guaranties the
observability preserved nature of both interconnected picture of physical-chemical reality.
5. Conclusion
As the classical quantum chemistry had proposed a series of principles and rules to
operate in describing the atomic, molecular samples and the reaction mechanisms [68], the
modern quantum physical-chemistry also likes to unitarily characterize the quantum nature of
the chemical and biochemical bonding and transformation on the base of the electronic
density [69].
While searching for an adequate expressing of the electronic density of atomic and
polyatomic forms of matter through an entire arsenal of quantitative techniques such as are
the computational methods of the self-consistent field, of the pseudopotentials, of the matrices
and their combinations, and of the graph theory [70,71], the resulted electronic densities can
be then properly integrated or differentiated to provide density functionals, e.g., the total
energy, the bond energy, the promoting energy, the solvation energy, reactivity indices, etc.
[72], as well as the localization functions or the electronic basins of stability [73,74].
However, the conceptual chemistry evolves through developing specific objects
expressing the reality of chemical reactivity, eventually at the valence levels by means of the
frontier electron movements. In this context, the electronegativity stands as the benchmark as
well as the forefront of the modern conceptual quantum chemistry since it may be related and
correlated in principle with any many-electronic systems behavior in isolated and reactive
environment.
Moreover, considered jointly with its companion as hardness, arisen as the second order
controlling factor of the total or valence energy expansion, constitute one of the most
powerful conceptual binom in Chemistry with whose help either chemical bonding or the
reactivity or even biological activity may be modeled in an elegant yet efficient analytical
framework [75-77].
As such, the present review unfolds the most intriguing aspects of electronegativity and
hardness, from their density functional forms, when clarifying their absolute and chemical
systematic realizations; the observability character was approached by means of the second
quantization formalism according which electronegativity is indeed revealed as the minus of
the chemical potential or even more as the negative of the eigen-energies for fully occupied
states thus affirming the plenty of observability, while the hardness still preserves the
quantum hidden character for such circumstance along the vacuum state, with proved no
observability for factionary occupancy.
Finally, the common electronic origin of reactivity and electrodynamic fields allows for
advancing the one-to-one correspondences of electronegativity and hardness with the main
undulatory fields and of their electronic characteristics in matter leaving with a sort of
electric-magnetic unification of fields through their correspondence with the
electronegativity, while furnishing the proper framework in which new or generalized
chemical reactivity equations are provided with the fruitful perspective of characterizing the
chemical transformation of matter with consistent quantum-relativistic information contents.
All these conceptual aspects and analytical formulations aim for unification of the
chemical bonding and reactivity by means of electronegativity and hardness indices, within
the most celebrated and not yet completed theory of Chemistry.
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1269-1310.
Chapter 12
PHYSICS AND CHEMISTRY OF CARBON IN THE LIGHT

OF SHELL-NODAL ATOMIC MODEL
G.P. Shpenkov*
FIRMUS S.A.R.L., 33 bd Princesse Charlotte MC, 98000 MONACO
Abstract
The first review devoted to the structure of the carbon atom and all its isotopes in view of
shell-nodal atomic model, and derivation of intra-atomic binding energy of nucleons in its
stable isotope is presented. It is shown that the main role in the formation of molecular
and crystal structures (their geometry) belongs to nodal nucleons, but not electrons, as is
commonly regarded. Electrons define only the strength of interatomic bonds.
1. Introduction
According to dialectical physics [1] with its axiom on the wave nature of all physical
phenomena in the Universe, an internal (spatial) structure of individual atoms [2], symmetry
of crystals [3], and the nature of Mendeleevs periodic law [4] are described by a classical
(not Schrdingers) wave equation
(1)
-Function represents in this case the density of potential-kinetic phase probability of

occurrence of events in wave spaces.
All elementary particles, including electrons, protons, and neutrons, are regarded in
dialectical physics as pulsing microobjects [5]. Interactions between them and with an
*
E-mail address: gshpenkov@janmax.com
278 G.P. Shpenkov
ambient space, more correctly exchange of matter-space and rest-motion (matter-space-time

for brevity), are realized at the fundamental frequency
(2)
inherent in microobjects at the atomic and subatomic levels; where
(3)
is an elementary quantum of the rate of mass exchange (called in modern physics the electron
charge), and
is the electron mass.

The fundamental frequency shows its worth everywhere. In particular, it defines the
quantum of specific resistance of atomic spaces that is found in the integer and fractional
quantum Hall effect [7], etc.
The fundamental frequency is connected with the fundamental wave radius
(4)
which defines average atomic diameters and, hence, average internodal distances (lattice
parameters) in ordered material structures (crystals); where
is the basis speed of exchange of matter-space-time at the atomic and subatomic levels (the
speed of light c is equal to the above speed).
The wave exchange of matter-space-time is in the nature of all physical phenomena.
Accordingly the probability of possible states has the wave character and reflects the states of
rest and motion. The possibility of rest and motion gives birth to the potential-kinetic field of
reality, where rest (potential field) and motion (kinetic field) are inseparable linked between
themselves in the unit potential-kinetic field. The mathematical image (measure) of the wave
of possibility is the wave of probability; the latter was called [9] the phase probability. Thus
the density of phase probability is the complex function
(5)
The density satisfies the wave equation (1), which in this case is called the wave
probabilistic equation.
Physics and Chemistry of Carbon in the Light of Shell-Nodal Atomic Model 279
Interference of waves of the exchange form standing waves in bound domains of space
[8]. Potential nodes of these waves are natural places of equilibrium disposition of
constituents of atoms and molecules - nucleons. An equilibrium disposition of nucleons in the
nodes inside of individual atoms correlates with the disposition of atoms in molecules and
crystals.
The wave equation (1) admits particular solutions in the form
(6)
where is the particular solution of the Helmholtz equation
(7)
is the wave number. The wave equation (1) describes both spherical
and cylindrical wave fields of matter-space-time.
The general form of the solutions of Eq. (1) for a spherical (longitudinal, central)
component of , in spherical polar coordinates, is
(8)
where
(8a)
is the spatial factor of the wave function (6);

The radial component of the spatial factor describes the density of potential-
kinetic probability of radial displacements, the polar component - the polar
displacements, and - the azimuthal displacements.

At integer values of the wave number m, an elementary solution of the wave equation (7)
has the standard form:
(9)
Two terms in (9) are the potential and kinetic spatial constituents of function. They
reflect polar opposite features of the function - its potential and kinetic character,
respectively.
The half-integer solutions of (7), for , where have the form
280 G.P. Shpenkov
(10)
where
(11)
(12)
From (12) it follows that the polar extremes of half-integer solutions are in the equatorial
plane.
All spatial components are determined with the accuracy of a constant factor A, imposed
by boundary conditions, which have no influence on the peculiarity of distribution of the
nodes on radial spheres. The superposition of even and odd solutions defines the even-odd
solutions. Odd solutions describe the nodes, lying in the equatorial plane of atomic space. In
this plane there are also solutions in the form of rings in space (shown below).
The solution (9) describes the kinematic structure of standing waves of wave physical
space, namely it yields a spatial geometry of disposition of specific points (nodes and
antinodes) in which function takes the zero and extremal values.

The disposition of principal potential polar-azimuth nodes (obtained in spherical polar
coordinates) reflects the discrete geometry of probabilistic radial polar-azimuth wave
spherical shells at . They are determined by the elementary solutions:
(13)
where is the constant factor.

The conjugated kinetic nodes are determined by the function
(14)
If potential nodes are the points of rest, the kinetic nodes are the points of maximal
motion (oscillation).
The relative radius of characteristic shells (the shells with the zero or extremal
value of radial functions ) is defined by the roots of Bessel functions: and , for
potential and kinetic components, respectively, where is the order of Bessel

functions and q is the number of the zero or extremum. Since , the radii of
the shells (spheres) of zeros and extremes are, respectively:
and .
A great set of characteristic shells corresponds to each number l of the radial function.
Zero values of the wave spherical field of probability define the radial shells of zero
probability of radial displacements (oscillations); they are the shells of stationary states.
According to the obtained solutions (9) [1-4], characteristic shells of the carbon atom are
defined by the following quantum numbers: and .
Radial functions of the even solutions (9), defining the characteristic shells of the carbon
atom, are presented in Table 1 (through their relative values Rl /A) and in Figure 1.
Table 1. The radial functions of even solutions for the carbon atom
0 (sin i ( cos)) /
1 (( -1 sin cos) i ( -1 cos sin)) -1
2 [((3 -2 1) sin 3 -1 cos)) i ((1 3 -2) cos 3 -1 sin))] -1
Elementary solutions for the polar functions have the form
(15)
where is the coefficient depending on normalizing conditions, and are

Legendre adjoined functions. Elementary linearly independent solutions for the azimuthal
functions have the form
(16)
where is an initial phase of the azimuth state. The first component of the function (16) is
potential, the second one is kinetic:
(17)
(18)
Both solutions, (15) and (16), define the potential-kinetic polar-azimuth function
(19)
282 G.P. Shpenkov
Figure 1. Plots of the radial spherical functions of the carbon atom: potential (a) and
kinetic (b).
Table 2. The reduced polar-azimuth potential functions of the carbon atom
l m
0 0 1
1 0
2 0
If the normalizing factor of the above functions is assumed to be equal to the numerical
unit, these functions are called the reduced functions. The reduced polar-azimuth potential
functions, , for the carbon atom are presented in the Table 2; their graphs are
drawn in Figure 2.
Figure 2. Graphs of the polar-azimuthal functions of the carbon atom.
The contour plots of potential components of the density of probability (13) for the
carbon atom are presented in Figure 3. Pictures presented here are the sections of (i.e. the
sections of the product of the three functions: radial , polar , and azimuthal
) in the plane .
It should be noted that the pictures demonstrated in Figure 3 are, in accordance with the
solutions, interference images of modes of standing waves in a three-dimensional spherical
space.
A characteristic feature of the shell at l = 2, m = 0 is an existence of a toroidal vortex-
ring. Obviously, it plays an important role in physical and chemical processes at the atomic
and molecular levels. We assume that it is responsible for a series of unique properties of
graphene - an atomic size thickness layer of graphite found in the last years. Therefore, we
show this ring once more in Figure 4 in two projections: for a section along the z-axis (in a
plane perpendicular to the plane (x, y), as in Figure 3), and additionally for a section z 0 in
a plane (x, y).
284 G.P. Shpenkov
Figure 3. Contour plots (an interference image) of the sections for the potential density of probability
in the plane for the space of the carbon atom.
The next peculiarity of the solution is an existence of the nodes along the z-axis which we
call polar nodes. The 2n and 2s, north and south, polar nodes, corresponding to l = 2, are
indicated in Figure 4.
Polar components of the space density of probability define characteristic
parallels of extremes and zeroes on radial spheres (shells). Azimuth components
define characteristic meridians of extremes and zeroes. Potential and kinetic polar-azimuth
probabilities select together the distinctive coordinates of the disposition of extremes
(antinodes) and zeroes (nodes) on the radial shells.
Figure 4. The solution (13) of the wave equation (7) for the spherical shell of the carbon atom with the
wave (quantum) numbers : (a) for a section along the z-axis (in a plane perpendicular
to the plane (x, y)), (b) for a section z 0 in a plane (x, y); 2n and 2s are, respectively, the north and
south polar nodes belonging to the shell.
The solutions for of the

probabilistic wave equation (1) presented in the form indicating the relative space disposition
of potential extremes-nodes - discrete elements of the shell nucleon structure of the carbon
atom - are drawn schematically in Figure 5. Numbers 1, 2, 3, , 6 are the ordinal numbers of
the principal polar-azimuth nodes coinciding with the atomic numbers of the elements Z of
the periodic table.
Every principal node with the ordinal number Z bounds, to the definite extent, all
previous shells with their nodes. Having the specific spatial structure, every such a locally
bounded object is distinguished from all others by the specific unrepeatable properties. A
totality of discrete units (nodes) of the wave probabilistic field in the object is considered as
an element (atom) of the field.
It turns out that the distribution of nodes in a standing wave spherical space, described by
the wave equation (1), also defines the distribution of dense matter (elementary particles) if
material spaces are considered. The particles are in nodal points of the space (presented, in
particular, in Figure 5 for the space of the carbon atom) because they tend toward equilibrium
state. Nodes for them are something like potential wells. It will be recalled in this connection
286 G.P. Shpenkov
that the wave equation for atomic spaces is the equation of microsystems. It does not describe
the motion of isolated microobjects, but it describes the wave processes at the definite level of
space on the whole, determining the space structures as unified systems.
Figure 5. A schematic drawing of the nodes and a toroidal vortex ring in the carbon atom: 0, 1N, 1S, 2N,
2S is the ordinal number of the polar potential-kinetic nodes (located along the z-axis, m = 0); 1, 2,, 6
is the ordinal numbers of principal polar-azimuthal potential nodes. The nodes 1 and 2 belong to the
internal spherical shell, l = 1; the nodes 3, 4, 5, and 6 are located on the external spherical shell, l = 2.
Analyzing the structure of crystals at the end of 18th century, R.J. Hay (1743-1822) [11]
came to the conclusion that it is necessary to consider atoms as elementary molecules, an
internal structure of which determines the crystal structure of solids. As masses of atoms are
multiple of the hydrogen atom mass, following Hays ideas makes it reasonable to suppose
that any atom, like the elementary Hays molecule, is the H-atom molecule.
Actually, as was shown by comprehensive analysis of direct and indirect consequences of
the solutions for the wave equation (7) [3], nodes of intratomic space are completed by H-
atoms to which we refer protons, neutrons, and hydrogen atoms; therefore, atoms of the shell-
nodal atomic model are regarded as H-atom quasispherical molecules. The simplest hydrogen
atom (protium) is an elementary brick of the Universe at the atomic level (the basis
particle of the atomic level). Protium has also a complicated internal structure which is
defined, following dialectical physics, by the solutions of the same wave equation (1).
However, it consists of elementary particles of the deepest level of the Universe -
subatomic [16-18].
Thus, Figure 5 is a schematic image of the disposition of nodes (and a toroidal vortex-
ring) in the wave spherical shells of the space of the carbon atom regarded as an elementary
molecule of H-atoms.
Principal azimuth nodes of the wave space of atoms are marked by ordinal numbers.
These numbers coincide with ordinal numbers of the elements of Mendeleevs periodic table.
A conducted comprehensive analysis showed uniquely that the number of H-atoms, which
can be localized in one node of an atom, is equal to or less than two.
All polar nodes (corresponding to m = 0) are potential-kinetic nodes. Being potential and
kinetic at the same time, they are the nodes of rest and motion simultaneously. Therefore,
particles of matter settled by a reason there will be in a disturbed nonequilibrium state. Thus,
the function describes, following the shell-nodal atomic model, the density of probability of
concentration of matter in nodal points of limited domains of the wave spherical space of
standing waves.
Every atom represents a system of spherical shells with discrete points-nodes of wave
space completed by H-atoms. It means that atoms have not a customary nucleus as is assumed
in modern physics based on the quantum mechanical (QM) Rutherford-Bohrs atomic
(nuclear) model [10, 11].
Being essentially different from QM and, respectively, Rutherford-Bohrs model, the new
molecule-like (shell-nodal) atomic model is in well agreement with all well-known
experiments (including Rutherfords experiment on scattering of - and -particles in
substance [12]) that we have already time to consider beginning from 1996, the year of the
first publication on dialectical physics. Moreover, this model, along with the dynamic model
of elementary particles [5], reveals the nature of a series of phenomena misunderstood until
now (see for example [1, 6, 13, 14]), including so-called forbidden symmetries found
recently in natural minerals [15].
The relative mass of atoms is defined by the total number A of H-atoms located in nodes
of spherical shells of a concrete atom:
(20)
were k and i are the numbers of polar (m = 0) and polar-azimuthal shells,

respectively; is the number of polar nodes of k-th polar shell; and are the
number of principal and collateral polar-azimuth nodes, respectively, of i-th polar-azimuthal
shell; , , and are the numbers of multiplicity, i.e., filling of the nodes
( ). (Collateral polar-azimuth nodes are in atoms that have the shells
corresponding to quantum numbers . The first atom in this series with l = 3 is silicon,
the atomic number )
Thus, generally, following the physical shell-nodal atomic model, atoms represent the
bounded microsystems of characteristic spherical shells with nodal points, where the wave
function has the zero and extremal values, expressing the discrete structure of these shells.
The number of potential (or, in equal degree, kinetic) polar-azimuth extremal points (nodes) Z
indicates the ordinal (atomic) number of the concrete atom. The principal constituents of
atoms are H-atoms located in the potential nodes.
Carbon and its compounds, especially with hydrogen and oxygen, are the most studied
substances with a great variety of different structures, which they form. Therefore it is in
order and a case in point to show an advantage of the aforementioned physical shell-nodal
atomic model, already essentially developed (see References), considering as an example the
structure of the carbon and oxygen atoms, their isotopes and some typical compounds that is
the goal of this review.
288 G.P. Shpenkov
2. An Internal Structure of Carbon and Oxygen Atoms and their

Isotopes
Thus, following the shell-nodal atomic model, atoms have an internal shell-nodal
structure defined by the simplest solutions of the wave equation (1). The nodal structure of
the carbon atom and its polar-azimuth functions are shown in Figure 6.
Figure 6. (a) Plots of potential polar-azimuth functions (l = 0, 1, 2;

), (b) symbolic designation of polar nodes on radial shells (b), and (c) the
symbolic designation of the carbon atom.
The carbon atom has two polar-azimuth spherical shells (l = 1, 2; ) with six
potential polar-azimuth nodes completed every by two H-atoms. All they are in one plane:
two potential nodes are in the inner spherical shell (l = 1), and four potential nodes are in the
outer spherical shell (l = 2). In the center of this structure (in the origin of spherical polar
coordinates), there is an empty node (l = 0, m = 0). The rest four empty nodes, potential-
kinetic polar (l = 1, 2; m = 0), are located along the z-axis. A toroidal vortex-ring (at l = 2, m
= 0) is in the plane (x, y) with the axis of symmetry z.
Kinetic nodes, the nodes of maximal motion (they are not shown and will not be
considered here), are in a perpendicular plane with respect to the plane of the disposition of
potential nodes (compare (13) and (14)).
The main mass of hydrogen in Nature at all its levels is in coherent states, in particular, in
the form of coupled atoms hydrogen molecules H2. Coupled H-atoms in polar-azimuth
nodes define an equilibrium state of atomic (polar-azimuthal spherical) shells. The condition
of coupling is inherent not only for H-atoms in nodes of individual atoms, but also for atoms
linked in molecules and crystals; we shall touch this subject further.
Individual properties characteristic for an element of the ordinal number Z are keeping
for its isotopes. Shell-nodal atomic model reveals this peculiarity showing the structure of all
possible isotopes. Following the shell-nodal atomic model, the structure of isotopes is
dependent on the filling of empty polar potential-kinetic nodes (located along the z-axis, at m
= 0) by H-atoms and on the multiplicity ( = 1 or = 2) of filling the principal potential
nodes in the external spherical polar-azimuth shell. Of course, structures with incompletely
filled principal potential nodes cannot be equilibrium, and as metastable states they are
characterized by a definite lifetime. Thus, the geometry of external polar-azimuth shells and,
hence, specific strong intraatomic nodal bindings in isotopes do not change only during the
lifetime of the unstable, in this case, atom.
Figure 7. A schematic image of the filling of nodes in the lightest ( ), heaviest ( ), stable (
and ), and unstable (radiogenic, ) isotopes of the carbon atom.
The nodal shell structure of carbon presented in Figure 6 is not changed until each of the
four polar-azimuth nodes of an external shell contains at least one H-atom. As was mentioned
above, such a state with unpaired single H-atoms in the nodes will not be equilibrium and,
hence, is temporal, short-lived.
Hence, following the shell-nodal structure depicted in Figs. 5 and 6, the uniquely possible
lightest unstable isotope of carbon is of the mass number 8 (the total number of H-atoms).
The order of filling the nodes in this isotope is shown in Figure 7.
It should be noted that the above described filling of only external nodes by one H-atom,
in the lightest unstable isotope of carbon, is inherent as well in the lightest isotopes of most
atoms of the periodic table having external integer shells.
Carbon is made up of isotopes with masses 12, 13 and 14. An isotope of carbon can
be obtained under condition of filling a central vacant node in the carbon with one H-
atom as shown in Figure 7. This isotope is stable. Apparently, a specific configuration of
290 G.P. Shpenkov
internal fields and internodal bindings in provides a stable state of a single H-atom in the
central polar-azimuthal potential-kinetic node.
Filling of the central node in with two H-atoms, or filling of two vacant polar nodes
in its first shell (l = 1, m = 0) by one H-atom per node, leads to two possible forms of the
carbon isotope (see Figure 7), which both are unstable, radiogenic. The half-life of
is 5730 years. This is a long-lived isotope, apparently, because of a specific symmetry of

the filled nodes and, hence, due to a specific symmetrical structure of its resulting binding
fields.
The maximal mass number of carbon cannot exceed 22 in any way. This fact follows
from the solutions presented above. Actually, the total number of the nodes in the carbon
atom (excluding polar-azimuthal kinetic nodes which are not shown here): axial potential-
kinetic polar and principal potential polar-azimuth, is 11. Multiplicity of filling of the nodes,
does not exceed 2. Accordingly, the maximal number of H-atoms in the nodes of the
carbon atom cannot exceed 22: 11 nodes . In fact, the carbon is the heaviest
artificially produced short-lived isotope of carbon [19]. It is obtained forcibly by filling all
vacant polar nodes, as is shown in Figure 7, by the neutron exposure on accelerators with
paired H-atoms.
The matrix of polar-azimuth discrete structure of the carbon atom, a matrix of the nodes
(excluding kinetic nodes), , has the form
(21)
Matrix elements show the number of nodes in the shells corresponding to a definite
values of l (the first row, l = 0; the second row, l = 1; and the third row, l = 2) and m (the first
column, m = 0; the second column, m = 1; and the third column, m = 2).
The matrices of filing the nodes by H-atoms in the stable , lightest , and heaviest
isotopes of carbon (shown in Figure 7) have the following forms:
(22)
The shell-nodal structure of possible isotopes of the carbon atom (from lightest to
heaviest), originated from the solutions of the wave equation (1), is shown in Figure 8.
Figure 8. The nodal structure of possible carbon isotopes (solutions of the wave equation (1)).
292 G.P. Shpenkov
The structure of carbon atom, being spherical (as generally, any atom), looks like
plane, because all potential polar-azimuth nodes with H-atoms inside of them are situated in
the same plane. Accordingly, due to specific geometry of disposition of the nodes, carbon
atoms can form the plane hexagonal structure pertinent to graphite. The symbolic designation
of carbon in Figure 6 reflects such a plane geometry of arrangement of all six potential
polar-azimuth nodes and shows the shortest directions of exchange (interaction) between
them. Thus, each carbon atom is associated in shell-nodal atomic model to one of the exo-
pentagonal bonds of the truncated icosahedrons.
Figure 9. Plots of the potential polar-azimuth functions (l = 0, 1, 2;
) and (s = 2), and their nodal points on radial shells and
of the oxygen atom. An initial phase of the azimuthal state (a) and (b) for
the external half-integer shell at s = 2; (c) the symbolic designation of the oxygen atom (for ).
The spatial shell-nodal structure of the oxygen atom and its polar-azimuth functions,
originated from the shell-nodal atomic model, are drawn in Figure 9. We see that in
comparison with the carbon atom (Figure 6), the oxygen atom has a half-integer external
shell with two potential polar-azimuth nodes lying in the equatorial plane ( , see Eq.
(12)); the rest shells (l = 0, 1, 2; ) are the same as in the carbon atom.
Six potential polar-azimuth nodes (at ), completed every by two H-atoms, lie in
one plane: two potential nodes are in the shell at l = 1 and the four potential nodes are in the
shell at l = 2. Two external potential polar-azimuth equatorial nodes (at s = 2), 7th and 8th, can
be whether in the same plane with internal nodes or in the perpendicular plane with respect to
the disposition of the rest nodes, as is shown in Figure 9b. Such positions of the nodes are
determined by an initial phase of the azimuthal state that is admitted by the solutions of (1).
All kinetic polar-azimuth nodes (not shown in Figure 9), the nodes of intensive motion
(therefore they are empty), are in the perpendicular plane with respect to the plane of
disposition of potential nodes, as in the carbon atom.
The structure of all possible isotopes of the oxygen atom, as every atom in the shell-nodal
atomic model, is uniquely defined by the multiplicity of filling of both external potential
polar-azimuthal nodes and polar potential-kinetic nodes. The relative masses of the isotopes
calculated on this basis coincide with the experimental data; they are presented in references
[2, 4]. For example, from the aforementioned solutions it follows that the maximal mass
number of oxygen is 26: the total number of all its nodes (excluding, of course, kinetic) is 13
and maximal multiplicity of their filling is hence, 13 . Actually, is the
heaviest artificially produced short-lived isotope of oxygen [19]. It is obtained forcibly by
filling of all 5 vacant polar nodes in with paired H-atoms, like in the case of producing of
the carbon isotope considered above.

Because all nodes inside of the oxygen atom are situated in the same plane (we mean the
case with presented in Figure 5.3a), the spherical structure of oxygen atom looks like
plane. Therefore, because of specific geometry of disposition of its nodes, oxygen atoms
can form the plane hexagonal structure pertinent, in particular, in snow crystals [20]. The
symbolic designation of oxygen presented in Figure 9c reflects such a plane geometry of the
arrangement of all eight potential polar-azimuth nodes and shows the shortest directions of
exchange (interaction) between them.
A matrix of polar-azimuth discrete structure of the oxygen atom, or a matrix of the nodes
(excluding kinetic nodes), , has the form
(23)
The matrices of filing of the nodes by H-atoms in the stable , lightest , and
heaviest isotopes of the oxygen atom have the following forms:
or
(24)
294 G.P. Shpenkov
It is to the point to note that contrary to particular solutions of Eq. (1) which uncover the
shell-nodal structure of matter (atoms), Schrdingers quantum mechanics solutions led to the
notion of electron structure (electron configuration) of atoms which, as turned out, is
the conceptually unfounded notion [10, 11, 21]. Moreover, Schrdingers solutions do not
give any information about the nature and structure of atomic isotopes. This is the very
important fact, which along with many other results already obtained in the framework of
dialectical physics, proves the credibility of the shell-nodal atomic model. Estimates of
binding energies in shell-nodal atomic structures and their compounds, presented in the last
sections of this paper, also confirm this.
3. Graphite and Fullerenes

Graphite is a modification of carbon crystallized in the laminated hexagonal structure. A
unit cell of graphite consists of three layers. The atoms of carbon on the top layer and bottom
layer are at the same lateral positions. The middle layer is shifted relative to the top and
bottom layers.
We will follow the shell-nodal pattern of the carbon atom expressed graphically by the
symbol (Figure 6c). We do not know what kind of carbon is responsible for the formation
of graphite, atomic, C, or molecular, C2. Therefore, the same designation will be applied to
the carbon molecule C2 as for the carbon atom C. There are suppositions that the C2 radical is
responsible for the formation of graphite [22]. And it was found experimentally that the
carbon dimer C2 is in fact the major observable product of C60 fragmentation. Being a very
effective growth species, C2 can rapidly incorporate into the diamond lattice leading to high-
film growth rates [23].
Our calculations of lattice parameters, results of which are presented below in Figure 10,
give an answer to the question: what are elementary bricks in graphite, C or C2?
Following the shell-nodal atomic model and assuming that the lattice constants of crystals
accepted in modern physics are precise and congruent to reality, we should accept that an
elementary building block in carbon crystals, including graphite, is the diatomic molecule
of carbon, C2. Let us consider this question.
Under accepted designations of C and C2, hexagonal layers of graphite have the structure
shown in Figure 10. In this figure, lattice constants of graphite indicated in brackets
correspond to imaginary lattice parameters if one accounts that the crystal lattice is formed
from single carbon atoms, C.
When we consider C2-based structure of graphite, we have six-multiple overlapped
atomic nodes (except of boundary nodes) with 12 overlapped H-atoms per node belonging to
three linked carbon dimmers.
For all that let us assume that the structure presented in Figure 10 is formed from single
carbon atoms, C. Then it takes place the three-multiple overlapping of every vertex (node) of
bound carbon atoms (one internal node with two external nodes), excepting boundary atoms
where two-multiple overlapping of external nodes occurs (Figure 11).
It means that every (except boundary) nodal point (vertex) depicted in Figure 10 belongs
to three individual carbon atoms. Every vertex contains 6 overlapped H-atoms, because we
need to take into account the coupled H-atoms filling every of the six nodes of .
Figure 10. (a) An elementary cell of graphite; (b) the structure of bindings in a layer of graphite
(graphene). The overlapping of external atomic nucleon shells of carbon dimmers is realized orderly
along the shortest bindings between internal and external nodes of different carbon dimers.
Figure 11. Two- and three-multiple overlapping of the nodes characteristic for linked carbon dimmers
C2 in graphene, a one-atom-thick crystal layer of graphite. The two types of 2-multiple overlapping are
realized on the edges of the carbon crystal.
Thus, taking into account the above assumption on the C-based structure of graphite, we
should distinguish among a vertex representing in shell-nodal atomic model three-multiple
overlapped atomic nodes (with 6 overlapped H-atoms), belonging to three different carbon
atoms, and the vertex (node) representing in the standard QM (nuclear) atomic model one
carbon atom (holding 12 nucleons in its nucleus).
Figure 10b and Figure 11 show a one-atomic layer of graphite. The latter called graphene
was obtained quite recently and is intensively studied at present [24]. Unsaturated two-
multiple overlapped external nodes of C2 dimers on different edges, especially zigzag-like
edges, must have unusual physical and chemical properties as chemical radicals. Actually, the
zigzag edge of a graphene nanoribbon possesses a unique electronic state and the chemical
reactivity.
An average density of graphite is . At the above density and three
multiple nodal overlapping of single carbon atoms, lattice constants of graphite have to be
296 G.P. Shpenkov
and (shown in Figure 10 in brackets). An average

length of bindings corresponding to these parameters must be . However,
the above values do not coincide with the accepted data for graphite shown in Figure 10
without brackets: and ; and bond lengths are
equal to and , respectively. The latter data completely coincides with
the calculated data only for the case when the lattice is formed from C2 units.
Thus, the complete coincidence of calculated parameters with the table values can be
achieved if we will take into account the previous coupling of individual carbon atoms
themselves at the atomic level with the formation of two-atomic molecules C2 (as H2, N2, O2,
etc.) and the following formation of crystals from them as elementary units. In this case we
have the six multiple overlapping of every node (with 12 overlapped H-atoms) and arrive at
the coincidence of the aforementioned parameters with the table values. The coupling is the
natural property of matter at all levels. Remember, the coupling of H-atoms, constituents of
atoms, occurs at the subatomic level as well, in intra-atomic nodes.
A scheme of overlapping of nodes of two carbon atoms resulted in the formation of the
C2 molecule is shown in Figure 12. Two-multiple overlapping of atomic nodes leads to the
nodes contained every by four H-atoms per node. Just the same number it has the helium
atom belonging to one of the balanced atomic structures (along with neon and argon).
Apparently, the latter fact provides the more stable thermodynamic state of C2 with respect to
the state that has an individual carbon atom.
The following is noteworthy. The lattice constants of graphite shown in brackets in
Figure 10 can prove to be verisimilar because of the following highly plausible situation. The
existing X-ray and neutron scattering analysis (along with others) of crystals and molecules is
not so simple matter in spite of the use of power modern computers and perfect techniques.
The gauging of diffraction images takes into account the accepted atomic model and the
density of substance known from the experiment. A solid-state theory based on the QM
atomic model identifies every node of a crystal lattice (or a molecule) with one atom, which is
regarded as the only center of scattering of incident particles or waves by this atom.
Figure 12. Formation of the C2 molecule: overlapping (confluence) of all approaching nodes (and
toroidal rings not shown here) of two carbon atoms in the unit whole. (A symbolic image of C 2 does not
differ from the symbolical designation of a single C atom drawn in Figure 6).
Actually, it is assumed that every peak of electron density, in X-ray crystallography at the
determination of atomic positions, corresponds to the definite position of a node with one
(whole) atom [25]. A precise calculation of atomic positions and lengths of interatomic bonds
uses the iterative method. The last is based on the comparison and fitting of measured and
calculated (proceeding from the accepted atomic model) intensity of reflected beam so as
long as will not be achieved an adequate correspondence of two sets of the values. Possibly,
if only the X-ray analysis will be based on the use of shell-nodal (i.e., multi-center or
molecule-like) atomic model, the gauging could be different, depending on the multiplicity of
overlapping of atomic nodes belonging to various atoms. It means that the three multiple
overlapping of nodes (vertices) of tree carbon atoms, just as presented in Figure 10, can be
real and, hence, deserves a special examination. A present assuming that the lattice constants
of crystals accepted in physics are precise and congruent to reality, we must accept that an
elementary building block of graphite is the C2 diatomic molecule.
The pictures presented show that interatomic (intermolecular) bindings in graphene are
realized along the bonds of external nodes of external shells and nearby internal nodes of
internal shells. Every hexagonal circle with 4 double bindings is surrounded with 6 similar
hexagonal circles. We see also that single bindings between the first and second nodes of
internal shells (responding to ; Figure 6b) nowhere overlap. The next
characteristic feature of graphene is its crystallographic anisotropy. The z-axes of all
elementary carbon formations (C2) of a one-atomic/molecular-thick layer form straight
parallel continuous chains of polar nodes along the direction perpendicular to the bonds
between 1st and 2nd internal nodes (Figure 6, 11, and 12).
Figure 13. (a) An unfolded structure of buckminsterfullerene C60; (b) a fragment showing the
overlapping of the nodes belonging to 5 spherical molecules C2 resulted in three-multiple overlapping
of their nodes in two verticies.
298 G.P. Shpenkov
In order to verify the above described peculiarities of nodal bindings in carbon structures,
found in graphite, it is interesting to consider the structure of other carbon compounds. Let us
turn now to the structure of fullerenes considering them in the light of the shell-nodal atomic
model as well.
Fullerenes are regarded as a molecular form of a pure carbon (a kind of microclusters)
representing a high symmetrical structure hollow inside. They are formed by the regular
polygons of strained atomic bindings because of their bending under the formation of cage-
like structure of carbon atoms, characteristic for fullerenes.
The most known among fullerenes is C60 molecule (called buckminsterfullerene), which
is well detected by mass-spectrograph. Complicated structural analysis has led to the
conclusion that this molecule has 60 vertices, and their bindings form 20 hexagons and 12
pentagons. Such a structure reminds in form a football pattern (see Figure 13).
If one follows the shell-nodal atomic model then we should accept that elementary
building bricks of the C60 molecule must be carbon dimers C2, but not carbon atoms C.
The spherical closed pentagonal/hexagonal monomolecular shell has the rotational
symmetry of order 5 forbidden in crystallographic space of plane symmetry group and highest
possible icosahedral point-group symmetry [26].
The conclusion about the structure of buckminsterfullerene, accepted in physics, rests on
the concept of quantum mechanical (mono-center) atomic model, according to which one
node (vortex) of a crystal lattice corresponds to one atom (containing 12 nucleons in its
nucleus).
Let us suppose that the aforementioned spherical structure with 20 hexagons and 12
pentagons is realized on the basis of shell-nodal atomic model with use of 30 carbon atoms,
but not carbon molecules C2, in the capacity of elementary bricks (they are designated by
the same symbol , see Figure 6 and 12). In this case, the above structure of 60 vortices,
depicted in Figure 13 in the unfolded form, will be characterized by a three multiple
overlapping of all vortices (nodes). We will arrive at the hypothetical C30 molecule, because
only 30 carbon atoms are needed for the formation of 60 such vortices. Obviously, this case
contradicts to the mass-spectrographic data.
The six multiple overlapping (every of 60 vertices-nodes) only leads to C60 molecule with
the above shell-nodal atomic structure of carbon. This is realized on the basis of coupled
carbon atoms, participating as elementary structural units at the formation of C 60 just like it
takes place at the formation of all crystal structures on the basis of carbon, including graphite
considered above. Thus, the symbol in Figure 13 represents two coupled carbon atoms, the
carbon dimer C2. Just then we have the right to state that the above structure belongs to C60
molecule. The length of single bindings in such C60 molecule is ,
double bindings , as in graphite in the same case formed from the
coupled carbon atoms.
If one supposes that the case of non-coupled atoms with three multiple overlapping of
their nodes is real then we should recognize that the molecule C60 called buckminsterfullerene
has actually 120 vertices. This is very likely because of possible errors at an extremely
complicated procedure of deciphering of intricate diffraction images of C60 molecule (as
generally all fullerenes), and mainly due to the aforementioned gauging, accomplished with
regard the nuclear (mono-center) structure of atoms. Thus, at the current stage of the
development of atomic physics, we cannot exclude completely that the structure presented in
Figure 13 with 60 vertices is an image of the C30 molecule, but not C60.
The overlapping of atomic shells at the formation of carbon crystal structures occurs
along the directions of bindings between the nodes of two shells, external and nearest internal,
for both graphite and fullerenes. Internal bindings of internal shells of carbon dimers
(between the nodes 1 and 2, corresponding to l = 1 and , see Figure 6b) overlap only
once at the coupling of carbon atoms and the formation of dimmers (see Figure 12).
4. The Shell-Nodal Structure of Diamond

Diamond is a modification of carbon crystallized in a face-centered cube. The
coordination number of diamond is 4. Therefore the structure of diamond is more friable in
comparison with cubic structures characteristic for metals. Diamond can be artificially
obtained from graphite under temperature and pressure.
The disposition of all polar-azimuth nodes in one plane (inherent in the carbon atom
under normal conditions and keeping in graphite) does not keep under aforementioned
extremal conditions. The one-planar disposition of all atomic nodes is broken. The internal
plane with the 1st and 2nd polar-azimuth nodes of an internal shell (Figure 14a) is turned
about the z-axis by an angle of about (with respect to the plane of disposition of the
rest four external polar-azimuth nodes belonging to the outer shell, Figure 14b). This is
admitted by solutions (9) of the wave equation (7), in which it enters the phase angle .
Figure 14. a) A plane structure of carbon atom (and carbon molecule C2 as well); b) a shifted (turned)
position of an internal shell (with nodes 1 and 2) around the z-axis by the phase angle ; c)
the bindings (marked by broken lines) between the shifted internal nodes 1 and 2, belonging to different
carbon dimmers, resulted in the face-centered cube structure of diamond.
300 G.P. Shpenkov
Figure 15. (a) A hexagonal-wavy structure of crystallographic planes in diamond; (b) a hexagonal-wavy
circle built from 3 carbon units (dimmers, C2); (c) the bindings (marked by dashed lines) between
hexagonal-wavy layers resulted in the face-centered cube structure; (d) an elementary cell of diamond.
As a result the plane hexagonal structure of graphite layers is transformed into the wavy
hexagonal structure, which enables bindings between them in the bulk face-centered cube
structure. The direct interaction between 1st and 2nd nodes (drawn by broken lines in Fig
14c) of different coupled carbon atoms, belonging to nearby layers, is realized in this case.
The bindings between the deformed (wavy) neighboring layers of the hexagonal
structure, leading to the formation of diamond structure, are shown in Figure 15. We see that
hexagonal circles are inherent in both graphite and diamond (Figure 15a). However, if they
are planar in graphite, they are wavy in diamond (Figure 15b,c). Thus, the specific hexagonal
structure originated from the specific geometry of disposition of nodes in the carbon atom,
pronounced in graphite, keeps also in diamond in its crystallographic planes (Figure15a).
The aforementioned similarity relates to multiplicity of overlapping of nodes as well.
Peculiarities of overlapping of the nodes in graphite were considered in a preceding section.
Similarly, the parameters of diamond presented in brackets in Figure 15 correspond to a
hypothetical case of non-coupled single atoms, participating supposedly as elementary units
at the formation of a diamond lattice. A three-multiple overlapping of atomic nodes of
different carbon atoms takes place in this case. The parameters indicated in brackets do not
agree with the data accepted in physics.
Obviously, if only a structural analysis would be based on the shell-nodal (i.e., multi-
center or molecule-like) atomic model, the gauging would be different; depending on the
condition of what is accepted in the capacity of an elementary building block of crystal
lattices a molecule-like atom or a carbon dimer, C or C2.
Assuming as in the case of graphite that the lattice constants of crystals accepted in
physics are precise and congruent to reality, we must accept that elementary building
blocks in diamond (as, generally, in all carbon crystals) are diatomic molecules of carbon,
C2.
5. The Formation of Bindings in Hydrocarbon Compounds

A carbon frame is the basis for hydrocarbon molecules. An external shell of the carbon
atom (l = 2, , see Figure 6) with four potential polar-azimuthal nodes is entirely
completed by coupled H-atoms. The next subshell ( ) of the same shell, l = 2, with
four empty nodes belongs to the neon atom, Ne, the atomic number Z = 10. Neon has all
completely filled subshells ( , ) of the shell l = 2. Intermediate solutions
(atomic numbers Z = 7, 8, and 9, respectively) relate to the atoms: N, O, and F. They have
half-integer external shells with polar-azimuthal nodes lying in the equatorial plane.
Empty nodes of the next external shell, which is outside the completed shell of the carbon
atom, are in an equatorial plane as shown in Figure 16a,b (designated by dotted lines). The
empty shell outside the carbon atom is simultaneously a vacant shell for the carbon
environment. This shell plays a role in the formation of molecules. Four empty nodes of the
shell can absorb H-atoms from the outside. By this way, the chemical level of bonds is
realized and hydrocarbon molecules are formed as a result. Accordingly, this shell is called
the improper shell of carbon.
Thus, when the improper shell is drawn into a process of interchange (interaction) with
hydrogen, hydrocarbon molecules are formed. The resulting structure of the improper shell
repeats the discrete nodal structure (geometry) of the external shell of the corresponding atom
to which this shell is proper. In a case of chemical adsorption of four H-atoms by the nodes of
the improper shell of carbon, the methane molecule CH4 is formed (see Figure 16c). The
conditional designations of the structures under consideration are drawn on the right side of
the figures.
A structural analog of the methane molecule is the neon atom (Z = 10). The latter has the
same geometry of the disposition of nodes as the methane molecule CH4 drawn in Figure 16c.
But external nodes of the neon atom have fully completed by coupled H-atoms equatorial
nodes strong bound with the rest nodes of neon in comparison with the chemical level bonds
of the nodes of the improper shell of the carbon atom filled with single atoms at the formation
of methane. The next possible nodal structure of CH4, when two nodes of the improper shell
absorb coupled H-atoms, H2, is shown in Figure 16d.
Moreover, the radial solutions of the wave equation (1) give a series of radial shells (see
Figure 3 and 4) slowly damped in amplitude (in the radial direction), with alternating zero
amplitude values determined by a series of zeros of Bessel functions [28]. These shells are the
proper shells for the atom but of the second, third, etc. order. The nearest (second order)
proper polar-azimuthal shell of carbon (l = 2, ), following the first order completely
filled external shell, with four empty nodes of the same polar-azimuth angular orientation, is
shown in Figure 16a,b by dotted lines. The nodes of the second order proper shell of carbon
are in a perpendicular plane with respect to the aforementioned nodes lying in an equatorial
plane of the improper shell.
302 G.P. Shpenkov
A case of the participation of the second order proper radial shell in the formation of
molecular bonds, resulted in a plane structure of the disposition of all potential constituents in
methane molecule, is shown in Figure 17.
Figure 16. The carbon structure (a, b) with two nearest proper and improper spherical shells and their
potential polar-azimuthal nodes designated by dotted lines; (c, d) two of the possible ways of the
formation of the methane molecule CH4. (Polar nodes are not shown here).
Figure 17. (a) An internal structure of the carbon atom , and (b) a possible polar-azimuthal
structure of methane molecule CH4; all chemically adsorbed individual H-atoms are in one plane with
the completely filled with coupled H-atoms proper potential nodes of carbon.
The possible structure of some hydrocarbon compounds is demonstrated in Figure 18.

Under the formation of a great number of carbon based molecules with C C bonds, two- and
three-multiple overlapping of polar-azimuthal nodes belonging to different interacting carbon
atoms (or domers) takes place. An overlapping of polar-azimuth nodes is realized along the
external and internal bonds of external and internal atomic shells, respectively, belonging to
contacting carbon atoms, as shown in Figure 18.
Two-multiple overlapping of the nodes of single H-atoms, characteristic for a
homologous series of saturated hydrocarbons and having the general formula CnH2(n+1), is
shown in the first row in Figure 18. The three-multiple overlapping of the nodes of single H-
atoms, similarly as coupled H-atoms in graphite, fullerenes, diamond (shown in previous
sections 3 and 4, see Figs. 10, 11, 13, 15) and in other carbon crystals, is also realized in
cyclic hydrocarbon molecules (the second and third rows in Figure 18).
Figure 18. The structure of bindings in some typical hydrocarbon compounds based on the shell-nodal
atomic model.
An overlapping occurs with both carbon atoms and carbon dimers (see Figure 19). In
gaseous carbon compounds (as for example, in ethane C2H6, shown in Figure 18), single
304 G.P. Shpenkov
carbon atoms are overlapped as a rule. Dense carbon compounds, as for example benzene
C6H6 (Figure 19c), are formed from carbon dimmers C2. And such compounds, as for
example cyclohexane C6H10 and cyclooctadiene C8H12 (see Figure 18) are composed from
both single carbon atoms, C, and carbon dimmers, C2; their positions are indicated in
Figure 18.
From Figure 18 it follows that among cyclic hydrocarbons CnH2n (cycloalkanes), where
, the more stable is cyclohexane C6H12. The equilibrium geometry of atomic bindings
in all six bound carbon atoms is not deformed; hence cyclohexane is not a strained compound.
The most deformed intratomic bindings in carbon (with respect to the equilibrium structure
originated from solutions of the wave equation (1)) are observed in cyclopropane C3H6 and
cyclobutane C4H8. This is why these compounds are highly strained ones. They have maximal
superfluous enthalpy (formation heat) among cycloalkanes: 37.674 and 26.377 kJ/mol,
respectively; for comparison, cyclohexane has 0 kJ/mol.
The direction of C C bonds in hydrocarbon compounds and the character of
overlapping of their potential polar-azimuthal nodes for a case of single carbon atoms is
demonstrated in Figure 19a (two-multiple overlapping), for the carbon dimmers in Figure
19b,c.
Figure 19. A schematic view showing how C C bonds in hydrocarbon compounds are formed, and the
character of overlapping (two- and three-multiple) of polar-azimuthal nodes for the case of single
carbon atoms (a) and their dimmers (b, c).
From the figures presented it follows that, at the formation of compounds, the internal
nodes, 1 and 2, of connecting atoms never overlap between themselves. In all cases these
nodes are overlapped only with the nodes belonging to external shells of nearby attached
atom, as for example, it is shown in Figure 19a, where an internal node 2 (or 1) of one carbon
atom is overlapped with the external node 3 (or 6) of a nearby attaching atom.
A three-multiple overlapping is realized with carbon dimmers, C2, at the formation of
carbon crystals. In this case (see Figure 19b), one internal node of one dimer is overlapped
with two external nodes belonging to two nearby dimers. For example, an internal node 2 (of
the 1st dimer) is overlapped with the node 4 (of the 2nd dimer) and the node 6 (of the 3rd
dimer).
Two-multiple overlapping of dimmers resulted in a closed hexagonal ring with six

vertices-nodes is characteristic feature for the carbon frame of the benzene molecule
(Figure 19c).
Figure 20. A schematic view of self-binding (assembling) of two-dimensional carbon compounds.
A schematic view of self-binding (assembling) of two-dimensional carbon compounds on

the basis of carbon dimmers, C2, such as graphene and benzene, is presented in Figure 20.
Nature uses the method of self-assembly, self-organization that resulted in complexity of
306 G.P. Shpenkov
nature. The structure of carbon crystals is strongly deterministic. For example, characteristic
feature of the graphene is the fact that all its constituent carbon dimmers, C2, are arranged in
such a way that they form straight continuous chains of potential-kinetic polar nodes along a
crystallographic direction coincident with joined z-axes of linked dimers. It means that the
graphene is crystallographicly and, hence, physically anisotropous. Apparently, owing to such
a structure, presented in Figure 20, graphene possesses unusual physical and chemical
properties found recently experimentally [24].
A carbon frame of the benzene molecule, C6H6, has the form of a flat hexagonal ring,
which is closed without a strain. Its formation from carbon dimmers C2 and a resulting
structure are demonstrated in Figure 20.
An ideal conjunction of all bonds conditions a high stability of benzene rings. It is well-
known that the benzene molecule behaves as a closed superconductor. Apparently, this
feature occurs due to the junction around its center of three chains of empty polar potential-
kinetic nodes. Thus, unique physical properties of the benzene molecule are determined by
the specific nodal structure shown schematically in Figure 20.
Thus, the structural features of carbon compounds, which we have already considered,
are naturally and logically explained in the framework of shell-nodal atomic model,
originated from the solutions of the wave equation (1).
6. Shell-Nodal Structure of Oxygen Compounds

Let us consider now the formation of oxygen compounds, including some its compounds
with carbon. The shell-nodal structure of the oxygen atom is presented in Figure 9. The
external shell of oxygen is half-integer with two polar-azimuth nodes in an equatorial plane
(according to the solutions (10) at s = 2) filled in with coupled H-atoms. An external quarter-
integer shell at s = 1belongs to the nitrogen atom, 7N; the external fractional shell at s = 3
belongs to the fluorine atom, 9F. The entirely completed external integer shell at l = 2 and
belongs to the neon atom 10Ne. The latter contains four external potential polar-
azimuthal nodes (numbered as 7, 8, 9, 10 in Figure 21). Thus, the half-integer external shell
of oxygen is intermediate between the entirely completed external integer shells of carbon (l
= 2, , Figure 6) and neon (l = 2, , Figure 21).
The neon atom with the proper external shell in an equatorial plane, contained four
completed equatorial nodes (at l = 2, ), belongs to one of the balanced atomic
formations. The external shell with indicated in brackets parameters is simultaneously the
resulting balanced shell for molecular compounds formed with the atoms N, O, and F (atomic
numbers Z = 7, 8, and 9, respectively) having every a partially filled (fractional) external
shell. Accordingly, this shell, proper for neon, is regarded as improper for nitrogen, oxygen
and fluorine atoms.
Correspondingly, empty improper nodes of the external shell of the aforementioned
atoms are active centers of adsorption of H-atoms from environment. They provide the
chemical level of interatomic nodal bonds owing to the full filling of the improper (vacant)
nodes of the improper shell without breakdown of the individuality of every of interacting
atoms.
Figure 21. Plots of polar-azimuth functions and nodal points on radial shells of the neon atom.
Figure 22. A conditional image of the formation of water molecule H2O, and the density of probability
(contour plots) of the localization of substance (H-atoms) in the external shell for the planes x = 0, y
= 0, and z = 0; the dashed smaller arrows in the pictures indicate the main directions of external
internodal bindings inherent in the water molecule.
It should remind that when the improper shell of an atom is drawn into process of
exchange (interaction) at the chemical level of bindings, and improper nodes are filling due to
adsorption of single or coupled H-atoms, a new atom does not form. Just a molecule with the
308 G.P. Shpenkov
shell-nodal structure, repeating the discrete geometry of the atom (neon in our case) with the
balanced external shell, is formed.
In particular, the water molecule H2O can be formed in result of adsorption of two
individual H-atoms by two improper (empty) nodes, 9 and 10, of the improper shell of
oxygen as shown in Figure 22.
In the framework of shell-nodal atomic model, the water molecule can be regarded as a
structural analogue of a short-lived isotope of neon (1672 ms half-life [23]). Actually,
both the isotope and the water molecule have the same atomic mass, 18, the same geometry of
disposition of the nodes and the same multiplicity of filling of all nodes. However, of course,
they have not the same strength of bindings in their proper and improper external shells,
respectively.
The shell-nodal structure of individual water molecule is not entirely completed not all
its nodes have paired H-atoms. Therefore this structure is not completely equilibrium. Such a
structure will continuously aspire to form bindings with hydrogen and other water molecules
by joining their half-completed nodes till the coupling of single H-atoms in them will not be
achieved.
If we take a look at the water molecule in the direction along the x-axis, we find the
hexagonal structure of disposition of its nodes with six radial directions of exchange
(interaction) in the plane x = 0, designated by smaller (dashed) arrows in Figure 22. Two
other directions of exchange connecting two improper nodes of oxygen, 9 and 10, are in the
plane y = 0, along the x-axis. The specific nodal structure of the H2O molecule enables the
formation of the great variety of possible chemical (and, hence, relatively weak) internodal
bindings between different H2O molecules; and, hence, it provides the great variety of
resulting intermolecular structures in a liquid state (water) that is clear observed
experimentally in a frozen state (in ice crystals). In particular, the nodal structure of oxygen,
apparently, determines numerous symmetric-asymmetric hexagonal forms of snowflakes,
short-range order of liquid water and long-range crystalline order of ice, dynamic and
thermodynamic anomalies of water, etc.
Water is the most abundant compound on the Earth and a major constituent of all living
organisms. It is still the most enigmatic liquid on the Earth, apparently, because of the
aforementioned specific nodal structure of the oxygen atom and its bonds with hydrogen.
The radial solutions of the wave equation (1) give a series of slowly damped in
amplitude, in radial direction, radial shells (shown, for example, for the carbon atom in Figure
3 and 4) with alternating zero values determined by a series of roots of Bessel functions (see
Eq. 9 and Table 1). The half-integer solutions are determined by the solutions (11) and (12),
where s = 1, 2, 3, is actually the number of proper potential polar-azimuthal nodes entering
in an external fractional shell of a corresponding atom. The distribution of the density of
probability (in different plane sections of the water molecule) for the external shell is shown
in Figure 22.
The formation of oxygen O2 molecules (just like carbon ones) can be realized by different
ways as shown, for example, in Figure 23. The possible nodal structure of the oxygen
molecule O2, when the two-multiple overlapping of completed external proper nodes,
belonging to two individual oxygen atoms takes place, is demonstrated in Fig 23a. Two
improper nodes of oxygen are depicted by dashed circles. In a resulting molecule, all nodes
(except of improper) are in one plane. The molecule obtained has four empty improper nodes.
Figure 23. Two possible ways of the formation of the oxygen molecule O2.
Figure 24. (a) One more possible way of the formation of oxygen O2, and the possible nodal structure
of carbon oxide CO, carbon dioxide CO2, and the ozone molecule O3; (b) the symbolic designations of
the compounds distinguished by the two-multiple overlapping of proper nodes of the constituent atoms.
Another possible structure of oxygen molecule O2, shown in Figure 23b,c, is formed with
the participation of improper nodes. The overlapping of completed proper and empty
improper external nodes of interacting atoms leads in this case to the bulk structure of the
obtained oxygen molecule. The nodes of constituent oxygen atoms in the resulting molecule
are in mutually perpendicular planes. The molecule obtained has three empty improper nodes.
The resulted structure is not therefore fully completed, just like the structure presented in
310 G.P. Shpenkov
Figure 23a, that stipulates its chemical activity to form bindings with other atoms and
molecules.
We cannot also exclude the third way (not shown in Figure 23) analogous to the way of
the formation of the C2 molecules shown in Figure 12, when all nodes of two approaching
oxygen atoms are mutually overlapped in pairs.
Another one more possible way of the formation of the oxygen molecule O2, which is
realized by two-multiple overlapping of completed proper nodes, is demonstrated in Figure
24a. The formation by this way of a triatomic molecule of oxygen, ozone (or trioxide), O3, is
shown in this figure as well. The similar way, apparently, is characteristic for the formation of
chemical compounds of oxygen with carbon, CO and CO2, as also shown in this figure.
The analogous interatomic bindings (just like above considered for oxygen and carbon
compounds) take place for nitrogen monoxide (or nitric oxide) NO and nitrous oxide (or
nitrogen hemioxide) N2O. The possible structures of hemioxide N2O are shown in
Figure 25a,b.
Figure 25. Two possible ways of the formation of hemioxide N2O: (a) an intermediate (unfolded) image
of one of such ways, (b) another of the possible nodal bindings in the hypothetical structure of N2O.
The equatorial densities of probability (contour plots) are drawn for external shells of separate
atoms, and (the upper row, left and right); for the shell at l = 2, (the section for z
= 0); and for the external shell of the resulting formation (l = 3, ).
The beginning stage of one of the possible ways of the formation of N2O is shown in
Figure 25a. The nitrogen atom has one proper node in its external fractional shell, filled with
coupled H-atoms, and three empty improper nodes. Two nitrogen atoms can be attracted
every by their external proper nodes to the improper nodes of the oxygen atom (located along
the x-axis) and stay there as shown in the figure.
There are other ways of the formation of N2O. For example, the overlapping of two
external proper nodes of oxygen with improper nodes of two nitrogen atoms, respectively, at
the beginning stage of the formation of the molecules, is also possible. Two associated
nitrogen atoms (left and right) have rotational degrees of freedom (around the joined nodes).
Turning around, they can change situation and form the bonds between themselves and
oxygen, turning about the overlapped nodes up to overlapping either single nodes or pairs of
nodes belonging to their internal shell (at l = 2, ) as, for example, shown in
Figure 25b.
The next but very enlightening example of the formation of oxygen compounds in view
of their shell-nodal structure is the aluminum oxide Al2O3. Its structure, admissible by the
solutions of the wave equation (1), is presented in Figure 26 in unfolded and closed forms.
The atomic number of aluminum is Z = 13. It means that it has a fractional external shell
at l =3 next to the inner shell at l = 3, m = 0. This shell contains 3 proper nodes filled by
paired H-atoms lying in the equatorial plane.
Improper vacant nodes of every from three conjugated oxygen atoms (designated by
hollow circles in the figure) are joined with external proper nodes of two aluminum atoms, as
indicated in Figure 26d by arrows. By this way it is achieved a perfect compact arrangement
of all overlapped nodes of two aluminum atoms (situated up and down opposite to each other,
Figure 26e) and three oxygen atoms, seated symmetrically between them. A stable neutral
formation, as if five individual neon spaces were tightly embedded and bound together,
reminding a perfectly associated cogged joint, is achieved in this case.
A formation of the nodal structure of carbon and oxygen compounds presented above
allows us to note the following. The characteristic feature of carbon in all its innumerable
compounds is the fact of the existence of two- and three-multiple overlapping of joined nodes
of constituent atoms or dimers. The three-multiple overlapping takes place in most cyclic
carbon compounds (Figure 18) and in all crystallographic forms of carbon as for example:
graphite (Figure 10), diamond (Figure 15), graphene (Figure 11 and 20), and fullerenes
(Figure 13). Remember, three (or two) multiple overlapping of completed nodes means (see
for example Figure 13b and Figure 19) that an overlapped nodal point (a joined node) belongs
to three (or two) individual atoms, C, or to three (or two) carbon dimmers, C2. And taking
into account the coupling of H-atoms in the nodes of the carbon atom, every such a joined
node contains from 6 (or 4) H-atoms (when single atoms are overlapped) to 12 (or 8) H-atoms
(when carbon dimmers are overlapped).
Compared with carbon compounds, the formation of oxygen compounds is mostly
characterized by only two-multiple overlapping of the completed nodes of individual atoms.
According to shell-nodal atomic model, the overlapping of completed nodes occurs
mainly in such a way that resulting internodal-interatomic (chemical) bindings are realized
just along the principal intra-atomic internodal (strong) bonds (Figure 18) existed between
external nodes (belonging to external shells) and conjugated nearby internal nodes (belonging
312 G.P. Shpenkov
to internal shells) of interacting atoms. Considered examples of the formation of compounds

based on the carbon and oxygen atoms confirm this peculiarity.
Figure 26. Two images (a and b) of the nodal structure of the atoms O, Ne, and Al and their conditional
designations (c) for different projections; the unfolded (d) and closed (e) conditional images of the
resulting structure of the Al2O3 compound.
The next peculiarity characteristic for all compounds is that single bindings between the
1st and 2nd internal nodes of an internal shell (corresponding to l = 1, ) of
constituent atoms (or dimmers) never overlap (see Figs 9 - 11, 13, 15, 18 - 20, 24 - 26).
Thus, on the basis of shell nodal atomic model, originated from solutions of the wave
equation (1), all structural features of chemical compounds, which we have already
considered, are naturally and logically revealed. It should be noted also that resting on the
dynamic model of elementary particles and the aforementioned atomic model, physical
phenomena already found are also well described, revealing unknown earlier regularities and
features (see References).
7. Intra-Atomic Bindings and the Binding Energy of the Carbon

Atom
Unlike the conventional quantum mechanical (mono-center) nuclear model, the shell-
nodal atomic model is molecule-like, i.e., multi-center. Its atom consists of H-atoms (to which
we refer proton, neutron and hydrogen atom) which are not all in one central point, nucleus. It
is the principal discrepancy with the common nuclear (mono-center) atomic model. The main
role in the new atomic theory, based on the shell-nodal atomic model, belongs to nodal H-
atoms, constituents of atoms, but not to electrons particles of the second order in magnitude
(mass) with respect to H-atoms. A was shown above, interatomic chemical bindings of
different atoms are realized along the characteristic directions defined by the specific
geometry of disposition of nodes with coupled H-atoms within them (Figure 27).
Exchange interactions of nodal H-atoms are responsible for the formation of both intra-
atomic and interatomic bonds, for the origination of different atoms and molecules, solids and
liquids. Electrons define only the strength but not directions of chemical bindings between
nodes, belonging to outer shells of different interacting atoms. Let us show this from another
side basing on general estimates of exchange interactions related to both intra- and
interatomic binding energies.
Figure 27. (a) A schematic view of internodal nucleon (nuclear) bonds in the carbon atom ; and
(b) characteristic internodal distances (between their centers) determined by the roots of Bessel
functions.
As was mentioned above, the new atomic theory rests also on the dynamic model of
elementary particles. In accordance with this model, elementary particles, being pulsing
microobjects, do not have the rest mass. The mass of the particles, as dynamic microobjects,
has associated character [5] and is defined by the formula
(25)
314 G.P. Shpenkov
where is the radius of a pulsing wave spherical shell of a particle; is

the absolute unit density; is the wave number corresponding to the
fundamental frequency of the atomic and subatomic levels (see (2)), which is the
fundamental frequency of the field of exchange of the levels (it is the frequency of
electrostatic field); herein c is the basis speed of exchange of matter-space-time at the
subatomic level equal to the speed of light.
We will assume that external and internal spaces of H-atoms are delimited by the Bohr
radius , so that the mass of H-atoms calculated from Eq.
(25) is ;
The rate of mass exchange (or, in other words, exchange charge of the H-atom [5])
responsible for internodal bindings between atomic constituents, H-atoms, is equal to
(26)
The rate of mass exchange of such a value determines the high stability of individual
atoms. Actually, the energy of interchange (interaction) of two separate H-atoms (situated in
two conjugated nodes of the same atom) being apart at the distance
(that is the length of double bindings in graphite, see Figure 10), is equal to
(27)
This value correlates with the experimental data for the binding energy of neutron in a
carbon nucleus and with the threshold energy of (, n) reactions [30] equal to . If
we shall take the length quoted from [31], corresponding to the
isolated double binding in C = C = C and CH2 = C = O structures, the obtained internodal
energy of interaction of constituent H-atoms of (following from Eq. (27)) will
practically coincide with the above threshold energy of (, n) reactions. Accepting
(indicated in brackets in Figure 10), we arrive at the energy
that is close to the threshold energy of (n, 2n) reactions in
isotope [30] (p. 887), etc.
The energy of interchange (interaction) of two separate H-atoms situated in two
conjugate nodes of the same atom [3] being apart at , is equal to
. The taken distance r is the length of a single binding between the internal
nodes 1 and 2 (see Figure 10b or 19a). This distance is also equal to an averaged
characteristic length of different bindings with participation of oxygen (S O, C O, N O,
B O, etc. [31]). The obtained energy correlates with the experimental value for the binding
energy of neutron in an oxygen nucleus and with the threshold energy of (, n) reactions in
the nucleus, equal to [30].
Calculated from the formula on the mass difference, , the binding energy of
the carbon atom , equal to , mainly depends on the energy of its nucleus
consisting of 12 nucleons. Let us show how this energy can be derived in the framework of
shell-nodal atomic model which has not a conventional nucleus ascribed to atoms by modern
physics. The derivation of the binding energy presented below one should regard as an
estimation, because it was conducted on the basis of some suppositions regarded as
preliminary axioms[18].
Basing on solutions of Eq. (1), we must take into account only those shortest internodal
bonds in the carbon atom which are distinguished by the shortest distances between wave
shells of internodal nucleons. Angular directions of such bonds are conditioned by the space
geometry of polar-azimuthal functions (see Figure 2 and 6). The symbolic designation of
carbon (introduced in Figure 6c) reflects a plane geometry of arrangement of all six
principal potential polar-azimuth nodes and shows the shortest directions of exchange
(interaction) between them. Just along these directions (except along the bonds between the
internal nodes, 1 and 2), shown in Figure 27a, the chemical bonds between nucleon nodes of
different atoms are realized at the formation of carbon molecules and crystals [29].
Regularities of wave processes are described by the Bessel functions that influence the
strictly definite structure of material spaces at all levels. Five internodal bonds (1 2, 1 3, 1
5, 2 4, 2 6, see Figure 27), responsible for the binding energy in the carbon atom, have
the same length r1 which is defined by the root of Bessel functions [
28] (as in a case of the helium atom):
(28)
i. e., , where r0 is the Bohr radius; (see
(4)).
All other characteristic internodal distances in the carbon atom: r2, r3, and r4 shown in
Figure 27b are not arbitrary as well. They are defined by the following roots, respectively:
(29)
Hence,
(30)
The binding energy in an atom is attributed to three causes and consists of:
316 G.P. Shpenkov
(1) the binding energy of paired nucleons in nodes, i.e., in essence, the energy of
deuterons;
(2) the binding energy of nucleon nodes with atomic shells to which these nodes belong;
and
(3) the energy of internodal exchange (interaction) of nucleons.
Thus, the first constituent must take into account the energy of coupling of two nucleons
in a node. We will not describe its derivation here in the framework of shell-nodal atomic
model; it is not the matter in question here. The latter is considered in detail in [18]. We will
use the value equal to the deuterons binding energy 2.224 MeV per node obtained from the
formula on the mass defect, :
(31)
We have the right to take this value assuming that according to shell-nodal atomic model
the coupled protons and neutrons in nodes are in the form of the deuteron D (
The second constituent of the binding energy is defined from the following conditions. In
a spherical atomic field, radial amplitudes of oscillations of H-units in nodes of the n- atomic
shell are determined by the expression
(32)
originated from solutions of Eq. (1) for the radial function [1], where
(33)
and are Bessel functions. The constant A is equal to
(34)
Then, assuming that (atomic mass unit), at the

level of the fundamental frequency e, the energy of oscillations takes the form:
(35)
where is the roots of Bessel functions,

The root defines an equilibrium distance
between two potential polar-azimuthal
nodes of an internal atomic shell of carbon. Hence, according to (35), for the 1st and 2nd
nodes (Figure 27) situated in the internal atomic shell, the binding energy of the nucleon node
with the atomic shell is
(36)
Thus, the second constituent of the binding energy (36) takes into account the bond of a
node with the atomic shell where this node is located.
A transition from one n-shell into another is defined by the following energy of the
transition:
(37)
Transitions of nucleons from the internal shell to the external shell, where four nodes are
located, are defined by the above formula. For and , we have
.
The binding energy for every of the four nodes of the external shell is
(38)
According to the DM, and the law of the universal exchange, the energy of exchange
(interaction) of particles at atomic and subatomic levels is defined by the formula
(39)
where and are exchange charges of interacting particles (pulsing

microobjects).
The third constituent of the binding energy of the carbon atom , the energy of
internodal exchange, is determined by the formula (39). According to the latter, an elementary
binding energy, caused by exchange interaction between two nodes a distance r1 apart, is
(40)
318 G.P. Shpenkov
The exchange energy (40) of the quantum of nucleon exchange of the 1st
node (Figure 27a) expends on three equal bonds with 2nd, 3rd, and 5th nodes; and the 2nd
node expends on the bonds with 1st, 4th, and 6th nodes. Hence the binding energy per node
(we mean 1st and 2nd nodes here) is
(41)
Every node of the 3rd, 4th, 5th, and 6th nodes are connected only with one node (1st or
2nd). Hence, the binding energy per node (for nodes from 3rd to 6th) is
(42)
Thus, we have the following internodal binding energies between the nodes of the
numbers
(1-2):
(43)
(3-1), (5-1), (4-2), (6-2):
(44)
Thus, the total energy of internodal exchanges is
(45)
A resulting sum of all constituents of binding energy of the carbon atom , calculated
for the exchange charge of the proton, qp: (31), (36), (38), and (45), is
(46)
Calculations for the exchange charge of a neutron give

.
Subtracting the energy , that have the four valent electrons of the
carbon atom , from the value (46), we arrive at the energy of the carbon ion :
(47)
We see that the binding energy of the carbon ion , obtained here on the basis of
shell-nodal atomic model and dynamic model of elementary particles, is in well agreement
with the binding energy of the nucleus of the stable carbon isotope , ,
calculated from the formula .
It should be noted at the conclusion that the shell-nodal atomic model allows
understanding the physics of atomic reactions caused by an inelastic interaction of high-
energy particles with substance. Actually, main structural units of the shells are potential
nodes with coupled H-atoms (and, of course, empty kinetic nodes not considered here),
representing by themselves deuterons. The d-, p-, and n-radiation occur when nodal H-atoms
tear off from their nodes. Besides, outgoing important elementary constructions of shells,
such as structural edges of two nodes completed with the two pairs of H-atoms, form -
radiation. Under powerful impacts, it takes place a splitting off of external shells of heavy
atoms, resulted in the formation of lighter elements. Consequently, such elementary
splinters, as p, n, and t ( ), also appear.
8. Interatomic (Molecular Level) Binding Energies

In accordance with the shell-nodal atomic model, we consider atoms as quasi-spherical
multiplicative molecules of H-atoms. The word multiplicative means that particles (H-
atoms), constituted these elementary molecules, are characterized by strong intra-atomic
internodal bonds (analogous in value to common nuclear). Accordingly, we call them
multiplicative bindings.
Ordinary molecules with relatively weak (chemical) bonds (analogous to cohesive or
adhesive bonds), we call additive molecules. They are related to the electron level of
bindings. For example, if deuterium D (an isotope of the hydrogen atom containing two H-
atoms) is the multiplicative molecule then the hydrogen molecules H2 is the additive
molecule. Accordingly, in the latter case we have relation with additive bindings.
Let us estimate the electron level of bindings, the level of additive bindings. The energy
of electron binding is equal to
(48)
where
(49)
is the minimal quantum of the rate of mass exchange, the electron exchange charge;
(50)
320 G.P. Shpenkov
is the absolute unit density;
is the fundamental wave radius (see (4)).

The energy obtained, , predetermines the electron work function of solids. For
instance, the electron work function of mono- and polycrystals of Al, B, Bi, W, Fe, Co, and
Cu is within [32, 33].
The energy (48) practically coincides with the dissociation energy of the molecules: H2
( , HD ( ), HT ( ) and close to the dissociation energy of the
molecules O2 ( ) and OH ( 4.4) [30] (p. 425), etc. The energy of electron
binding (48) correlates with the break energy of bindings in molecules and radicals. For
instance, it is equal to in reactions and ; in
, it is .
The binding energy (of the electron level) per mole of substance defines the characteristic
break energy of chemical bonds
(51)
where NA is the Avogadro number.

A definite energy is spent upon tearing off the H-atom from a node of the improper shell.
In accordance with the experimental data [34], this energy is equal to
for CH4 and for C2H4 that is consistent with the obtained value (51).
Obviously, in a case of breaking of two bonds simultaneously, the break energy must be
approximately twice as much. Actually, a breakdown of O2 molecule with two similar bonds
requests about . The additive bindings (of the electron level)
show its worth in the molar heat capacity of molecules and other phenomena considered in
detail in [1].
9. Conclusion
We should not only calculate all the results [37], but also reveal and understand the
genetic code of structural variety in Naturecomprehend Nature, where the above
considered carbon and oxygen and their constituent hydrogen atoms dominate. Therefore,
creation of physical atomic models is inevitable. The imaginable physical atomic models
must be non-contradictory, clearly comprehensible, and well agreeable to common sense,
logic and the experimental data. The shell-nodal atomic model described here responds to
these requirements.
A new atomic theory based on shell-nodal atomic model and dynamic model of
elementary particles accounts for all physical phenomena, related to atomic structure, which
we already had time to consider [1]. First of all it predicts theoretically the number of all
possible isotopes, including the ultimate oneslightest and heaviest (shown in this report for
carbon), revealing their internal structure. The latter was a large gap in our knowledge that
existed till now due to invalidity of quantum mechanical atomic theory (QM) dominated
currently in modern physics. The shell-nodal atomic model, taking the first steps, has been
considered here in general outline by the very important examples of the structure of carbon
and oxygen atoms.
The shell-nodal (multi-center) structure of atoms reminds the nodal structure of spherical
resonant cavities having internal oscillating electric and magnetic mode fields. They are
described by Bessel functions. Such resonant cavities can exist in free space even without
physical material guiding the wave [36]. All types of elementary crystal formations represent,
in essence, the elementary nodal structures of standing waves in a limited three-dimensional
wave physical space.
All atoms with , including the above described carbon and oxygen atoms (Z = 6
and Z = 8), like their basic constituents H-atoms (Z = 1), have an internal structure defined by
solutions of ordinary wave equation (1), reminding R.J. Hays elementary molecules [35].
The physical shell-nodal (molecular-like) atomic model enables simpler and convincing
elucidation of the formation of chemical compounds in comparison with an abstract and
intricate explanation based on the QM atomic model. As turned out the main role in the
formation of molecular and crystal structures belongs to nodal H-atomsconstituents of
atoms. Electrons define only the strength but not directions of chemical (additive) bindings.
The crystal structure of graphite, diamond and buckminsterfullerene is characterized by
either three-multiple overlapping of nodes belonging to 3 carbon atoms, or to six-multiple
overlapping of nodes belonging to 6 carbon atoms (3 carbon dimmers, C2). We cannot
uniquely state now, which one of the two possible overlaps, three- or six-multiple, is closer to
reality. In the light of the discovery of shell-nodal atomic structure, both above cases are now
equiprobable. An additional investigation on conformity of the commonly used gauging
(accepted in the structural analysis with due account of nuclear atomic model) to the shell-
nodal atomic model has become topical; this must resolve in the future above duality. It is
necessary for a precise verification of lattice parameters and binding lengths, accepted
currently in modern physics, in view of the new concept on the intra- and interatomic
structure.
The new theory operates with exchange charges. This enables revealing the nature of
nuclear and chemical bindings from one theoretical concept, the universal law of exchange
(related to gravitational, electromagnetic, and strong interactions [1]). The rate of mass
exchange of H-atoms, or exchange charge of H-atoms, defines the nature of multiplicative
intra-atomic bindings (called in modern physics strong or nuclear). The electron exchange
charge, the minimal quantum of the rate of mass exchange, is responsible for additive
(interatomic, or chemical) bindings. Estimations of the energy of interactions between
eigennodes of an atom, having the shell-nodal spherical structure, and between nodes of
different interacting atoms, are entirely consistent with the experimental data.
322 G.P. Shpenkov
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29th Microwave Power Symposium, Chicago, Illinois, July 25-27, 1994.
[24] A.K. Geim and K. S. Novoselov, The Rise of Graphene, Nature Naterials, 6, 183-191
(2007).
[25] Russell S. Drago, Physical Methods in Chemistry, W.B. Saunders Company, 1977.
[26] R.E. Smalley, The Third Form of Carbon, Naval Research Reviews, December (1991),
p. 3-14.
[27] C.S. Yannoni, P.P. Bernier, D.S. Bethune, G. Meijer, J.R. Salem, NMR Determination
of the Bond Length in C60, 113. Journal of the American Chemical Society, (1991), p.
3190-3192.
[28] F.W.J. Olver, ed., Royal Society Mathematical Tables, Vol. 7, Bessel Functions, part.
III, Zeros and Associated Values, Cambridge, 1960.
[29] G. P. Shpenkov, The Role of Electrons in Chemical Bonds Formations (In the Light of
Shell-Nodal Atomic Model), Molecular Physics Reports, 41, 89-103, (2005).
[30] Tables of Physical Quantities, Reference Book (in Russian), edited by I. K. Kikoin, M.,
Atomizdat, 1976, pp. 891-892.
[31] A.J. Gordon and R.A. Ford, The Chemists Companion: A Handbook of Practical Data,
Techniques and References, A Wiley-Interscience Publication, 1972.
[32] A.P. Babichev, et al., Physical Quantities, Reference Book, Atomenergoizdat, Moscow,
1991, Table 23.1, p. 568, in Russian;
[33] H.B. Michelson, The Work Function of the Elements and Its Periodicity, Journal of
Applied. Physics, Vol. 48, No 11, pp. 4729-4733, (1977).
[34] V.I. Vedeneev, et al., The Chemical Bond Brake Energy (in Russian), Moscow, 1962;
A.P. Babichev, et al., Physical Quantities, Reference Book, Atomenergoizdat, Moscow,
1991.
[35] R.J. Hay, Essai dune Theorie sur la Structure des Crystaux, Paris, 1784; Traite
Elementaire de Physique, Paris, Imp. Delance et Lesueur, an XII, 1803.
[36] R.F. Harrington, Time-Harmonic Electromagnetic Fields, McGraw-Hill, 1961.
[37] P.A.M. Dirac, Classical Theory of Radiating Electrons, Proc. Roy. Soc., 1939, V. 168,
p. 148.
Chapter 13
MOLECULAR MODELING OF THE PEANUT LECTIN -

CARBOHYDRATE INTERACTION BY MEANS
OF THE HYBRID QM/MM METHOD
Alexei N. Pankratov1,a, Nikolay A. Bychkov1

and Olga M. Tsivileva1,b
1
Division of Analytical Chemistry and Chemical Ecology,
Institute of Chemistry, N. G. Chernyshevskii Saratov State University,
83 Astrakhanskaya Street, Saratov 410012, Russia
2
Laboratory of Microbiology, Institute of Biochemistry and Physiology
of Plants and Microorganisms, Russian Academy of Sciences,
13 Entuziastov Ave., Saratov 410049, Russia
Abstract
The search and analysis of literature devoted to the problem of molecular modeling of protein-
carbohydrate systems and protein-ligand interaction were performed. The hybrid QM/MM
method was established to be the most appropriate for modeling the proteins interaction with
different ligands. Within the framework of this method, the force fields AMBER and
CHARMM were used until 2000 and during the period 2000-2005, respectively, while the
most recent works deal with the force field OPLSAA as preferable one and UFF to a lesser
extent.
Using the Brookhaven Protein Data Bank, the adequate model of lectin was selected for
modeling interaction in the systems lectin-carbohydrate.
By means of the QM/MM method, modeling of peanut lectin interaction with seven
carbohydrates, the molecules of which incorporate D-galactose and D-glucose chains, was
carried out. Therewith the amino acid fragments of carbohydrate binding site along with the
carbohydrate molecule served as the quantum chemical subsystem.
As a criterion of carbohydrate specificity, the value of formation energy of the complex
(conjugate) lectin-carbohydrate from its composing parts was proposed. The theoretical
a
E-mail address: PankratovAN@chem.sgu.ru, PankratovAN@info.sgu.ru.
Web: sgu.ru/node/44087, sgu.ru/faculties/chemical/pankratov
b
E-mail address: tsivileva@ibppm.sgu.ru
326 Alexei N. Pankratov, Nikolay A. Bychkov and Olga M. Tsivileva
substantiation of dominating specificity of peanut lectin to -anomeric digalactoses, as well as

of higher specificity to galactose derivatives than to glucose derivatives, was presented.
The AIM-analysis of interaction between hydroxyl groups of carbohydrate and polar
(amide, carboxylic, hydroxyl) groups of protein was performed. The above interaction was
shown to obey a criterion of hydrogen bonding. The analysis of electron density topological
properties pointed out the dominating role of aspartic and glutamic acid residues in protein-
carbohydrate binding.
The results of molecular modeling carried out correlate to the experimental data on the
carbohydrate specificity, as well as on the contribution to this specificity made by the
carbohydrate anomers nature and by the L-glutamic acid chains. The latter confirms a
predictive power of the approach used as a whole, the energy of formation of the protein-
carbohydrate conjugate as a criterion of carbohydrate specificity, as well as the electron
density in the bond critical point and Laplacian of this quantity in respect to establishing the
amino acid residues principal for the lectin activity manifestation.
1. Introduction
At present, chemistry has made great strides toward the transformation of covalent and
ionic compounds chemistry into the supramolecular chemistry, which deals with complexes
and associates, in which the mutual components disposition is provided by the non-covalent
bonds [1].
Within the framework of supramolecular chemistry, there is a field of science concerned
with biospecific interaction.
Biospecific interaction (enzyme - substrate, antigen - antibody, protein - carbohydrate,
hormone - receptor, etc.) constitutes the basis of current methods and approaches in analytical
chemistry (immunochemical methods of analysis, affinity chromatography and others), in
which specificity is realized as a highest degree of selectivity.
Affinity (biospecific) labeling is a powerful tool for the proteins research.
Biospecific polymeric adsorbents are used in medicine, biochemistry, and the food
industry.
Supramolecular chemistry gains special importance when being applied to living objects.
Supramolecular chemistry involves such essential definitions as recognition, self-
organization and self-assemblage. All these phenomena occur in living organisms at the level
investigated by molecular biology.
Basic biochemical knowledge assigns nucleic acids and proteins the decisive role in
information flow in biosystems. Connected by the genetic code the transcribed portions of the
genome govern the expression of a complex set of messages on the level of polypeptides [2].
When however aspiring to understand intra- and intercellular recognition processes
comprehensively, the two biochemical dimensions established by nucleic acids and proteins
are not sufficient to satisfactorily explain all molecular events (e.g., in cell adhesion). To
bridge this gap, consideration of further code systems is essential. In contrast to nucleic acids
and proteins, branching of chains is a common feature of the glycan part of cellular
glycoconjugates (glycoproteins, glycolipids). On defining the role of glycans as hardware in
information storage and transfer, it should be noted that oligosaccharides surpass peptides by
more than seven orders of magnitude in the theoretical ability to build isomers [3].
Thus, the capacity for information storage has been extended to the third biochemical
dimension established by so-called carbohydrate code. After introducing first the concept of
Molecular Modeling of the Peanut Lectin 327
the sugar code on the level of sequence and conformation, carbohydrates gain their place as
ideal candidates for generating compact units with explicit informational properties [2].
The message of coding units of the sugar code, in the interplay with sugar receptors, will
trigger post-binding signaling and the intended biological response. Information stored as
sequence and shape will have to be grasped. Translating and transmitting it into intended
responces is the task of decoding devices. They should specifically recognize coding units
established by glycans. Therefore, in addition to physicochemically serving roles to control
folding, oligomerization and access of proteolytic enzymes [4-8], oligosaccharides in glycan
chains can be likened to the postal code in an address to convey distinct messages read by
suitable receptors [2].
The above bioinformation potential of carbohydrates is realized due to biospecific
carbohydrate-protein interaction. The carbohydrate-binding proteins (sugar receptors just
mentioned) are classified into enzymes responsible to assemble, modify and degrade sugar
structures, immunoglobulins homing in on carbohydrates as antigens, and lectins. The latter
class encompasses all carbohydrate-binding proteins, which are neither antibodies nor are
they enzymes which couple ligand recognition with catalytic activity to process the target [9,
10]. Lectins are proteins capable of specific recognition and reversible binding to
carbohydrate moieties of complex carbohydrates without altering covalent structure of any of
the recognized glycosyl ligands [11].
Carbohydrate-protein complexes are formed in the initial steps of a large number of
physiological and pathological processes, which range from cell-pathogen interaction, to cell-
cell recognition, to tumor metastasis, etc. Interference with these recognition events could be
used to modulate or alter signal transmission, or to prevent the onset of diseases.
Molecular recognition by specific targets is at the heart of the drug discovery process.
The synthesis of functional sugar mimics capable of antagonizing oligosaccharides at the
protein receptor level has attracted a great deal of attention as a way to develop drugs with
good stability and synthetic availability [12, 13].
The study of the role of the lectins and lectin-like receptors in the immune system is a
topic of current interest [13]. The immunity-related reactions are known to be controlled in
their early stages by the interaction of proteins with oligosaccharides, often in the form of
glycoconjugates [14-17]. This interaction is realized mainly via lectins or lectin-like
substances capable of recognizing the specific carbohydrate determinants in the cellular
structures. Organelles self-assembling process is accompanied by the above interaction, too
[18].
Therefore, the protein-carbohydrate interaction is extremely important in living systems.
Typical contributions to such kind of ligand binding originate from hydrogen bonding,
electrostatic effects, hydrophobic interaction, medium effects and depend on molecular
conformations, pH of medium, state of the reactants - protein and carbohydrate (protolytic,
tautomeric equilibria, etc.), presence of metal ions, and other factors [19].
Until now, mechanism of the majority of those reactions is not understood thus
presenting a great scientific and practical challenge.
The investigations in this field involve both experimental and computer-assisted
approaches.
For the directive design of appropriate conjugates, promising are the methods of
molecular modeling (molecular dynamics, molecular mechanics, quantum chemistry).
Because of the voluminous size of protein systems, the QM/MM method should be
reasonably applied as combining the powerful aspects of quantum chemistry and molecular
mechanics.
The goal of the present work is molecular modeling of the lectin interaction with
carbohydrates by means of the QM/MM hybrid method.
In the course of investigations, the following tasks have been formulated:
1. To search and analyze literature on the simulation methods concerning the protein-
carbohydrate interaction. To choose the most appropriate variant of the QM/MM method for
modeling the lectin-carbohydrate interaction, as force field and theory level for the quantum
chemical computations.
2. To conduct the selection of model protein in compliance with the following criteria:
lectin nature, known spatial structure, determined saccharide specificity, lack of lipid and
carbohydrate moiety in the molecule.
3. To carry out the analysis of three-dimensional structure of the model protein. To
highlight the binding site(s), as well as the peptide regions critical for binding site. To outline
the quantum chemical and molecular mechanical subsystems.
4. To perform computations of the lectin complexes with different carbohydrates, to
compare the values of energy of conjugates formation with the lectin affinity to saccharides.
To conclude on the predictive power of the calculation method used.
5. To realize the AIM analysis. To elucidate the amino acid residues mostly essential for
the lectin-carbohydrate bonding. To discuss the results obtained in the light of the published
literature data.
The present work has been done following the practice of two lines of scientific inquiries
given below:
The establishment of quantitative structure - property relationships in the series of

inorganic, organic, organoelement, coordination compounds; the statement of the
reactivity interrelation to the molecules and nanoclusters electronic structure in the
ground and excited states on the basis of refining the understanding of electronic
effects, electronegativities of atomic groups, hydrogen bond, generalization of the
views on reaction mechanisms (including oxidation and reduction, nitrosation,
nitration, azo coupling, halogenation, alkoxylation, condensations, other
electrophilic, nucleophilic and radical processes, complexation, ligand exchange,
molecular and ionic association, dissociation, tautomerism and dual reactivity,
isomerization, proton, hydrogen atom and hydride ion transfer), regioselectivity of
homolytic (oxidative and reductive) coupling reactions for the substances of different
classes; study of the medium influence on chemical processes occurrence;
development of the theory of analytical reagents action; molecular modeling of
biospecific protein-ligand interaction, development of physical chemistry of
morphogenic proteins of higher fungi; systematization and generalization of
information about Web resources on natural sciences, on ecology (Professor Dr. Sc.
Alexei N. Pankratov);
Research into the physiology and biochemistry of edible cultivated mushrooms, the
functions and biological activity of glycopolymers and carbohydrate-binding proteins
of xylotrophic basidiomycetes, the role of carbohydrate-binding glycoproteins in the
processes of fungal vital activity, the biosynthesis and characterization of lipophilic

compounds of mycelial fungi (Leading Researcher Dr. Sc. Olga M. Tsivileva).
2. Methodology of Theoretical Study

The initial geometry of protein was gained from the Brookhaven Protein Data Bank
(RCSB PDB) [20].
The molecular modeling was performed by means of the QM/MM hybrid method [21]
(quantum chemical method was PM3 [22-24], force field was OPLSAA [25]) using the
FireFly programs package in the modified version by Dr. James W. Kress [26].
In order to convert the initial PDB file the programs TINKER V 4.2 [27] and Force Field
Explorer [28] were used, and for viewing and analyzing the polypeptide chain the Protein
Explorer V 2.80 program [29].
AIM analysis was carried out by the AIMALL program [30] with the wave function
deduced using the Hartree - Fock method for the basis set of 3-21G [31, 32], by the program
from the PC GAMESS V 7.1.F package [33] for geometry found using the QM/MM method.

3.1. Choice of the Force Field for Molecular Mechanics Computations
Basing on the analysis of works published starting from 1995 up to now (not cited here
because of insufficient place) we have generalized the data on force fields used in the
QM/MM method (Figure 1).
Figure 1. Frequency of force fields use: 1 - CHARMM, 2 - AMBER, 3 - OPLSAA, 4 - UFF, 5 others.
Within the framework of the QM/MM method, the force fields AMBER [34] and
CHARMM [35, 36] were used until 2000 and during the period 20002005, respectively,
while the most recent works deal with the force field OPLSAA [25] as preferable one and
UFF [37] to a lesser extent.
More than a half of papers, which authors exploit the QM/MM method, involves the
quantum chemical methods of DFT group [21].
3.2. Choice of Subject under Study and Initial Approximation Preparation
We have pursued the search for lectins. From all the lectins characterized by three-
dimensional structure (59 proteins) in the Brookhaven Protein Data Bank (RCSB PDB) [20]
we have selected the peanut protein with 2PEL PDB-code (Figure 2). This lectin has been
treated as a model since it is adequately explored experimentally, displays the specificity to
galactose [38-40]. The works on studying this lectin assisted by the quantum chemical
methods are absent, so far as we know.
Figure 2. Peanut lectin macromolecule complexed with 1,4--D-digalactose (one fourth of the
elementary cell of the crystal).
Besides, accessible are structures of this lectins complexes with 1,3--D-digalactose,

1,3--D-digalactose, and D-galactoso-1,6--(N-acetyl-D-galactosamine) [39].
For convenience, in Figure 2 the color of polypeptide chain changes gradually from red
into blue (red is for -end, blue is for N-end). The polypeptide chain is visualized by means
of tubular model, carbohydrate molecule and ions of elements-metals by means of ball model.
In the lower-left part of Figure, the moiety of red balls denotes the molecule of 1,4--D-
digalactose. In the lower part, large red balls denote: on the left - calcium ion, on the right -
manganese(II) ion. Hydrogen atoms are not shown.
Unit cell of the protein crystal structure incorporates 4 identical (both in composition and
conformation) polypeptide chains, each of those involves calcium and manganese (II) ions.
The polypeptide chain consists of 3446 atoms (232 amino acid residues). Within those, two
sections were chosen, including the binding site. The first section comprises the amino acid
residues from 79-th to 134-th (775 atoms), the second one from 210-th to 215-th (84 atoms)
(Figure 3). The end-point fragments of the boundary amino-acid sequences were terminated
(by the addition of hydrogen at N-end, oxygen at -end, types of atoms were changed in
compliance with the force field). The initial PDB-file was converted by means of the TINKER
V 4.2 and Force Field Explorer programs, polypeptide chain was scanned and analyzed using
the Protein Explorer V 2.80 program.
Figure 3. Simulated part of peanut lectin macromolecule complexed with 1,4--D-digalactose. Brown
balls represent carbon atoms, blue - nitrogen atoms, red - oxygen atoms, gray - hydrogen atoms.
In Figure 3 the carbohydrate molecule is arranged on the right, that is why large violet
balls denote, in contrast to Figure 2, on the left - manganese(II) ion, on the right - calcium ion.
The further conversion into a format compatible with PC GAMESS/FireFly was
performed by means of the special software created by ourselves (Nikolay A. Bychkov).
Metal ions were described additionally to the basic program. Carbohydrate molecules were
converted in a manner analogous to polypeptide chains.
3.3. Separating Out the Quantum Chemical Subsystem
As a result of the polypeptide chain analysis conducted using the Protein Explorer V 2.80
program, we decided to construct the quantum chemical component (Figure 4) from the
amino acids 80-83 (aspartic acid, proline, alanine, aspartic acid), 125-129 (tyrosine, serine,
asparagine, serine, glutamic acid), 211 - serine.
Carbohydrate simulations were quantum chemical in all the cases.
Figure 4. Quantum chemical subsystem of peanut lectin macromolecule complexed with 1,4--D-
digalactose. The atoms numbering is given. Brown balls represent carbon atoms, blue - nitrogen atoms,
red - oxygen atoms, gray - hydrogen atoms.
Metal ions simulations were made within molecular mechanics.

The tentative computations and AIM analysis were performed. In consequence of this
analysis it emerged that the residue 83 - aspartic acid did not form hydrogen bonds with
carbohydrate, that is why we decided to transfer this residue into the molecular mechanics
part.
3.4. Computations by Means of the QM/MM Method
It is known [39] that the lectin under our study displays specificity to D-galactose. That
specificity is regularly considered being exemplified by disaccharides derivatives. Few works
report [39, 40] on the preferable specificity of peanut lectin to -anomers of such compounds.
We attempted to substantiate theoretically the given lectins carbohydrate specificity.

This has become the topic of a large body of computations at different theory levels.
QM/MM-computation of the system assisted by personal computer with a AMD Athlon
XP+ 2666 processor and 1 Gb ROM, when considering the quantum chemical part at the
semiempirical 3 level in single point takes time on the order of several minutes, at the
HF/3-21G level on the order of one hour and a half, at the HF/6-31G(d,p) level on the order
of 6 hours. The geometry optimization at the semiempirical level takes about 750 iterations
and several days. Therefore, the geometry optimization at a high level of theory at the given
hardware instrumentation should be impossible. Since the quantum chemical part carries a
charge 2, the DFT method is hardly applicable in the given case because of poor
convergence, this fact being inspected for the instance of B3LYP with the 3-21G and 6-
31G(d,p) basis sets.
It was decided to apply the semiempirical PM3 method, and to describe the molecular-
mechanics part by the OPLSAA force field. The geometry optimization was carried out by
the standard gradient technique.
In the software package FireFly the molecular mechanics block is compatible only
incompletely with the quantum chemical block in the case when the semiempirical methods
of quantum chemistry are involved. For this reason, in the course of our study the geometry of
molecular-mechanics subsystem was not optimized, i.e. was fixed and extracted from the
Brookhaven Protein Data Bank (RCSB PDB) [20]. Nevertheless, by means of the QM/MM
method we have obtained the results (see below) in compliance to the experimental data.
Moreover, fixing the coordinates of atoms entering the molecular-mechanics subsystem leads
to the considerable economy in calculation resources and computations duration. Provided
that the challenge and sufficient calculation resources appear, the above results could be
refined at the high theory level.
Table 1.Carbohydrate part of the lectin-carbohydrate systems
Lectin-carbohydrate system* Carbohydrate part**

2DV9 D-Gal--1,3-D-Gal
2DVD D-Gal--1,3-D-Gal
2DVB D-Gal--1,6-D-Gal
2PEL D-Gal--1,4-D-Gal
2DV9+ -D-Gal
2DVD+ -D-Gal
2PEL+ D-Glc--1,4-D-Gal
*
Sign + means that the carbohydrate part of the system is modified against the analog referred to
in literature
**
Carbohydrate residues abbreviations: Gal - galactose, Glc - glucose
Table 1 refers to the carbohydrate parts of peanut lectin conjugates by their abbreviations
adopted conventionally in the international scientific literature and in the Brookhaven Protein
Data Bank (RCSB PDB).
Computations of all the lectin-carbohydrate conjugates were performed. On the basis of
optimized geometry of each complex, the initial approximation has been chosen for
computing the isolated molecular systems of protein and carbohydrate. Therefore, every
estimation of the formation energy of one or another complex involves the particular value of
energy of the protein molecule adopting a somewhat distinct conformation in a given case.
Consequently, each the value obtained implies hard work.
According to the X-ray data [39] used as the initial approximation, the peanut lectin
secondary structure is organized predominantly by a -type (Figure 3). Fixed geometry of the
molecular-mechanics subsystem conserves such the protein structure, thus providing the
computations correctness.
The results of computations using the QM/MM method are shown in the Table 2.
Table 2. Values of full energy (a.u.) of molecules of peanut lectin, carbohydrates and
their complexes
Energy
System Protein Carbohydrate Conjugate
of complex formation, kcal/mol
2DV9 444.5731264 183.2695074 627.8721643 18.5
2DVD 444.5800379 183.4243216 628.0294127 15.7
2DVB 444.5725665 183.2717943 627.8778614 21.0
2PEL 444.5470548 183.3017077 627.8765784 17.5
2DV9+ 444.5731264 97.5640462 542.1622761 15.7
2DVD+ 444.5800379 97.6897403 542.2972807 17.2
2PEL+ 444.5470548 183.0882028 627.8765784 12.9
Analyzing the data obtained one should remember that the computations have been
carried out with no allowance for solvent, that is why the experimental value of conjugation
energy appears to be more positive by the quantity of dehydration of the binding site and
carbohydrate. However, over the series of carbohydrates this quantity alters only slightly, thus
the comparative studies could be performed with no regard to the medium effect.
Provided that the complexation energy serves as a criterion of carbohydrate specificity,
the data obtained display the lectins preferable specificity to 1,6--D-digalactose. The lowest
specificity is observed toward 1,4--D-glucoso-D-galactose. The difference between
complexation energies with these two carbohydrates consists about 8 kcal/mol.
The latter value does not exceed the computation error for heats of formation of the C-,
H-, N-, O-containing substances [22, 23, 41, 42]. However, even if this quantity exceeds, due
to the presence of calcium and manganese atoms in the protein subunit, the error of the
quantum chemical method [24], so one of reactants (lectin) being the same and other reactants
(carbohydrates) being structurally similar, as well as the complexes structures being alike-
typed and relatively close to each other, enable one in accordance with the relativization
principle [43] to compare the energy characteristics of the lectin-carbohydrate adducts
without taking into consideration the basis set superposition error (BSSE) [44-46].
Moreover, the necessity of the BSSE correction is controversial [47, 48]. The authors of
[48] have performed a theoretical and numerical analysis of the different counterpoise
correction (CP) schemes potentially applicable to correct for the BSSE in the neighborhood
of transition structures of chemical reactions. The analysis proved that neither of them is
satisfactory: all CP versions result in either discontinuous potential surfaces or yield different
energies for the same species in various reactions.
In relation to the criterion of complexation energy, the series of carbohydrate specificity

occurs to be the following:
-1,6-D-digalactose > -1,3-D-digalactose > -1,4-D-digalactose

-D-galactose > -D-galactose = -1,3-D-digalactose >
> -1,4-D-glucoso-D-galactose.
It has been stated experimentally [49] that the lectin shows higher specificity toward -
methylgalactopyranoside as compared to its -form (inhibiting ability referred to inhibiting
ability of lactose being equal 2.5 and 1.25, respectively); as for disaccharides, the affinity is
better toward -anomers, therewith the lectin is mostly specific to the -1,3 disaccharides
derivatives.
Consequently, our work renders the theoretical substantiation for the peanut lectins
highest specificity to -anomeric digalactoses, as well as the higher specificity toward
galactose derivatives than to glucose derivatives.
3.5. AIM Analysis
Richard F.W. Bader has developed the current quantum theory of electronic structure of
molecules from the viewpoints of analysis of the electron density topological properties. This
theory is called Quantum Theory Atoms in Molecules (AIM) [50-54].
According to the Baders theory, a molecule could be divided into fragments (atoms) by
zero-flux surfaces, which obey the equation:
(r).n = 0,
where (r) is electron density depending on nuclei coordinates r, n is unity vector normal to
surface.
Points on the zero-flux surface, for which
(r) = 0,
are called critical.

The positive value of electron density at the Bond Critical Point (BCP) (b) and the
negative value of Laplacian of electron density at BCP (2b) testify to the electron charge
concentration within inter-nuclei region and to the electron charge depletion towards nuclei,
i.e. to the occurrence of strong chemical bond.
Contrary, the negative b value and the positive 2b value serve as the evidence in favor
of the electron charge concentration on nuclei and its depletion in the inter-nuclei space, i.e.
testify to the absence of binding.
Within the framework of topological theory of electron distribution, the BCP (3, 1) is
the point of electron density field gradient for a given nuclei configuration, in which
(r,q) = 0, local maximum toward two directions and local minimum in the third direction,
i.e. the saddle point in three dimensions. Here r is a rank of BCP (the number of non-negative
eigenvalues of the matrix of second derivatives), s is a signature (algebraic sum of signs of

eigenvalues). The BCP exists between every pair of the adjacent bound atoms, its position
reflecting the bond polarity. The position of BCP for A-B displaces toward A and thus
reserves the greater bulk of electron density for the B atom, provided that B is more
electronegative than A.
The hydrogen bond formation is accompanied by the BCP appearance between the
hydrogen atom and the atom - proton-acceptor, which are bound by the bond pathway. This
BCP possesses the characteristic properties of interaction within a closed shell: the value of
electron density at BCP (b) is relatively moderate, and the Laplacian of electron density
(2b) is positive, those point out to the exhausted electron density in the direction from
interatomic basin toward the interacting nuclei ([55-64], etc.).
We have realized the AIM analysis of the protein, carbohydrate and conjugates in the
instance of the system 1,3-?-digalactose with lectin.
For the pairs of atoms, one of which enters the lectin composition, and another the
composition of -1,3-D-digalactose, among which the hydrogen bonding occurrence could be
presumed, we have analyzed, at the HF/3-21G theory level, the electron density (b) at the
BCP and the Laplacian of electron density at BCP (2b) (Table 3).
Table 3. The b & 2b values (a.u.) at the bond critical points
Numbers of atoms* b 2b
44152 0.0435 0.156
12895 0.0222 0.092
119130 0.0154 0.084
9154 0.0492 0.138
68139 0.0057 0.032
*
According to Figure 4
In Table 3, O44 is an oxygen atom from COOH group of L-aspartic acid residue; H95 is a
hydrogen atom from CONH2 group of L-asparagine residue; H119 is a hydrogen atom from
OH group of L-serine residue; O9 is an oxygen atom from COOH group of L-glutamic acid
residue; H68 is a hydrogen atom from OH group of L-tyrosine residue; H152, H154 are
hydrogen atoms from OH groups of D-galactose residues; O128, O130, O159 are oxygen
atoms from OH groups of D-galactose residues.
The greater is the electron density at BCP, the stronger is the hydrogen bond.
Consequently, one could conclude on the formation of 5 hydrogen bonds, therewith two of
them (44152 and 9154) outstand as being stronger than others.These strongest
hydrogen bonds appear between the oxygen atoms from carboxylic groups of aspartic and
glutamic acids and the hydrogen atom from hydroxyl group of galactose residue. Weaker
hydrogen bonds occur between the hydrogen atoms from amide group of asparagine and the
oxygen atom from OH group of galactose fragment, between the hydrogen atoms from
hydroxyl group of serine and oxygen atom from OH group of galactose residue.
Thus, the results of the AIM analysis show that the aforesaid mentioned interaction
hydrogen atom - heteroatom (between the carbohydrate hydroxyl groups and polar (amide,
carboxylic, hydroxyl) groups of the protein) satisfies the criteria of hydrogen binding.
The authors of the work [65] have attempted a comparison of carbohydrate specificity of
the natural peanut lectin and the lectins of its artificial mutants, in which the L-glutamic acid
residue (129-th amino acid residue) was replaced by other amino acid chains. It has appeared
that such the substitution causes a substantial increase in the inhibiting concentrations of
carbohydrate, i.e. the worse specificity (Table 4).
Table 4. Inhibiting concentrations (mmol/l) of various carbohydrates for the lectins of

peanut and its artificial mutant
Carbohydrate Lectin Mutant

D-Galactose 3.84 6.65
D-Galactosamine 2.80 9.26
N-Acetyl-D-galactosamine 6.94
D-galactoso--1,4-D-glucose 1.37 2.45
D-Galactoso--1,3-N-acetyl-D-galactosamine 0.10 0.35
The above result agrees with our data on the AIM analysis carried out.
In general, the results of molecular modeling we have performed confirm a predictive
power of the QM/MM method as a whole, the energy of formation of the protein-
carbohydrate conjugate as a criterion of carbohydrate specificity, as well as the electron
density at the bond critical point and Laplacian of this quantity in respect to establishing the
amino acid residues principal for the lectin activity manifestation.
Acknowledgments
The authors would like to thank Dr. James W. Kress (President of The KressWorks
Foundation, Chairman and Chief Executive Officer of KressWorks) for valuable advice and
discussion, and Dr. Donna Dennis (Nova Science Publishers, Inc., Editorial Production
Manager) for careful proceeding with the manuscript
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Chapter 14
ELECTRON DENSITY DISTRIBUTIONS

OF HETEROCYCLES: A SHORTCOMING
OF THE RESONANCE MODEL
Ricardo A. Mosquera*, Marcos Mandado, Laura Estvez

and Nicols Otero
Departamento de Qumica Fsica, Universidade de Vigo,
36310-Vigo, Galicia (Spain)
Abstract
Electron density distributions obtained for several heterocycles (indoles, 1,3-azoles, and
anthocyanidins) at diverse computational levels were analyzed with the Quantum Theory of
Atoms in Molecules (QTAIM). The results computed for some of these compounds, or for
their protonated species, indicate that qualitative partial atomic charges obtained by using the
resonance model do not provide a reliable description for those electronic distributions.
Overall, total QTAIM atomic charges are more related to electrostatic interactions than to
concerted movements of electron pairs.
Introduction
The resonance model (RM) is still one of the most often employed tools for explaining
the mechanism of chemical processes or predicting their products. The study and application
of this model consumes a significant amount of time for chemistry students. Nevertheless
diverse evidences found by several research groups point to its inadequacy to describe the
evolution of the electron density in various simple chemical processes. Even, RM cannot
explain some experimental facts like the evolution of pKas along certain series of organic
compounds. Conformational equilibria, protonations or hydride additions are examples of
simple processes where the resonance model leads to explanations that contradict those
obtained using modern quantum chemical methods for the electron density analysis. Among
*
E-mail address: mosquera@uvigo.es
344 Ricardo A. Mosquera, Marcos Mandado, Laura Estvez et al.
them, the quantum theory of atoms in molecules (QTAIM) [1-3] can be considered as a very
reliable one, as it is based exclusively on the basic principles of Physics without introducing
any other hypothesis.
Several QTAIM studies have contradicted well known and generally accepted
conclusions of the RM. To the best of our knowledge, Wiberg and Laidigs work on the
origin of ester and amide resonance [4], can be reported as the first serious difference between
QTAIM results and RM explanations. This work shows that in diverse R-CO-XR
compounds, comprising formamide (XR=NH2), formic acid (XR=OH), methyl formate
(XR=OCH3), etc., the atomic electron population of nitrogen/oxygen, N(X), is smaller in the
transition states for the C-X rotation than in the corresponding planar conformers. In contrast,
N(O) remains nearly constant along this process. According to the RM, the non-planar
geometry of transition states for C-X rotation breaks the electron delocalization along the
O=C-X unit (usually represented by resonant forms: O=C-X OC=X+) present in the
planar conformer. Clearly, RM predicts that, at transition states and with regard to
conformers, N(X) should be larger, as the OC=X+ form should have a negligible weight, and
N(O) should be smaller. These results, obtained initially at the HF level, were confirmed later
at the MP2 level [5]. Slightly later, Slee and MacDougall observed that the comparison of
QTAIM atomic electron populations, N(), of allyl ions and the corresponding neutral
compounds is not in line with the evolution of electron density expected with the resonance
model [6]. In this context, it should be mentioned that the publication of the first of Wibergs
papers on ester/amide resonance led to a long argument about the reliability of QTAIM
atomic populations [7], ended by clear demonstrations of unreliability of the basic postulates
against QTAIM charges [8,9]. Moreover, the same kind of contradiction between RM
predictions and QTAIM relative charges observed for simple amides and esters was also
obtained for thioformamide [10].
In the same vein, Glaser and Chao obtained that the electron density distributions of
diazonium ions are inconsistent with the commonly used Lewis structure R-N+N and would
be better represented by a combination of two unconnected structures: R+NN and R+N-
N+ [11,12]. Also, the acidity sequence followed by dimethyl sulfide, sulfoxide and sulfone,
cannot be explained by the RM, which reverses the order. In contrast, QTAIM atomic
populations explain the real sequence and provide no evidence for the delocalization of the
charge from the anionic carbon in the rest of the anion [13].
In the second half of the 90s our group started a systematic study on protonation
processes of oxygenated compounds employing QTAIM as basic tool for analyzing the
evolution of the molecular electron density (computed at diverse computational levels: HF,
B3LYP, MP2 and sometimes QCISD) along the protonation. This study comprised carbonylic
compounds [14,15]. linear [16,17] and cyclic ethers [18,19]. The general conclusion obtained
was that the positive charge was mainly concentrated on the proton while the oxygen formally
attached to it does not reduce its electron population, as postulated by a classic protonation
scheme shown in Figure 1. On the contrary, N(O) increases upon protonation, gaining
electron density from the remaining hydrogen atoms in the molecule, as had been previously
proposed by Stutchbury and Cooper [20].
Electron Density Distributions of Heterocycles 345
+ H
O O
+ H+
R1 R2 R1 R2
Figure 1. Classic mechanism of protonation for carbonyl compounds.
+
+H
+310
-25
-39 +406
b -83
a -76
-47
-112 -105
-105
-112
Figure 2. Evolution of atomic electron population, N(), upon protonation of propanone. All values in
au multiplied by 103.
Later on, our work was extended to other systems of practical interest, as uracil and
cytosine [21-23], and to compounds without oxygen, like nitriles [24]. RM was only able to
predict the stability sequence of protonated forms and explain the changes exhibited by most
of the bond properties upon protonation. Even, both the O- and N-protonated forms of uracil
and cytosine are found to be better described by RO-H+ and RN-H+ forms than by the
classical RO+-H and RN+-H structures. Again, according to the QTAIM analysis the electron
charge gained by the proton is mainly provided by the other hydrogens of the molecule. The
study of several model systems, like vinylketone, methyl formiate and N-methyl formamide
[22] led us to explain the previously reported stability sequence of uracil [25] and cytosine
protonated forms, as well as the evolution of atomic electron populations. Thus, we developed
an alternant model, not based on the resonance concept but mainly on electrostatic
interactions [22,23], which we think can be applied to any protonation. This model is based
upon the following points: i) the donation of electron population is easier when the atomic
number is smaller; ii) the closer the distance to the proton is, the easier the electron donation
will be; iii) the donation of electron population between bonded atoms follows the direction
of the bond. The orientation of the bond with regard to the proton can make the electron
transference easier (if the electron density approaches the proton), or more difficult (if the
electron density moves away from the proton) (see, respectively, hydrogens labeled a and
b in Figure 2); and iv) -transferences are generally easier than ones, when both are
possible.
At this point, we should highlight that other modern methods for electron density
analysis, like the Hirshfeld scheme [26], recently implemented for several computational
levels [27], which was employed to analyze several simple oxygenated compounds [28],
provide different absolute values for the evolution of atomic electron populations, N(), but
the same qualitative description, contradicting RM expectations.
As protonation can be considered as a model for electrophilic attacks, we have also
studied how activant and deactivant substituents modify the evolution of electron density in
this process. QTAIM analysis carried out for the protonation of a set of aniline derivatives,
indicate that most of the electron density gained by the proton is provided neither by the
nitrogen atom nor by activant substituens like OH [29]. In a similar way, the acidity of phenol
derivatives can be rationalized on the basis of atomic QTAIM properties, but not on the RM
predictions [30].
On the other hand, the evolution of molecular electron density upon hydride addition,
(simple model for nucleophilic attacks), computed both with QTAIM or Hirshfeld methods,
has been shown to display general trends that are also not in line with RM predictions
summarized in the scheme shown in Figure 3 [31,32]. Thus, we observe that most of the
electron density provided by the hydride is not taken by the oxygen. In fact N(O) never
reaches 0.2 au, whereas for the carbon attached to hydride N(C) always exceeds 0.4 au and
N(H) goes from 0.44 au to 0.53 au in the compounds hitherto studied. When the study is
repeated using other anionic nucleophiles (CN-, OH-) the results do not change substantially.
-O
O H
H- +
R1 R2 R1 R2
Figure 3. Classic mechanism for hydride addition to carbonyl compounds.
Among the discrepancies observed between RM predictions and relative atomic charges,
we highlight the specific behavior of heteroatoms, X, reducing the extent of electron
reorganization with regard to that displayed when they are replaced by carbons [22]. In fact
C-X bonds were found to act as barriers to -electron reorganization, precluding (or reducing
substantially) the transference of electron density throughout them [22,33]. We think of
interest to show if the discrepancies previously described for pyrimidine and purine bases
[21-23], affect in general to all heterocycles. In particular, this chapter reports a detailed
comparison between the RM predictions and conclusions derived from the QTAIM analysis
carried out for the protonation (in some cases also other processes) of diverse heterocycles:
indoles, 1,3-azoles, and anthocyanidins.
Short Overview of QTAIM

QTAIM has been included among the topological methods for analysing of the electron
G
density function, (r ) . As in any topological analysis, the localization of singular points
plays a basic role. In this case we have singular points in the real space spanned by the 3
G
coordinates representing the position of any electron, r , that can be classified as: i) Local
maxima, also called electron density attractors, whose coordinates correspond very
approximately to those of the nuclei in the molecule; ii) Along every bond there is a saddle
G
point with two negative eigenvalues of the Hessian matrix of (r ) . These points are also
called bond critical points or BCPs. Inside each ring, we observe other kind of saddle points,
whose Hessian matrix present two positive eigenvalues, and are called ring critical points
(RCPs). Finally, in polycycles with cage structure, we observe the presence of relative
minima, one per cage, named cage critical points (CCPs).
The topological analysis also looks at the gradient paths of the electron density. They
form a vector field where every group of field lines ends at a different nucleus. These groups
of lines are delimited by surfaces given by what is known as the zero flux condition (1),
which is rigorously derived [34] from Schwingers principle of stationary action [35]. These
G
surfaces intersect with a certain vanishing limit of (r ) (e.g. 10-5 au), defining the atomic
basins that are disjoint regions of the space. In this context, an atom can be defined as the
joint of a nucleus and its electron basin. The integration of the proper density function within
the atomic basin provides the atomic properties, like the atomic electron population (2), the
atomic electron kinetic energy (3) or the atomic volume (4).
G G G
(r ) n (r ) = 0 (1)
G G
N ( ) = (r )dr (2)

{2[ (r , r )] }
1 G G G G
K ( ) = (r ) dr
2
G G
r =r (3)
4
G
v( ) = dr (4)

G 1 2 G
L(r ) = (r ) (5)
4
Turning back to critical points, it has to be said that the conduction of the eigenvector
associated to the positive eigenvalue of every BCP gives rise to the atomic interaction lines or
bond paths. According to Bader's original formulation of QTAIM, bond paths are the physical
representation of chemical bonds [1]. Nevertheless, the interpretation of bond paths in certain
systems (biphenyl, inclusion complexes of He in adamantane, etc.) has risen significant
controversies [36-42]. Other points requiring careful attention when performing QTAIM
analysis are: i) The obtention of non-nuclear attractors, usually found in systems with very
weak bonds, [43-48]; ii) The calculation of atomic energies by correcting kinetic energies
using the molecular virial ratio, , may lead to artifacts when the later quantity experiences
important variations [49]. This problem can be reduced employing (rG ) distributions that
closely verify the virial theorem [50], what can be achieved using self consistent virial scaling
(SCVS) optimizations [51]; iii) Finally, the quality of atomic integrations should be tested,
checking that summations of atomic energies and atomic electron populations recover within
negligible differences, respectively, total electronic energy and the number of electrons in the
molecule. Moreover, each atomic integration should be performed providing absolute
G
integrated values of the L( r )function (5) nearly below 10-3 au. In fact, L() and N() display
linear correlations within a certain range of L() values [52].
Computational Details
Electron densities were computed in all cases for completely optimized geometries at the
G
same computational level with Gaussian03 program [53]. Topological QTAIM (r ) analysis
was performed with the program AIMPAC [54]. When necessary, two-centre delocalization
indices (DIs), (,), [55-57] and QTAIM based 5- and 6-centre DIs, 5 and 6
respectively, [58,59] were also calculated using a program developed in our group [60]. In all
cases DFT delocalization indices are computed as approximations using HF expressions, as
the Fermi hole density cannot be defined strictly in DFT framework. The accuracy achieved
in the calculation of the QTAIM atomic properties was checked as usual. Thus, summations
of the N() and atomic energy, E(), values for each molecule never differ from total
electron populations and electronic molecular energies by more than 510-3 a.u. and 4.0 kJ
mol-1, respectively. No atom was integrated with |L()| > 2 10-3 a.u.
Indoles
Indole has been studied intensively in chemical literature because of both its structural
and practical importance. Thus, details of its molecular structure can be found elsewhere (see
for instance [61,62] and references therein). Experimental evidences [63-66] and
computational results [61,67,68] reveal that C3 is the preferred protonation site both in gas
phase and solution, contrasting with pyrrole, which prefers C2 [69,70].
Our study comprises a detailed analysis of all possible protonations of parent indole [71]
and how the protonation affinity (PA) of every site is affected by including one activating or
deactivating substituent (-CH3, -F, -NH2, -NO2) at different positions [72]. In the first case,
B3LYP/6-311++G(2d,2p) 6d and MP2/6-31++G(d,p) electron densities were considered for
indole and all its protonated forms, named with the IUPAC carbon number where the proton
is attached. The geometries obtained at B3LYP and MP2 levels are very similar in all cases,
as well as most of relative atomic properties for the protonation process. The highest change
in bond lengths is 0.013 au, whereas differences in bond angles are never higher than 0.3.
Thus in the second study we restricted ourselves to B3LYP calculations. Also, for the sake of
simplicity we are only detailing the results obtained for the parent molecule, whereas we just
summarize the main conclusions obtained for derivatives.
The protonations of parent indole at bridge carbons (C8 and C9) were not studied, as the
corresponding PAs were reported to be much less than the remaining ones [61]. PAs shown in
Table 1 (named by the position where proton is attached) were computed transforming the
energy difference into enthalpy, including the corresponding unscaled B3LYP ZPVE, BSSE
(which was found negligible) and thermal correction at 298.15 K.
G
QTAIM N() values of indole computed from B3LYP (r ) show that, with the
exception of N1 and its neighbors, the atoms are nearly neutral. N1 has a strong negative
charge (-1.067 au), while C2, C8, and H10 are charged positively (+0.329, +0.340, and
+0.390 au, respectively). The main differences with MP2/6-31++G(d,p) values occur in the
atoms displaying strong charges, which MP2 tends to increase. Thus, N1 is even more
negative (-1.333 au), and C2, C8, and H10 more positive (+0.428, +0.422, and +0.452 au,
G
respectively). The symmetry of indole allows partitioning (r ) into and components.
We notice that even the carbon atoms that lose total electron population have nearly 1 au of
population. Therefore, when we exclude N1, the atomic charges are mainly due to
displacements. N1 displays a strong negative charge (-1.350 and -1.588 au at B3LYP and
MP2 levels, respectively) and a slight positive charge (+0.283 and +0.254 au with B3LYP
and MP2, respectively). If we only consider the population, we could say that it agrees with
the results expected from the application of the RM. Thus, most of the eleven isovalent
resonance structures that can be written for indole place a positive charge on the nitrogen
atom [71]. Also, according to nine of them, all carbon atoms should have negative charges.
However, it is only displayed by C3, C7, and C9, while the rest of the carbons are positive in
terms of charge.
Table 1. PA, (in kJ mol-1) and relative 5 and 6 indices for the protonated species (in
G
au), Qzz and [2 (r ) ]SCC- values (both in au) for protonation sites in neutral indole
G
PAB3LYP PAMP2a 1026b 1025b Qzz() [2 (r ) ]SCC-
1 832.3 827.5 2.11 -0.15 -2.53 -1.414
2 870.7 842.6 0.60 0.10 -3.40 -0.158
3 891.6 884.2 2.03 0.31 -3.74 -0.136
4 858.3 835.4 0.14 1.56 -3.30 -0.143
5 858.3 835.3 0.12 1.15 -3.46 -0.148
6 861.4 833.5 0.13 1.10 -3.38 -0.143
7 846.7 826.9 0.11 1.66 -3.47 -0.161
a
Thermal and ZPVE corrections taken from the B3LYP/6-311++G(2d,2p) 6d frequency calculation.
b
B3LYP/6-311++G(2d,2p) values, 6 and 5 indices for indole are 1.6310-2 and 1.3410-2 au
respectively.
If the electron delocalization is described correctly by the RM, we should find significant
DIs between nonbonded pairs of atoms that bear charges in one of those resonance structures
(nitrogen and all the carbon atoms), and the corresponding values could be employed to
weight them. The highest index found is (N1,C3) (0.166 au). Other important nitrogen
delocalizations are found with C9 and C7 (0.119 and 0.086 au respectively). The rest of the
(N1,C) values are in the same order or even smaller than the (N1,H) ones. In contrast, there
are some important DIs between carbon atoms, like (C4,C7) (0.100 au), which correspond to
the delocalization of the carbons in the 6 member ring, or (C2,C8) and (C2,C9) indicating
delocalizations between rings. Most of (N1,C3) corresponds to delocalization, while for
(N1,C9) the delocalization only represents a half of the total one, meaning that the electron
lone pair of the nitrogen delocalizes better in the direction of C3. The three pairs of atoms
arranged in para in the benzene ring (C4-C7, C5-C8, and C6-C9) display also important
delocalizations (larger than 0.071 au). The highest delocalization between rings occurs in
the pair C2-C4 (0.035 au), while the bridge carbons have noticeable delocalizations with
atoms from both rings.
PAs calculated for 1-7 agree with the experimental fact that C3 is the preferred
protonation site and N-protonation is the least suitable. The values obtained with both
computational levels (Table 2) are also in line with the gas phase experimental one (933.4 kJ
mol-1 [73]). According to Baders criteria [74], the protonation should be favored where
(rG ) is less retained in the ring. This is measured by the atomic quadrupolar electric tensors,
Q(), and especially by Qzz(), the eigenvalue of this tensor associated with the eigenvector
perpendicular to the ring, e. The more negative Qzz(), the more concentrated the charge is
in the e axis, and the easier the protonation will be. Bader also related reactivity with
G
2 (r ) in the sense that more negative values indicate more reactive points for electrophilic
G
attack. So, another index to study is 2 (r ) at secondary concentrations of charge (SCC)
G
close to the atom (SCC-), [2 (r ) ]SCC-. A SCC corresponds to (3,-1) critical points for
G G
2 (r ) which also presents 2 (r ) < 0. The most interesting of them are the ones close to
G
(3,-1) points with 2 (r ) > 0, because they warrant a favorable route for the approximation
of the proton.
Calculated Qzz() values of indole (Table 1) show a qualitative correspondence with the
proton affinity. Therefore, the most negative value corresponds to C3, the most favored
protonation, while the least favored protonation, N1, displays the least negative Qzz(). The
rest of the carbons that can receive a proton have similar values of Qzz(). However, no
G
linear correlation was found with PAs. On the contrary, [2 (r ) ]SCC- values are not in line
G
with PAs (Table 1). e.g., the most negative [2 (r ) ]SCC- corresponds to N1, the atom with
the lowest PA, and the atom that displays the least negative value is C3, the preferred
protonation site.
n-DIs were shown to be a useful tool to investigate the local aromaticity in monocyclic
and polycyclic compounds [58,75]. Since the n-DIs measure the extension of the electron
delocalization to n atoms, when it is computed for all atoms of the ring, the larger the n-DI,
the more aromatic the molecule. However, because of n-DIs are defined as a product of n
overlap atomic integrals, the comparison of aromaticity of rings with a different number of
centres requires the inclusion of a scaling factor that weights the n-DIs, increasing 6
values. In this case, even unscaled 6 indices for the benzenoid ring are larger than 5 values
of the pyrrole ring (Table 1), indicating that the benzene ring is significantly more aromatic
than the pyrrole one. This fact also agrees with the pyrrole ring larger PAs.
Variation of atomic electron populations due to protonation, N(), computed at the
B3LYP level (Table 2) are very similar to those obtained at the MP2 one. The differences
obtained for N() with both levels never exceed 0.06 au. In general, there is also a good
linear correlation between N() and E() values [71]. Nevertheless, the remarkable
stabilization of N1 in protonation 3 makes C3 the preferred protonation site (Table 2). This
fact can be explained considering the small variation shown by N(N1) arises from an
important reduction of population (-0.754 au) compensated by a little larger increase of
population (+0.767 au). As the electron population is in average closer to the nucleus the
result is a significant stabilization.
Table 2. Most significant variations of atomic and group B3LYP energies (in kJ mol-1)
and electron populations (in au multiplied by 103) due to protonation
Group 1 2 3 4 5 6 7
E(C6H4) 4 483 124 370 573 340 595
E(N1) 332 18 -238 -94 -88 -78 -97
N(N1) -160 -47 13 -2 -12 -9 -8
E(H+) -1186 -1529 -1520 -1534 -1521 -1530 -1528
N(H+) 562 894 896 905 899 905 901
E(C4NH3) 37 349 323 248 266 258 256
A very noticeable difference among N-protonation and C-protonations is the electron

population gained by the proton (Table 2). Thus, the proton on the nitrogen atom has the
smallest atomic population, whereas the ones on the carbons are always around 0.33 au
larger. The proton on the N receives 83% of the electron population from the rest of the
hydrogens according to B3LYP electron densities (93%, from the MP2 results). In contrast,
the proton on the carbons receives only between 55 and 59% of the electron population from
the rest of the hydrogens. Moreover, most of the hydrogens lose more electron population
than carbon atoms. Also, in protonations 4-7, the highest donor to the electron population
gained by the proton is the neighbor hydrogen. Thus, as previously found in other cations and
anions [20,76], hydrogens allow a dispersal of the charge excess.
Contrary to what could be expected, the most important N() values are not shown by
the -carbon, but in C2 or C8 depending on the specific protonation site. Thus, protonations
3, 4, 6 decrease N(C2) and protonations 2, 5, 7 decrease N(C8) [71]. The role played by these
carbons can be explained considering the resonance structures of protonated indole. Two
points have to be remarked about them: i) The most stable protonation (3) is the only one that
allows two resonance structures that do not alter the electronic structure of the benzene ring,
in line with the high 6 value already commented; ii) the resonance structures favored by
N() values keep a positive formal charge connected to a formally neutral nitrogen (C+-N),
contrasting with the traditionally used N+-C structures. Thus, the two atoms that are losing
more electron density in C-protonations are the neighbors of the nitrogen, while global
N(N1) is almost negligible. Nevertheless, N1 experiences a strong / movement, loosing
electron density and gaining a similar amount of . The largest movements occur for
protonation 3 and the smallest for 4 and 7. Thus, except for protonation 7, N(N1) is higher
than N() for atoms C2 or C8 in the corresponding protonations, what agrees better with
traditional resonance structures. Finally, protonation at C2, the preferred protonation site for
pyrrole, reduces significanty the aromaticity of the benzenoid ring, destabilizing the
protonated species with regard to that formed by C3-protonation.
The activating/deactivating effects of CH3, -F, -NH2, and NO2 in indole were
quantitatively measured as PA values (Table 3) and, in general, agree with RM predictions.
The insertion of a methyl group into one of the carbons of the pyrrol or phenyl rings clearly
activates the electrophilic attack at all positions with the exception of the ipso one. The
specificity of ipso positions may be due either to steric hindrance or to electronic effects and
will be discussed below. As a general rule, it can be stated that methylation of a certain ring
mainly activate the carbons of that ring, indicating the prevalence of inductive effects for this
substitution. However, some exceptions to this rule can be observed in Table 3. Thus, the
most activated position of 6-methylindole is C2, which is quite far from C6. Also, the most
activated position of 4-methylindole and 7-methylindole are respectively C7 and C4. All
these evidences indicate that the activating ability of -CH3 cannot be solely explained by
arguments based on inductive effects.
The insertion of fluorine into the pyrrol or phenyl rings clearly disfavours the protonation
at all positions with the exception of C2 and C7 for respectively 3-fluorineindole and 4-
fluorineindole. The large inductive withdrawing (-I) character of fluorine is clearly reflected
on the ipso positions, displaying the most negative PAs for all the substitutions. N1 is an
exception to this rule that can be explained by its high electronegativity. Also, the behaviour
of fluorine derivatives cannot be uniquely explained by the -I character. Thus, PAs for
protonations at ortho and para sites are significantly less negative than the rest. This can be
explained accepting that fluorine has a small mesomeric electron-releasing character (+R).
The amino group is an example of -I and +R character. Thus, ipso positions are
significantly deactivated, showing negative PAs, whereas the remaining positions are
activated (large positive PAs). It must be noticed that the +R character of -NH2 is quite
important as can be derived from the high PA values of each substitution, which always
exceed 81.0 kJ mol-1. The position with the largest mesomeric effect is located in the
substituted ring. Thus, substitutions at N1, C2 and C3 mainly activate the pyrrol ring and
substitutions at C4, C5, C6 and C7 mainly activate the phenyl ring.
Finally, the nitro group is an example of inductive and mesomeric electron-withdrawing
character (-I and -R). The former is reflected on the PA values at ipso positions, which are
highly deactivated, in fact they are the most deactivated positions. The only exception is
observed for 2-nitroindole, where the most deactivated position is C3 and not C2. We think
that is due to the competitive inductive effects of the two attached nitrogens. Once again, the
position with the largest mesomeric effect is located in the substituted ring as happened for -
NH2.
According to traditional interpretations, inductive effects and mesomeric effects are
mainly related to variations of and electron populations respectively [77]. However, no
quantitative simple relationship has been found between N() values [72] and PAs, pointing
again that RM considerations are not able to predict the evolution of electron density. It
should be noticed that the summation of N() values for the heterocycle, N[R], is
negative for methylindoles (up to -0.017 au). Thus, contrary to what is generally accepted, the
QTAIM results point to an inductive electron-withdrawing character for -CH3 instead of
electron-releasing. These results probably stem from the slightly negative QTAIM charge of
Hs in methyl groups. The loss of electrons by the rings is partially recovered via donation
from -CH3. The N[R] remaining groups confirm the expectations, -F and -NO2 are highly
electron-withdrawing groups.
Table 3. B3LYP PAs for every site (1-7) [in kJ mol-1 with regard to those of indole
(Table 1)] for the 28 indole derivatives here studied
R 1 2 3 4 5 6 7
1 17.5 12.6 27.9 12.4 13.7 13.9 15.4
2 16.0 -2.7 29.1 20.5 15.7 23.3 13.6
3 21.7 25.8 -2.4 10.4 12.6 9.9 10.9
CH3 4 7.1 13.3 7.6 -7.6 21.2 10.1 24.9
5 11.0 14.5 11.8 21.2 -3.5 20.1 8.4
6 10.4 23.1 9.8 7.1 21.0 -4.3 20.8
7 8.3 9.8 7.5 21.3 11.3 18.8 -6.2
1 -9.1 -26.2 -16.7 -29.7 -21.9 -30.6 -17.9
2 -29.1 -41.0 -6.3 -8.2 -17.5 -4.2 -20.0
3 -8.3 4.7 -44.5 -16.2 -18.4 -20.2 -18.6
F 4 -20.1 -18.6 -17.8 -60.0 -5.0 -23.6 1.2
5 -14.9 -18.8 -13.1 -4.3 -63.9 -8.8 -25.9
6 -17.2 -3.8 -17.3 -26.3 -10.1 -60.7 -7.2
7 -18.8 -25.1 -19.8 -2.5 -23.5 -7.3 -58.4
2 18.4 -20.4 88.6 60.1 25.5 68.6 20.4
3 52.0 101.4 -16.7 22.8 26.9 19.9 22.5
4 16.9 37.2 15.4 -48.4 83.1 11.4 99.5
NH2
5 30.5 31.0 37.6 85.6 -41.7 63.3 16.0
6 27.6 76.1 23.3 11.7 64.5 -43.9 81.5
7 14.2 11.1 13.6 82.3 12.4 69.7 -24.2
2 -62.1 -80.9 -86.1 -70.9 -63.8 -76.1 -60.0
3 -84.2 -80.3 -90.1 -60.2 -64.1 -66.4 -62.7
4 -53.2 -58.3 -45.3 -78.7 -70.9 -59.6 -77.6
NO2
5 -58.4 -61.3 -56.8 -66.8 -90.3 -62.1 -65.6
6 -55.9 -69.0 -56.0 -62.3 -66.0 -85.4 -67.7
7 -48.2 -57.0 -48.4 -78.5 -65.4 -72.0 -89.8
1,3-Azoles
Azoles are defined as a class of five-membered heterocycles containing at least one
nitrogen atom (N3) and another heteroatom. We have applied QTAIM to analyze the electron
density of imidazole, N-methyl imidazole, oxazole and thiazole and how it evolves along
some of the main chemical processes: electrophilic and nucleophilic aromatic substitution
modelized, respectively, by protonation and hydride addition. Deprotonation of neutral
molecules to produce the corresponding anion is also among the most characteristic reactions
experienced by these compounds. This process is specially significant in the chemistry of
imidazoles and thiazoles, which have been extensively employed to give NCN and NCS free
carbenes [78]. All of these processes have been studied for gas and aqueous solutions,
represented, respectively by optimizations of the isolated species and with the Polarized
Continuum Model (PCM) [79].
Imidazole proton affinities, PAs, have been extensively computed at different theoretical
levels [80-86], while less data are available for the deprotonation energies of this compound
[80]. The computational studies carried out for oxazole and thiazole are scarce and
concentrate on PAs [80,81].
The study comprises the four neutral species shown in Figure 4 and all their
corresponding protonated (but that on N1 in 1-methylimidazole) and deprotonated species, as
well as those obtained upon hydride addition on C atoms. In what follows, n+Hm and n-Hm
refer to those species obtained, respectively, upon proton or hydride addition to the neutral
molecule n at atom m (Figure 4). Conjugated bases obtained upon deprotonation are denoted
as Bn-m.
n X
1 N-H
2 N-CH3
3 O
4 S
Figure 4. Atom numbering and nomenclature of 1,3-azoles here studied.
The electron densities were obtained in all cases for completely optimized geometries at
the B3LYP/6-311++G(2d,2p) 6d level and confirmed as true minima by vibrational analysis
carried out at the same level in gas phase. ZPVE and enthalphy thermal corrections (ETC) at
298.15 K were considered for computing gas phase PAs, deprotonation and hydride addition
enthalpies. The corresponding quantities for aqueous solution were computed correcting PCM
optimized energies with the ZPVE and ETC corrections obtained for the gas phase [87].
5-centre DIs [58], and FLU indexes [88] in planar molecules were also calculated. Both
5 and FLU values (Table 4) indicate that oxazole, which is considered the least aromatic
compound of the series, displays the lowest electron delocalization (minimum 5 and
maximum FLU) so in gas phase as in aqueous solution. These indices also indicate that the
electron delocalization of thiazole is significantly larger than that of oxazole, but only slightly
lower than that of imidazoles. Both indices agree that electron delocalization increases in 1-
methylimidazole with regard to imidazole. Nevertheless, 5 and FLU values obtained from
PCM computed electron densities indicate different trends. Thus, 5 indicates the electron
delocalization of the imidazole ring decreases in aqueous solution upon N1-methylation,
whereas the opposite trend is indicated by FLU values. Anyway, 5 differences between
imidazole and its N-methyl derivative do not exceed 810-4 au in PCM and 610-4 au in gas
phase.
Comparing electron delocalization indices computed for the same molecule with PCM
and gas-phase electron densities, we also observe 5 and FLU values display a common
trend (electron delocalization increases in aqueous solution) but in oxazole, where 5 values
again differ in a very small amount (310-4 au).
Table 4. 5 delocalization indices (in au and multiplied by 102) and dimensionless FLU
values for neutral species
102 5 102 FLU

Gas PCM GAS PCM
1 3.155 3.450 7.154 5.702
2 3.210 3.373 5.658 5.181
3 2.167 2.202 23.719 24.097
4 3.036 3.151 12.552 11.945
Both gas phase and PCM calculations indicate that N3 is the most favored protonation
site for the azoles here studied (Table 5), as expected according to experimental results [81-
82], whereas protonation at the other heteroatom (X1) gives rise to the least stable
protonation, contrary to what had been assumed for oxazole and thiazole in a previous paper
[80]. Concerning C-protonations, we notice that imidazole and N-methyl imidazole follow the
sequence PA(C5) > PA(C4) > PA(C2) in both phases, which diverges from that obtained in
the gas phase for imidazole using MP2/6-311G(2d,p) calculations [83]. This sequence
changes for thiazole, where PA (C2) exceeds that of C4 by less than 20 kJ mol-1. Finally,
oxazole follows the same sequence as imidazole in the gas phase and that of thiazole in
aqueous solution.
Table 5. Computed and experimental PAs (in kJ mol-1) for the diverse protonation sites
PA(gas) PA(PCM)
X1 C2 N3 C4 C5 Exp.a X1 C2 N3 C4 C5
1 698.0 769.9 904.1 772.0 786.5 942.8 959.9 1005.1 1138.5 1013.2 1019.8
2 - 801.7 925.6 805.6 814.2 959.6 - 1007.7 1137.0 1013.9 1020.5
3 624.1 706.4 836.7 702.1 729.5 876.4 924.0 944.3 1393.6 946.2 970.1
4 699.8 728.7 863.1 720.0 744.8 904.0 829.9 961.7 1471.4 956.9 978.8
a
Experimental data for the preferred protonation site taken from reference 73.
We notice that gas phase experimental and computed PAs follow the same relative
sequence for this series (r2= 0.997). Nevertheless, the values computed for the aqueous
solvated species with PCM indicate a different sequence with thiazole displaying the largest
PA followed by oxazole, whereas 1-methylimidazole and imidazole display the lowest PAs
(Table 5). If we exclude the gas phase PA computed for thiazole at S1, the only case where
protonation breaks the ring, we observe that the same sequence of PAs at the most stable site
is followed by the remaining sites. This observation cannot be extended to aqueous solution
(Table 5).
The protonation of 1,3-diazoles has no consequences on the planarity of the ring with the
exception of oxazole protonated at O1 which is non planar in gas phase, giving rise to the
lowest PA in the series. The non planar O1-protonated oxazole is 1.5 kJ mol-1 more stable
than the corresponding planar structure, which displays one imaginary frequency, in spite its
electron delocalization diminishes from 0.0040 au (planar form) to 0.0024 au (conformer).
We also notice that O1 protonation of oxazole in PCM produces a planar species, which is
only 0.1 kJ mol-1 more stable than the corresponding non planar singular point.
Both 5 and FLU values indicate that, in gas phase, the electron delocalization is
reduced significantly by most of the protonations but that on N3, where we observe a slight
increase of electron delocalization upon protonation with the exception of 1-methylimidazole.
There is a good linear correlation between 5 and FLU in gas phase (r2=0.86) that worsens
significantly (r2=0.51) for PCM calculations. In contrast, no significant correlation is
observed between PAs and variation of delocalization indices.
Looking at N() values and their evolution upon protonation (data not shown) we
observe: i) The largest positive charge of the most stable protonation of each molecule (and
for all protonations at heteroatoms excluding the ring-breaking protonation at S1) is
displayed by the proton what, as in previous studies [18,19,21-23,71,72], contradicts the
Lewis structure usually employed to represent protonated heterocycles; ii) In contrast, the
proton gains a substantial amount of electron population (between 0.85 and 0.875 au) at C-
sites; iii) Consequently, the most stable protonations of 1,3-azoles are accompanied by
smaller electron reorganizations in the molecule; iv) In all the protonations at N3, the electron
density lost by the hydrogens of the molecule represents more than 50% of that gained by the
proton. This percentage is reduced significantly in thiazole, what can be related to the
population provided by S1 (0.300 au) because of its large polarizability; v) In general, C-
protonations take place with hydrogen electron donations that represent less than 50%; vi)
Excluding protonations at X1 (the least favored ones) and C5-protonation of thiazole, the
electron population of the protonation-site, Y, is enlarged. In most of the cases this and the
proton are the only atoms displaying positive N() values. N(C6) values are also positive
for all the protonations of 1-methylimidazole. All of this can be explained because the
deformation experienced by the electron density distribution is continuous and displays its
highest intensities along the bonds, resembling the electron density flows through the set of
chemical bonds [23]. Thus, N(Y) is positive because atom Y is at a junction which receives
electron density through three bonds and sends it to the proton by only one. N(C6) is also
positive for all of the protonations at the ring of 1-methylimidazole as a consequence of the
electron density gained by this atom from its three attached hydrogens exceeds that lost by its
own basin through the C6-N1 bond.
We have observed that PCM calculations reproduce the experimental preferred
deprotonation site for these compounds (C2). Nevertheless, gas phase calculations predict that
deprotonation at C5 is favored over that at C2 for 1-methylimidazole by 8.3 kJ mol-1 (this
relative energy becomes -1.4 kJ mol-1 with PCM optimizations). 5 values show that the ring
delocalization is always smaller in the anions than in the neutral molecule. The decrease
observed for the deprotonation at C5 (-1.810-3 au with gas phase values) is significantly
smaller than those for C2 (-4.410-3 au) and C4 (-10.510-3 au) carbenes. This sequence of
delocalization reductions remains unchanged with PCM-optimized electron densities,
although the values become smaller (-0.910-3, -2.710-3, and -4.510-3 au, respectively). As the
relative sequence of 5 values is the same in PCM and gas-phase results, we infer that
electron delocalizations cannot be employed as the unique element to explain the
deprotonation preference in these compounds. Gas phase results indicate the basicity of
heteroatom at position 3 is always larger than that at 1. The difference between both
following the sequence: oxazole > imidazole > thiazole.
Anthocyanidins
Anthocyanins are a class of flavonoids that are responsible for the blue to red colors in
higher plants [89,90]. As no harmful effects have been established for them, anthocyanins are
useful as natural food colorants [91]. Also, anthocyanins have been reported to possess
antioxidant properties in vitro [92-94] and are considered important nutraceuticals whose
abundance in human diet has been related to lower incidence of diverse degenerative diseases
[95,96]. The flavylium cation, F, constitutes the basic skeleton of anthocyanidins in acid
media and pelargonidin cation, P, is the simplest natural anthocyanidin, with hydroxyls
attached to 3, 5, 7 and 4'. Both molecules present coplanar structures between the AC bicycle
and the B ring [97,98]. Several resonance structures, which localize the positive charge on
different atoms, can be drawn. According to RM, this set of structures indicates that the
positive charge of these cations is shared among diverse atoms (O1, C2, C4, C5, C7, C9, C2',
C4', and C6'). Nevertheless, only some of these forms are usually employed to represent these
cations, form I being the most widespread in literature. On the basis of Mulliken bond order
analysis of AM1 optimized structures Pereira et al. have proposed that canonical forms
represented by III in Figure 5 are predominant in the flavylium cation [98], with smaller
contributions from I and IV, whereas the participation of V and other forms leaving the
positive charge out of ring C, like VI, is negligible. The situation is modified in hydroxylated
compounds, like P, where the relative weight of forms leaving a positive charge on the
hydroxylated carbon increases [98]. Thus, form VI becomes specially significant for 4'-OH
derivatives, like pelargonidin [98,99]. In contrast, a recent paper by Woodford [100] interprets
the long C2-C1 bond distance obtained for the cations of a series of eleven anthocyanidins as
a lack of resonance conjugation between AC and B systems. Also, bond lengths within the C
ring are interpreted in that paper as favoring form III.
2' 3' 4'
8
+
B +
O 1' 5' O
7 9
2 6'
A C I II
3
6 10
5 4
O O
+ +
IV
III
O O
V VI
+
Figure 5. Some of the common Lewis structures employed to represent flavylium cations and atom
numbering.
The summations of N() values for the AC bicycle and B ring in the flavylium cation
indicate positive charges of 0.613 au in the former and of 0.387 au in the latter. This is neither
in line with Pereira et al. suggestion [98,99] nor with Woodford interpretation [100], pointing
to an important participation of the B ring in the distribution of the positive charge. Moreover,
respectively 66.4 % and 60.3 % of both positive charges are due to the electron population of
the hydrogens.
Interpretation of individual values of N() should be done carefully. In fact the most
positive charges are displayed by C2 and C9, what could be missinterpreted as indicative of
the predominance of IV and III. Looking at the value of N(O1) we realise this fact is mainly
due to the electronegativity of oxygen, as the total electron population of the C2-O1-C9 unit
is 20.071 au. That is, the COC region of AC bicycle displays a slight negative charge in
contrast to what is indicated by the canonical forms that are widespread used or proposed as
predominant by the theoretical studies hitherto carried out (I-IV).
As weak electron density attractor, hydrogens play usually an electron density sink or
supplier role [20], we have used the electron densities of every CH group to analyze the
relative predominance of the canonical forms shown in Figure 5. The most positive CH group
corresponds to C8 (0.124 au), which according to RM should not bear a positive charge.
Moreover, the third higher positive charge is displayed by the CH group at C3 (0.115 au). The
positive charge on ring B is distributed nearly uniformly among the CH groups, if we exclude
C6, which displays the lowest value (0.041 au) in spite it is one of the positions that should
display larger positive charges (C2, C4 and C6) according to the RM. We conclude the
inadequacy of the RM to describe the global electron density distribution of the flavylium
cation.
How does this picture evolve upon polyhydroxylation? All the carbons attached to
hydroxyl groups display lower N() values in P than in F [101]. Nevertheless, this cannot be
interpreted as a reinforcement of the role played by the resonance forms leaving a positive
charge on one of those carbons outside the C ring. In fact, the global charges on the C-O-H
fragments are less positive in P than the corresponding C-H charges in F [101]. Overall,
hydroxylation increases the electron density of these regions by 0.050 au. Part of this electron
density is taken from the C2-O1-C9 group, which is 0.021 au less negative in P than in F. The
most affected atom is H6', which loses 0.060 au in P with regard to F and becomes involved
in an intramolecular H-bond with O3. In contrast, N() values in some unsubstituted C-H
groups remain practically unchanged from F to P (those at C4, C6 and C2').
Polyhydroxylation also alters the distribution of the positive charge between AC and B
systems. Thus, a larger number of electronegative substituents on AC, increases the positive
charge of ring B (0.448 au) and that of AC decreases (0.551 au). Comparing with the
respective values in F we conclude an electron density transference of 0.062 au from B to
AC. Overall, once more, the resonance model cannot be taken as an indicator for global
electron density distributions.
As resonance forms are obtained by concerted movements of -electron pairs, they may
represent exclusively the -electron distribution. Therefore, it could be expected that atoms
bearing a positive charge in some of the resonance forms shown in Figure 5 should present
the lowest N() values. This is true for some atoms of F like: C2, C4, C7, C4' and C2'.
Neverhtheless, N(C6) is smaller than N(C5), although no resonance form displays a positive
charge on C6 and one can be written leaving the positive charge on C5. Also, N() values
for C3' and C5' are smaller than N(C9). In contrast, the fact that N(C4) > N(C9) agrees with
the RM, where four equivalent resonance forms V leave a positive charge on C4, while only
two equivalent forms of IV leave that on C9.
Grouping the formal -charges that can be obtained from the N() values, we observe
that almost half of the positive -charge is placed on the C2-O1-C9 fragment (+0.435 au),
more intensely on C2 and O1, indicating that resonance forms I, II and III are those that
provide a better description of the -electron distribution. The slightly negative charge
displayed globally by this region is obtained by a balance of and charges with opposite
signs. The rest of the AC system contributes with +0.338 au and the smallest part of the -
charge is placed on the B ring (+0.226 au). When these values are compared with the
corresponding global charges, the conclusion is that both regions display positive and
charges. and charges are approximately equal for the rest of AC, whereas the charge is
more positive than the one in ring B.
According to the RM, polyhydroxylation of F to yield P should reinforce the weight of
resonance VI-like forms. Looking at the N() values, we observe that C4' displays the most
positive atomic charge in P, highlighting the significance of a positive charge in this cation.
This atom is followed by C7 and both of them exceed the positive -charge at C2. Thus,
forms VI provides the best description for the -electron distribution of P in contrast with the
formulas commonly drawn for this cation in bibliography (I-III), which are those favored by
the RM according to the number of equivalent structures.
Taking into account the -electron donations of OH groups received by each ring system
(0.108 and 0.243 au for, respectively, B and AC) and the variations presented by the
summation of the corresponding N() values (0.046 and 0.305 au, respectively) we conclude
the polyhydroxylation takes place with an electron transference of 0.062 au from B to AC.
This value coincides with the global change of electron density indicated above, showing that
all that electron transference accompanying polyhydroxylation has character.
When the whole set of main natural anthocyanidins: pelargonidin (Pg), cyanidin (Cy),
delphinidin (Dp), peonidin (Pn), petunidin (Pt), and malvinidin (Mv) is considered with all
their acid/base forms (cation, neutral form and anion) we conclude that in ionic species the
charge is distributed on the whole molecule. Thus, the summation of the electron atomic
charge of the atoms of the B ring and those of the AC system shows that, for all the
anthocyanidins, the positive charge of the cationic forms is spread throughout the whole
molecule. Thus, over 44% of the charge is in the B ring. We also notice that more than 30%
of total positive charge is at the hydrogens. As stated above for flavylium and pelargonidin
cations, it is not possible to localize the positive charge on a specific atom or set of atoms.
Thus, the commonly drawn Lewis structures for these cations, in which the positive charge is
usually located at O1 or C2, are not supported by QTAIM results. O1, far from bearing a
positive charge, displays a significant negative one, and even summing the atomic population
of atoms C2, O1 and C9 (hereafter we refer to it as group) we found a negative formal
charge. Even, the relative electron population of the group in the cations with regard to the
neutral forms is only slightly depleted, between 0.063 and 0.075 au in gas phase along the
series of anthocyanidins, and between 0.065 and 0.088 au with PCM. In contrast, the largest
increases of positive charge upon protonation of neutral forms are obtained for the C-O group
which receives the proton and for the whole B ring (even when the protonation site is located
on the AC system q(B) exceeds 0.240 au in gas phase or 0.100 au in PCM).
For the anions, QTAIM analysis indicates the negative charge is mainly spread among
three regions of the molecule: the two C-O units where hydrogens have been removed
(averages are: -0.277 au for C5-O5, -0.275 au for C4-O4 and -0.317 au for C3-O3) and the
area, which varies from -0.146 to -0.226 au. Relative charges, with regard to the
corresponding neutral forms, indicate that more than 40% (more than 50% with PCM) of the
charge involved in the deprotonation process is taken from deprotonated C-O units. That is,
these groups act as electron density sinks. Also, the rest of the hydrogens receive a significant
amount of electron density (from 0.079 to 0.200 au) although most of them keep positive
atomic charges. Finally, the electron density gained by the region represents in all cases less
than 5%. Overall, as previously reported by Slee and MacDougall for allyl ions [6] QTAIM
net charges are not in accord with RM expectations and/or predictions based on simple
orbital models.
QTAIM analysis can also be employed to get insight about the enolate vs. quinonoidal
character of neutral species: The usually represented quinonoidal Lewis structure containing a
C=O double bond for representing the neutral form of anthocyanidins is mainly supported by
comparing bond lengths between the most stable neutral and cationic rotamers. Nevertheless,
several resonance structures displaying positive and negative sites -enolate-like structures-
can also be drawn for neutral anthocyanidins. Taking into account previously observed
shortcomings when resonance structures are employed for qualitative descriptions of electron
distributions, we think that the electron distribution of neutral anthocyanidins species should
be analyzed with some detail before accepting they bear a quinonoidal structure.
As a general rule, we observe that electro-neutrality is obtained by compensation of
substantially negatively charged areas ( group and deprotonated CO) and the rest of the
molecule, where all the atoms (if we exclude some exceptions) bear moderate positive
charges. It should be remarked that the charge of the deprotonated CO unit (COdep) is, in all
molecules and tautomers (named by the site where proton has been abstracted from the
cation), more negative than -0.206 au. Thus, looking at the most stable tautomers, we observe
the C4-O4 bond displays negative charge (-0.236 au) in the 4 tautomer of Cy whereas the
corresponding COH group in the cation is slightly positive (0.036 au) as it has been obtained
for the 4 tautomer of Dp (-0.277 au and 0.086 au, respectively) [102]. The same pattern is
observed in 5 for the remaining anthocyanidins. Thus, we find the C5-O5 bond goes from a
slightly positive charge in the cations (0.063 to 0.068 au) to a negative charge (-0.206 to -
0.210 au) in the neutral anthocyanidin. In general, q(COdep) is more negative than those found
for a carbonyl group in aliphatic systems [52] in spite of there are less surrounding hydrogens
(the atoms that act as electron donors) in anthocyanidins than in aliphatic aldehydes and
ketones. Although this could point to a significant weight of the enolate forms, we do not
observe the accompanying set of positive charges predicted by RM at: C2, C4, C5, C7, C9,
C2, C4 and C6, and neutral charges at: C3, C6, C8, C10, C1, C3 and C5. Clearly, some
QTAIM atomic charges are not in line with this rule, e.g. q(C1) > q(C2), q(C10) > q(C4),
etc. Overall, QTAIM results indicate that in spite of their geometry, neutral forms display a
certain enolate character, bearing a negative charge around the deprotonated oxygen but
counterbalanced in a different fashion than that expected from the typically enolate-like
resonance structures.
Acknowledgments
We are indebted to Spanish MICINN for financial support through project CTQ2006-
15500/BQU and to Centro de Supercomputacin de Galicia (CESGA) for access to its
computational facilities. M.M. thanks Xunta de Galicia for financial support as a researcher of
the "Isidro Parga Pondal" program. N.O. thanks University of Vigo for predoctoral
fellowship.
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Chapter 15
ELECTROMERISM IN SMALL MOLECULE

ACTIVATION BY METAL CENTERS
OF BIOLOGICAL RELEVANCE
Radu Silaghi-Dumitrescu*
Department of Chemistry and Chemical Engineering,Babes-Bolyai University,
11 Arany Janos str, Cluj-Napoca RO-400028, Romania
Abstract
Activation of small molecules, such as dioxygen, peroxide, or nitric oxide via mechanisms
involving ligation to metal centers of biological relevance is discussed. Emphasis is placed on
the means currently available for describing the problematic electronic structures of such
complexes in cases where electromerism phenomena are possible.
Introduction
Dioxygen binding to globins is central to human life and has as such been among the
most studied biochemical processes [1,2]. Figure 1 illustrates this reaction: the ferrous
histidine-ligated heme in globins (deoxy) binds dioxygen reversibly, to yield a ferrous-
dioxygen (oxy) adduct. Other reactions possible starting from these two states shown in
Figure 1 will also be discussed in subsequent sections; of main interest to us will be the
ferric-peroxo and the high-valent [Fe(V) and Fe(IV)] forms [3,4]. All of these species
feature electromerism phenomena. The following chapter discusses the means currently
available for unveiling the details of these complicated electronic structures, with emphasis
on the possibility of assigning them to one electromer, or to a defined mixture of electromers.
*
E-mail address: rsilaghi@chem.ubbcluj.ro
368 Radu Silaghi-Dumitrescu
O O OH
O O O
+H+ O N
N N N N -H2O N N O N
+e - N +H + N Fe +e- Fe
Fe Fe Fe N N
N N N N N N N N
X X X X X
"Compound I" "Compound II"
Fe(II)-O2 <> Fe(III)-O2

"Fe(II)-O2 <> Fe(III)-O22" Fe(III)-O2H formally Fe(V) formally Fe(IV)
"ferrous-dioxygen" "ferric-peroxo" "ferric-hydroperoxo"
+"R" +H-+
+O2 +HO2
- -"RO" +e
OH N
N N N N +H+ N
Fe - Fe Fe
N N +e N N -H2O N N
X X X
Fe(III)-OH
Fe(II) Fe(III)
Figure 1. Physiologically-relevant reactions of active site hemes with O2 and/or H2O2. R denotes an
organic substrate molecule. X may be a protein-derived cysteinate, tyrosinate or histidine ligand.
Ferrous-Dioxygen Species
The nature of the ferrous-dioxygen adduct has elicited interest due to the two main
electromers, Fe(II)-O2 and Fe(III)-O2-. Two key pieces of information have been used to
decide which one of these two electromers predominates in the globin version of this adduct.
Thus, the stretching frequency of the O-O bond in oxy hemoglobin, at ~1100 cm-1, is far
lower than the 1500 cm-1 value seen for molecular oxygen and consistent with a superoxide
moiety. Secondly, Mssbauer spectra are consistent with a ferric site as opposed to a ferrous
one; hence, the ferric-superoxo electromer is generally favored [1]. However, a discussion
remains as to whether a pure electromer is observed experimentally, and to what extent this
structure is modulated by changes in the first and second coordination sphere. Indeed, the oxy
adduct is seen with many other systems, ranging from cytochromes P450[5] to non-heme iron
proteins [6,7], and their reactivities, structures and spectroscopic features indeed suggest
different degrees of mixing between the possible electromers. In many of these complexes,
the oxy adduct is short-lived and its electronic structure is key to critical reaction
mechanisms. From these points of view, computational investigations can add significantly to
our understanding of dioxygen binding and activation.
With two main electromers suspected to contribute to the electronic structure of a
ferrous-dioxygen species and at least another one [Fe(IV)-peroxo] considered, it appears
that only multiconfigurational methods may address such structures computationally. Such
methods are not yet amenable for geometry optimization procedures, so that either a high-
resolution experimental structure or a density functional (DFT)-optimized geometry have to
be used for analysis of the electronic structure. Thus, in the most recent approach, using a
geometry computed at B3LYP level, CASPT2 (multiconfigurational second-order
perturbation theory) computes a contribution of 70% form the ferrous-dioxygen electromer,
with most of the remaining 30% due to the ferric-superoxo electromer [8]. However, this
procedure is still too demanding to be applied routinely to any given system of interest. On
the other hand, closer examination of the DFT geometry, which was taken as basis for the
Electromerism in Small Molecule Activation by Metal Centers 369
CASPT2 computation, reveals some interesting conclusions. Figure 2 thus shows a

comparison of oxygen-oxygen bond lengths and oxygen-localized spin densities computed
with two representative functionals for a few representative models; the HisH, SCH3- and
PhO- mimic the globin and heme oxygenase (histidine-ligated), cytochrome P450 (cysteinate-
ligated) and catalase (tyrosinate-ligated) active sites, respectively.[9] Since the dioxygenic
ligands in these three species are expected to be described as either molecular oxygen (bound
to ferrous iron) or superoxide (bound to ferric iron), or something in between, the computed
parameters for the OO ligands are indeed compared to those found, at the same level of
theory, for free O2 and HO2.[9]
0 1- 1-
O O O
O O O
N N N N N N
Fe Fe Fe
N N N N N N
N S O
NH
HisH/heme SCH3-/heme
PhO-/heme
% superoxide character - -
PhO /heme SCH3 /heme S=1/2 OOH
100%
UBP86, bonds HisH/heme
80% UB3LYP, bonds
UBP86, spin
60% UB3LYP, spin
40%
20%
S=1 O2
0%
Figure 2. Top panel: Structures and nomenclature for ferrous-dioxygen models employed in the
present study. In addition to the heme models, we examine the cd1 model based on the known
ability of cytochrome cd1 nitrite reductase to bind and reduce molecular oxygen. Bottom panel:
Percentages of superoxide and nitroxyl character derived from bond lengths and spin densities for
ferrous-dioxygen models with two different functionals, BP86 and B3LYP. Percentages are defined
with the general formula 100x[P(complex)-P(Oxidized Reference)]/[P(Reduced Reference)-P(Oxidized
Reference)], where the property P is either the bond length or the spin density on the O2 ligand;
Oxidized Reference is S=1 O2; Reduced Reference is S=1/2 OOH.[9].
It is important to note that of the two parameters investigated, O-O bond lengths and spin
densities, the former is the only one that is found to be relatively independent of the
functional used; the net spin density is seen to vary drastically with functional, such that
consideration of this parameter alone can lead to dramatically wrong conclusions. A strong
dependence of the spin density but not of the geometry on the dielectric constant of the
medium was also shown.[9] The DFT-computed bond lengths in fact appeared to yield an
indirect description of the electronic structure (% superoxide electromer) in reasonable
agreement with previous CASPT2 calculations, at a far smaller computational cost. This
agreement is surprising since the data shown in Figure 2 in fact come from ground state
calculations, whereas CASPT2 directly takes into account excited states; one may indeed
have expected a ground state calculation to yield either a pure ferrous-dioxygen or ferric-
superoxo description. A similar paradox is encountered with semiempirical calculations on
the same models, but not with Hartree-Fock.[10] A possible explanation is that
parameterization, more or less directly common to DFT and semiempirical methods, has
indirectly introduced excited-state information in the apparently ground-state results yielded
by density functionals and certain semiempirical methods, so that further application of more
expensive multiconfigurational methods on these ground-state geometries only rediscovers
information already introduced by parameterization. The validity of the DFT-derived
geometrical criterion for assignment of electronic structures in problematic electromerism
cases will further be exemplified in the following sections of this chapter.
Ferric-Peroxo Species
The one-electron-reduced versions of the ferrous-dioxygen adducts discussed in the
previous section (cf. Figure 1) are much shorter-lived, and for certain systems impossible to
detect: they rapidly (sometimes even at liquid helium temperature) protonate to produce a
ferric-hydroperoxo species.[3,11-15] Partly due to this fact, of the two electromers possible,
ferric-peroxo and ferrous-superoxo, the former is often preferred as terminology, and is as
such, only formally, used in tables below. Table 1 lists computed O-O bond lengths for the
one-electron reduced versions of the imidazole and methylthiolate models shown in Figure
2.[3] It is immediately apparent, based on this criterion alone, that a predominantly ferrous-
superoxo description applies here. Indeed, Table 2 then shows that the O-O bond lengths in
ferric-peroxo models are all shorter even compared to those computed for free superoxide, so
that no significant contribution from the ferric-peroxo electromer can be envisioned. By
contrast, in ferric-hydroperoxo models (cf. Figure 1) Table 1 shows O-O bond lengths similar
to those in free hydrogen peroxide. The geometrical conclusions are supported by DFT-
derived partial atomic charges and spin densities, all supporting a distinct superoxide
character in the ferric-peroxo models (Tabel 3). However, unlike the ferrous-dioxygen
case, where extensive experimental data was available for verification of hypotheses
formulated based on computations, data on ferric-peroxo adducts is mostly limited to EPR,
ENDOR and UV-vis spectroscopic data. In the case of the heme adducts illustrated in Tables
1 and 2, EPR spectra indeed are suggestive of spin density being located mainly away from
the metal, and ENDOR parameters for the oxygen atoms can be interpreted to be consistent
with a superoxo description.[3] By contrast, in non-heme ferric-peroxo adducts (not shown in
Tables here), where the O-O bond is computed to be distinctly more elongated than in the
heme cases, UV-vis spectra and possibly also EPR and Mssbauer parameters suggest clear
contribution from the ferric-peroxo electromer [16-19].
Table 1. Calculated bond lengths () for one-electron reduced versions of the models
shown in Figure 2. Hydrogen bond effects were accounted for by inclusion of one or two
water molecules (as indicated) interacting with the dioxygenic ligand.[3]
Formal description X Fe-O O-O

S=1/2 OOH - 1.35
S=1/2 OO- - 1.38
H2O2 - 1.48
HO2- - 1.57
Ferric-peroxo SCH3- 1.93 1.32
Ferric-peroxo imidazole 1.90 1.31
Ferric-peroxo, SCH3- 1.92 1.34
1 H-bond
Ferric-peroxo, imidazole 1.88 1.33
1 H-bond
Ferric-peroxo, SCH3- 1.94 1.35
2 H-bonds
Ferric-hydroperoxo imidazole 1.80 1.46
Ferric-hydroperoxo SCH3- 1.89 1.46
Ferric-hydroperoxo SCH3- 2.04 1.40
Table 2. Calculated Mulliken partial atomic charges and spin densities (the latter shown
in parentheses), for Figure 2 models [3]
Formal description X Fe O1a O2b

S=1/2 OOH - - -0.18 (0.29) -0.17 (0.72)
S=1/2 OO- - - -0.50 (0.50) -0.50 (0.50)
Ferric-peroxo SCH3 1.12 (0.80) -0.25 (0.41) -0.23 (0.59)
Ferric-peroxo imidazole 1.27 (0.03) -0.26 (0.38) -0.23 (0.40)
Ferric-peroxo, SCH3- 1.09 (0.39) -0.28 (0.38) -0.31 (0.38)
1 H-bond
Ferric-peroxo, imidazole 1.26 (0.17) -0.26 (0.40) -0.26 (0.43)
1 H-bond
Ferric-peroxo, SCH3- 1.05 (0.57) -0.34 (0.33) -0.39 (0.34)
2 H-bonds
Ferric-hydroperoxo imidazole 1.32 (0.76) -0.34 (0.24) -0.28 (0.07)
Ferric-hydroperoxo SCH3 1.09 (0.80) -0.36 (0.22) -0.34 (0.06)
Ferric-hydroperoxo SCH3 1.09 (0.64) -0.31 (0.14) -0.36 (0.35)
Ferric-hydroxo SCH3 1.05 (0.95) -0.34 (0.13) -
a
Iron-bound oxygen atom. bNon iron-bound oxygen atom. csolvated model, assuming =4.335.
Fe(IV)-Oxo and Fe(III)-Oxo Species

Fe(IV)-oxo species of the type illustrated in Figure 1 feature an electromerism case
different form the previous two, in that no internal geometrical parameter of the ligand (e.g.,
O-O bond) is available as a criterion for assigning electromers. Therefore, analysis of
molecular orbitals, partial atomic charges and spin densities remain as the only methods
available all bearing in mind the caveat provided by Figure 2 in this respect. Scheme 1
illustrates the molecular orbital diagram for formal binding of an oxo ligand to an Fe(IV)
center in octahedral environment. Key to the reactivity of this system are the degenerate *
orbitals, each singly occupied and reminiscent in this respect of the dioxygen molecule [20].
dx2-y2 eg

dxy t2g
Fe4+
px,py,pz
n-
X

Scheme 1.
Figure 3. Iron-oxygen * orbitals for an octahedral ferryl model, with four equatorial amine ligands and
an axial acetonitrile, illustrating a high degree of covalence [21].
Also reminiscent of the dioxygen molecule is the significant degree of covalence of these
orbitals in contrast with the ionic character seen with cognates of the oxo ligand such as
hydroxide or water; Figure 3 illustrates this aspect with DFT-derived plots of the two orbitals
[21]. Within such a framework, it is virtually impossible to assign electrons to either of the
two centers, and so the canonical Fe(IV)-oxo electromer is generally-accepted. Indeed,
Mssbauer spectra reveal the iron in such complexes to be highly oxidized [4,22,23]; even so,
recent experimental data revealing an unexpectedly high effect of covalence on iron
Mssbauer parameters have revealed that improper consideration of the covalence factor may
lead to assignments of iron oxidation states that are wrong by one or even two units [24,25].
In sharp contrast with the DFT results of Figure 3, Hartree-Fock and MP2 analyses of the
same system (Figure 4) reveal an entirely different picture: the * orbitals computed at non-
DFT levels reveal a clear hole on the oxygen valence shell, so that the oxygen ligand is now
described as oxyl (deprotonated version of a hydroxyl radical) while the iron is Fe(III). The
question remains, whether the DFT or the Hartree-Fock results describe these systems more
realistically; notably, the net electron densities obtained at the two levels of theory are
essentially the same: one full electron on iron from DFT, and two halves of electron on iron
from DFT.[21,26]
Figure 4. Iron-oxygen * orbitals at HF/6-31G** level, for the same model as in Figure 3 [26].
While the iron-oxygen covalence appears to hamper clear assignment of oxidation states
on the two partners in [FeO]2+, related systems such as [FeS]2+, [FeN] + and [FeN]2+ - all
formally Fe(IV) or Fe(V) do feature counterparts of the oxo ligand with different
electronegativity and hence different tendencies to engage in covalent interactions.[27]
Indeed, Table 3 shows that in an octahedral environment where the other five ligands are, for
simplification, water molecules, the various relatives of the [FeO]2+ system do exhibit
drastically different behavior in terms of localization of the * electrons: from the 45% seen
on oxygen in the Fe(IV)-oxo to the only ~10% seen with a nitride ligand, and with an
unexpected antiferromagnetic coupling in the Fe(V)-nitrido cognate. Table 4 further reveals
clear holes in the valence shels of the formally sulfide and nitride ligands (orbitals with
occupancies at 0.37), so that the corresponding systems can be interpreted, even at DFT level,
to be essentially Fe(III) and not Fe(IV) with the extra oxidizing equivalents lying on the
sulfide/nitride ligand. Additionally, stepwise elongation of the iron-oxo/sulfido/nitrido bonds
leads to an increase in Fe(III) character,[27] further arguing against a predominantly Fe(IV)
description at equilibrium.
Table 3. Optimized geometries and spin relevant densities for

[Fe(H2O)5O]2+,[Fe(H2O)5S]2+, [Fe(H2O)5N] + and [Fe(H2O)5N]2+ systems. All data is from
UBP6/6-31G** geometry optimizations [27]
Fe-Xa Fe X
[Fe(H2O)5O]2+ 1.64 1.12 0.92
[Fe(H2O)5S]2+ 2.06 0.89 1.13
[Fe(H2O)5N]+ 1.58 1.73 0.17
[Fe(H2O)5N]2+ 1.50 1.22 -0.37
a
X=O, N or S, respectively. baverage over 5 bonds.
Table 4. Relevant atomic orbital occupancies for [Fe(H2O)5O]2+,[Fe(H2O)5S]2+,

[Fe(H2O)5N]+ and [Fe(H2O)5N]2+ systems ( and values listed in each cell, in this
order). X is defined as in Table 3 [27]
[Fe(H2O)5O]2+ [Fe(H2O)5S]2+ [Fe(H2O)5N] + [Fe(H2O)5N]2+

Fe dxz 1.00-0.48 0.99 -0.60 0.99-0.46 0.62-0.46
Fe dyz 0.99-.50 1.00-.56 0.63-.46 0.63-0.48
Fe dxy 1.00-.00 1.00-.00 1.00-.99 1.00-1.00
Fe dx2-y2 0.29-.24 0.24-.21 0.97-.10 0.99-0.18
Fe dz2 0.45-.40 0.50-.43 0.57-.44 0.58-0.49
X px 0.98-.52 0.97-.37 0.92-.50 0.38-0.53
X py 0.97-.48 0.97-.41 0.37-0.53 0.39-0.53
X pz 0.66-.68 0.54-.58 0.51-0.61 0.52-0.59
An indirect test of the electronic structure is reactivity. Fe(IV)-oxo systems are known
to transfer an oxygen atom to organic substrates, with the reaction greatly facilitated by the
presence of a porphyrin ligand at the iron, carrying an extra oxidizing equivalent in the form
of a cation radical (the so-called Compound I state). Clearly, in order to accomplish this
transfer of an oxygen atom, the iron oxo ligand must at some point lose two electrons,
which implies an albeit transient Fe(II)-oxygen atom electromer. The other type ox
reactivity of Compound I and related species, hydrogen atom abstraction by the oxo ligand,
is consistent with the ferric-oxyl electromer (formally related to a hydroxyl radical) more so
than with the Fe(IV)-oxo (formally featuring a closed shell at the oxygen). On the other hand,
paradoxically, protonation of the iron-bound oxygen atom, which, as expected and as shown
in the next section, removes almost all of the spin density from the oxygen, is computed to
leave essentially unaltered the hydrogen-abstracting ability.[3]
Another way to assess the electronic structure of the Fe(IV)-oxo systems would be to
look at their one-electron-reduced counterparts- formally ferric-oxo. One such system, for
which a simplified model is shown in Scheme 2, is known experimentally. Figure 5 illustrates
that, in sharp contrast with the one-electron oxidized counterpart seen in Figure 3, the *
orbitals are now largely localized on the oxygen, which is cleanly described as oxo.
Consistent with this, the oxygen atom transfer reactivity of this species is much lower than
that seen typically with Fe(IV)-oxo systems.[28,29] Surprisingly however, Figure 6 reveals
yet another facet of electromerism in this system: the spin density on heme ferric-oxo systems
are indicative of one unpaired electron on the porphyrin ring, with the iron-oxygen moiety
described, ironically, again as Fe(IV)-oxo.[30]
H O
H
O H
O N
N Fe N
O
N
Scheme 2.
Figure 5. Molecular orbitals illustrating the Fe(III)-oxo interaction for the model shown in Scheme 2
[29].
Figure 6. Spin densities on imidazole-ligated S=1/2 and S=5/2 ferric-oxo models; white-positive, black-
negative) [30].
Non-Oxo Fe(IV) Species

The intricacies of the iron-oxygen covalence in the Fe(IV)-oxo system also prompt one
to examine related systems where the metal-ligand double bond (and hence the problem of the
two degenerate * orbitals) no longer exists. One class o such systems is illustrated in Figure
7. An added phenomenon of isomerization known experimentally, with the alkyl/aryl ligand
R migrating from the iron to the macrocycle, formally converts Fe(IV) to Fe(II) in these
systems without participation of an external redox partner.[31,32] Table 5 then shows that for
the Fe(IV) isomer with imidazole and methyl as axial ligands, there are clearly four orbitals
with occupancies close to 1, as expected of a formally Fe(IV) system.
1+ 1+ 1+ 1+
CH3 CH3 CH3 CH3
N N N N N N N N
Fe Fe Fe Fe
N N N N N N N N
N N S S
NH NH
Fe(IV) Fe(II)
Fe(IV) Fe(II)
Figure 7. Formally Fe(IV) models in heme organometallic complexes [32].
Table 5. Occupancies of iron d orbitals for models shown in Figure 7, from Mulliken
analyses. Axial ligands and formal oxidation states are labeled according
to Figure 7 [32]
Fe(IV), imidazole Fe(II), imidazole Fe(IV), thiolate Fe(II), thiolate

dz2 0.70 0.96 0.63 0.59
0.48 0.18 0.45 0.38
dxz 0.98 0.97 0.95 0.96
0.24 0.47 0.41 0.68
dyz 0.97 0.96 0.97 0.94
0.28 0.33 0.39 0.53
dxy 0.49 0.43 0.54 0.63
0.40 0.34 0.49 0.61
dx2-y2 0.94 0.94 0.83 0.69
0.92 0.92 0.80 0.66
However, the iron dz2, engaged in interaction with the methyl ligand, has an
occupancy of 0.70, suggestive of a fifth iron d electron and hence an electronic description
featuring Fe(III) engaged in covalent interaction with a methyl radical. A change of axial
ligand, from imidazole to thiolate, does not affect this description drastically. On the other
hand, the formally Fe(II) isomers (with the methyl radical migrated from iron to the nitrogen)
do differ significantly in electronic structure: the thiolate-ligated model features five d orbitals
clearly occupied (hence, ferric), while the imidazole-ligated cognate, with 6 d electrons, is
clearly ferrous [32].
Porphyrin Radical-Type Structures

The formally Fe(V) species shown as Compound I in Figure 1 is best described as a
[FeO]2+ moiety bound to a porphyrin cation radical; this is fully supported by experimental
data.[4] On the other hand, the porphyrin may engage in electromerism in a number of other
iron oxidation states.
Thus, the certain ferric porphyrins can isomerize to a Fe(IV) + anion radical state, both of
which are well characterized experimentally and computationally. More recently, attempts to
produce super-reduced states at the iron (Fe(I), Fe(0)) in hemes and related complexes have
led to the detection of species to which assignment of the electronic structure is still under
debate.[33-36] Figure 8 shows one set of models relevant for experimental data available;
consideration of CO and CO2 ligands is justified by the reactions observed, where CO2
appears to be reduced to carbon monoxide. Perhaps not surprisingly almost none of these
models are found to be described as clean Fe(0) systems.
O C
O O
C O C
N N N N N N N N
Fe Fe Fe Fe
N N N N N N N N
N N N N
N N N N
1 2 3 4
O
(H) (H)
O O
C C
(H) O (H)
O O
O C O
N N N N N N
Fe Fe Fe
N N N N N N
N N N
N N N
5 6 7
Figure 8. Formally Fe(0) models examined computationally [33].

Figure 9. Left: Metal-localized frontier orbitals in S=0 Model 1.Right: metal-localized frontier orbitals
in S=0 Model 4 [33].
For exemplification, Figure 9 lists molecular orbitals computed for the pentacoordinated
model: there are clearly four electrons missing from the iron d orbitals, and the system is
perfectly described as Fe(II) coupled to a two-electron reduced porphyrin. By contrast, Figure
9 also shows that the molecular orbitals computed for the model featuring an iron-carbon
bond between the heme and CO2, predicted by theory but yet to be confirmed by experiment,
indicate only two electrons to be missing from the iron d-shell, and hence a true super-
reduced state at the iron; orbital occupancies confirm this interpretation.
Metal-Nitric Oxide Complexes

Metal-nitric oxide complexes are important in biochemical pathways concerning the
nitrogen cycle (catalyzed entirely by metalloenzymes) as well as in nitrosative stress
processes.[37-41] A recent important example has been the hemoglobin-nitric oxide
interaction, thought to be important from a medical point of view.[42] With redox metals such
as iron or copper, M-NO adducts typically feature a second electromer, where an electron is
donated either from, or towards, the NO ligand, converting it into NO+ or NO-.[43]
In certain respects, this situation is reminiscent of the behavior of the dioxygen ligand
when bound to these metals, and, as such, nitric oxide has often been used a probe for
examining enzyme active sites, taking advantage of the unpaired electron of NO which makes
the resulting metal adducts more spectroscopically-amenable than their metal-dioxygen
cognates.[6,44,45] Figure 10 thus shows a few relevant formally Fe(II)-NO models, where a
second electromer is often invoked, Fe(III)-NO-.[9] The protocols applied are similar to those
seen in Figure 2, and it is again obvious that DFT-derived spin densities are not always
reliable, whereas assignments of electronic structure based on the internal bond length of the
NO ligand is considerably less dependant on the computational model used and hence much
more trustworthy.[9]
Figure 11 illustrates one aspect of the biological importance of copper-NO adducts: the
catalytic cycle of copper-containing nitrite reductases (CuNIR), where interaction of a
reduced Cu(I) center with nitrite leads to formation of a formally Cu(II)-NO adduct, which
indeed has a second electromer, depicted in the figure, Cu(I)-NO+.[38] The principle
illustrated in Figure 11 is in fact applied by all nitrite-reducing enzymes including those
employing iron: a reduced metal interacts with nitrite to yield a metal-NO adduct.[38,40] One
salient feature of the CuNIR catalytic cycle is the proposed bidentate binding of NO to Cu(II).
While this species has never been observed, its more stable, and more spectroscopically-
amenable cognate, Cu(I)-NO, has been characterized both spectroscopically and structurally,
and it did show the previously unobserved bidentate mode of ligation of NO to copper.[46]
EPR spectra of the Cu(I)-NO adduct showed a typical Cu(II) signal, suggestive of significant
contribution from the Cu(II)-NO+ electromer.[46] Both the structural and electronic structure
aspects warranted a detailed computational analysis of the Cu(I)-NO and Cu(II)-NO adducts.
Employing a simple model of the CuNIR active site (with the three protein-derived copper
ligands, cf. Figure 11, modeled as imidazoles), there was no evidence for bidentate ligation of
NO to the metal in either of the two oxidation states. However, using a larger model of the
active site, which accounts for sterical constraints (Figure 12, listed as +protein in Tables),
it was found that indeed bidentate binding of NO to Cu(I)-NIR is possible, in good agreement
with experiment [38].
Table 6 lists relevant geometrical parameters for the Cu-NO models. The larger Cu(I)-
NO model shown in Figure 12 features an NO bond length only 0.02 shorter than free NO-
at the same level of theory, and longer by 0.06 than in free NO. This already indicates, as
previously discussed, a significant Cu(II)-NO- character in good agreement with EPR
spectra; by contrast, Table 7 shows very little spin on the copper in the same model, again in
line with pitfalls previously seen in Figures 2 and 10. On the other hand, the Cu(II)-NO
model, which is directly relevant for the CuNIR catalytic mechanism, shows an NO bond
length 0.03 shorter than in free NO and 0.05 longer than in free NO+, suggesting
significant contribution from the Cu(I)-NO+ electromer. Here, too, if bidentate binding of NO
is enforced the NO, the nitrogen-oxygen bond lengths elongates, in fact reaching the exact
value seen for free NO at the same level of theory; this observation is important since this
species is know to decay via liberation of NO, not of NO+ [38].
O
O HN N
N
H2O OH2 N
Fe Fe
H2O O
OH2 N O
OH2
NH
[Fe(H2O)5(NO)]+2 [Fe(PCD)NO]0
O
HN
O N
N
N NH
N N
N Fe O
Fe O
N N
HN N NH
S
N
+1
[Fe(SOR)(NO)] [Fe(RDO)(NO)]+1
% nitroxyl character S=1 HNO

100% +1
UBP86, bonds [Fe(SOR)(NO)]
UB3LYP, bonds
80%
UBP86, spin [Fe(PCD)NO]
0
60% UB3LYP, spin
40%
20% +1
[Fe(RDO)(NO)]
+2
S=1/2 NO [Fe(H2O)5(NO)]
0%
Figure 10. Top panel: S=3/2 formally Fe(II)-NO models: PCD = model of the active site of
protocatechuate dioxygenase, featuring two tyrosine and two histidine ligands; SOR = model of the
active site of superoxide reductase, featuring four histidine and one cysteine ligand; RDO = model the
active site of naphthalene dioxygenase (a Rieske dioxygenase), featuring two histidine and one
aspartate ligand. Percentages of nitroxyl character are derived from bond lengths and spin densities for
ferrous-NO models with two different functionals, BP86 and B3LYP. Percentages are defined with
the general formula 100x[P(complex)-P(Oxidized Reference)]/[P(Reduced Reference)-P(Oxidized
Reference)], where the property P is either the bond length or the spin density on the NO-ligand;
Oxidized Reference is S=1/2 NO; Reduced Reference is S=1 HNO [9].
N
OH2 (H)O O
+ (H)NO2
Cu(II) Cu(II)
+ OH2 -
+e
- NO
N
+ O (H)O O
N
+ H+
Cu(I) - OH2 Cu(I)
Figure 11. Proposed mechanism for Cu-NIR [46].
Table 6. Calculated energies (a.u.), and relevant distances () for the

CuNIR-NO models [38]
Model Cu-O N-O

exp-NOa 1.95 1.46
Cu(I)-NO 2.84 1.19
Cu(I)-NO +proteinb 2.11 1.22
Cu(II)-NO 2.89 1.13
Cu(II)-NO side-onc 1.95 1.16
a
crystal structure, pdb code 1SNR. b model shown in Figure 12. cthe Cu-O bond was frozen at the distance
seen in the crystal structure, cf. entry 1 in Table.
Table 7. Calculated partial atomic charges and spin densities for models shown in Table
6. Spin densities are shown in italics [38]
Model Cu N O1 L
Cu(I)-NO 0.39 0.02 -0.08 -0.06
0.08 0.57 0.33 0.90
Cu(I)-NO +protein 0.40 -0.01 -0.12 -0.06
-0.03 0.73 0.31 0.90
Cu(II)-NO 0.45 0.22 0.15 0.37
Cu(II)-NO separated 0.48 0.21 0.20 0.42
Cu(II)-N) side-on 0.44 0.22 0.07 0.29
Cu(I)-OH2 0.37 - -0.53 -0.09
Cu(II)-OH2 0.59 - 0.53 -0.17
0.52 0.01 0.01
Figure 12. Large version of the Cu(I)-NO model, including selected side-chain and water (WAT) atoms
found near the NO ligand (~3-5 ). Protons are not shown, for simplicity. Heavy-atom coordinates
were taken from the crystal structure of the NIR-NO adduct, pdb code 1SJM [38].
Conclusion
A wide range of methods is available for exploring electromerism in complexes of metals
with small ligands, such as seen in dioxygen or nitric oxide activation. Spectroscopic methods
that probe the metal (EPR, Mssbauer) or ligand (resonance Raman, ENDOR) are in
continuous development and need careful choice of reference molecules. Much the same are
computational methods; in this latter respect, we have exemplified here how
multiconfigurational methods can be complemented by ground-state methods, where careful
analysis of geometries, molecular orbital plots, or orbital occupancies can again be very
reliable, provided proper reference systems are selected.
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Chapter 16
STRUCTURAL MODELLING OF NANO-CARBONS AND

COMPOSITES
Mihai Popescu* and Florinel Sava

National Institute R&D of Materials Physics, Magurele-Ilfov,
RO-077125, Romania
Abstract
The state of art in the field of nano-carbon object structures is presented. Simulations of the
structural configurations by a Monte-Carlo computing procedure are reported. New nano-
carbon objects were predicted on the basis of structural modeling data. A complex structural
configuration based on nano-carbons and a chalcogenide nano-object (arsenic sulphide
nanotube) has been modelled and its crystallo-chemistry was analyzed in order to demonstrate
the stability and importance of composite nano-objects for nano-technological purposes.
1. Introduction
The structure of the carbon nano-configurations is still poorly known and understood.
The nano-carbon species attracted the attention of the researchers in nano-devices, due to
their possible use in the nano-conductors (by filling carbon nanotubes with metallic atoms), in
the possible development of new superconductors (by filling the fullerene molecules with
alkali metals) [1], and in the utilization of the luminescence properties of doped fullerenes [2].
Recently, nano-objects were discovered in other systems, as e.g. molybdenum sulphides
[3] and arsenic chalcogenides [4]. In general, the low coordination covalent materials are able
to develop fiber, rings, closed tubes, ball-like configurations, or even complex configurations
at the nano-scale.
The problem of the formation and growth of nano-configurations in different materials is
still in its infancy.
*
E-mail address: pop_al.mihai@yahoo.com, mpopescu@infim.ro
388 Mihai Popescu and Florinel Sava
The presently available simulation techniques (semi-empirical, ab-initio and others) are
able to provide quantitative understanding of the formation and peculiarities of the structures
as a function of the structural arrangement of the atoms. A deep insight, at the atomic scale,
into various nano-objects will give the possibility to understand the essential physics of the
nanomaterials and will open the way towards various applications.
2. Structural Modelling Procedures

The modelling supposes a procedure for building rational structural models based on
calculations consisting in finding the structure of minimum free energy on the basis of inter-
atomic interactions chosen according to the crystallo-chemistry principles.
Three main methods are well-known:
- Molecular dynamics (MD)

- Monte-Carlo Metropolis (MCM)
- Reverse Monte-Carlo method (RMC).
The molecular dynamics is a simulation method which allows for predicting the time
evolution of a system with interacting particles and to estimate its relevant physical
properties. Thus, the positions and velocity of the atoms (particles) as well as the forces
acting upon them at every time can be known exactly. The particle trajectories are calculated
by resolving the motion equations for equilibrium and non-equilibrium situations.
By using the statistical mechanics are calculated the macroscopic properties of the system
as a function of time: pressure, caloric energy parameters [5, 6]. The method permits the
simulation of time-dependent phenomena: transport phenomena, growth processes, etc. The
method consists in several steps:
- choosing of an initial set of parameters (initial positions and velocities of all the
particles of the system)
- choosing the interaction potentials that govern the system and allow for the calculation
of the forces acting between the particles
- finding the evolution in time of the system by resolving the classical Newtonian
equations for all the particles. The equations are expressed as:
G G
d 2 ri
Fi (t ) = mi 2 (1)
dt
where F is the force that acts on the particle i at time t and is equal to the negative gradient of
the interaction potential U, mi is the atomic mass and ri is the position of the particle.
The interaction potentials determine the force field in the system. This force field can be
obtained by quantum methods (e.g ab-initio method, by using the Schrdinger equation), by
empirical methods (Lennard-Jones [7], Morse [8], Born-Mayer [9]) or quantum empirical
methods (embedded atom model [10], glue model [11], bond-order potential [12]). The
criteria for selecting the force-field are the accuracy, transferability and calculation speed. A
Structural Modelling of Nano-Carbons and Composites 389
typical interaction potential could consist of a number of bonding interaction terms (potential
for bond stretching, bond bending and bond torsion) and non-bonding interactions (van der
Waals, electrostatic).
The method has been improved by using the density functional theory (DFT) which leads
to more precise geometry and energies. The MD method that uses DFT (first principles) is
successful in the study of the dynamical processes but requires huge amounts of computing
resources.
The Monte-Carlo-Metropolis method has the following characteristics:
- the problem is treated in an analogous-probabilistic or statistical model.
- the probabilistic model is resolved by a numerical stochastic experiment; in a stochastic
process there is not a unique possibility of evolution in time of the processes, as is the case
when differential equations are used. Oppositely, there exists some uncertainty regarding the
evolution described by the distribution probability. This means that, notwithstanding the
knowledge of the initial conditions there exists more possibilities to continue the process,
some ways being more probable than others.
- the data are analyzed by using statistical methods.
The simplest procedure is the static Monte-Carlo one. In this method the atoms
trajectories are generated by random shifting of atoms in space, which leads, step by step, to
the minimization of the free energy of the system. This method does not permit the
investigation of the processes at the normal time scale. Temperature is not a variable
parameter and the system is, therefore, considered at T = 0 K. To accelerate the finding of the
minimum energy configuration it is better to choose firstly a set of initial coordinates.
The reverse Monte-Carlo method proceeds with the following steps:
- An initial configuration of points (atoms) are admitted (e.g. a set of N points within a
cube of side L). It is possible to use a a random three-dimensional configuration, a special
network or a set of coordinates from previous simulations.
- boundary periodical conditions are applied (e.g. the cube is surrounded by its image)
and one computes the pair distribution function, gs(r) (PDF, or radial distribution function
(RDF)).
- a new configuration is generated by moving randomly one or more simulated atoms. A
new PDF (RDF) is calculated: gs(r).
- the two PDFs, old and new one, are compared with the experimental gexp(r) for the
system under investigation by using Pearson test (2 criterion) or the least mean square
estimation of the difference between the two functions:
[g (r ) g (r )] [g (r ) g (r )]
nr nr
2 2
exp i S i exp i S i
2 = i =1
; '2 = i =1
(2)
2
E E2
where nr is the number of points ri and E is the experimental error.

- if < the new configuration is accepted. If > the new configuration is accepted
with a probability that follows a normal distribution, with width .
- if the new configuration is accepted, then this one is taken as initial configuration for
the next iterative step.
The procedure is repeated till the 2 decreases down to the equilibrium value and
oscillates around this value as in the case of the energy in the conventional Monte-Carlo
method.
3. Graphenes
3.1. Geometrical and Electronic Structure of the Graphene Nano-Object
Graphene is the constituent unit of the graphite crystal. It is formed by a a plane of

covalently bonded carbon atoms situated in the corners of the regular hexagons of side 1.415
. In graphite, the graphene sheet are held together by van der Waals forces at the distance of
3.354 . Fig. 1a shows the packing of the graphenes with the sequence ABABAB, in a
hexagonal lattice.
Figure 1. a. The hexagonal latticre of the graphite single crystal [from R. W. G. Wyckoff, Crystal
Structures, (Interscience) New York 1964, Vol. 1] b. The image obtained by STM (Scanning tunneling
microscopy, STM). It is observed the trigonal lattice of the pyrolitic graphite with very good
orientation. In the picture appear only the positions noted in part a of the figure by B (filled dots) [from
M. S. Dresselhaus and M. Endo, Carbon Nanotubes - Synthesis, Structure, Properties, and
Applications, M. S. Dresselhaus, G. Dresselhaus, P. Avouris (Eds.), (Springer-Verlag Berlin Heidelberg
2001, Springer Series: Topics in Applied Physics, Vol. 80), p.15].
Although the fullerene has been discovered in 1985, and the carbon nanotubes in 1991,
the prototype of these nano-objects, the graphene, (in greek: graphein = to write), has been
obtained as distinct object for physico-chemical investigations only in 2004. At that time,
Novoselov et al. [13-15] succeeded to make the transfer of a single graphite sheet from the
face c of the crystal to an appropriate substrate for performing measurements of the optical
and electrical properties of the carbon sheet.
The schematic of the structure of the graphene is given in Fig. 2. Such atomic structure is
formed due to the fact that during graphene formation process every atom modifies its
electronic configuration, from the fundamental state, with two electrons on the atomic orbital
2s and one electron on every orbital 2px and 2py, to the hybrid state sp2, with three electrons
on the hybrid orbitals sp2 (situated in the same plane, the angle between their axes being
120). The fourth electron is situated on the unhybridized orbital pz, having a lobe above and
other below the plane of the hybridized orbitals.
Thus, every carbon atom is covalently bonded with other three carbon atoms by three
molecular orbitals , formed by the unification of two hybrid orbitals sp2, for every molecular
orbital, and by a molecular orbital (partially filled), formed by the unification of the
unhibridized atomic orbitals pz. In fact, there exists only one molecular orbital , extended in
the whole graphene, with the maximum amplitude of the electronic wave above and below
the plane of the bonds. The electrons are delocalized.
The bonds are strong and they lead to frequencies of the optical phonons, much higher
than those observed in diamond carbon.
Figure 2. a) Illustration of the valence orbitals of the carbons in graphene: three hybridized orbitals sp2
in the plane of the graphene and the unhybridized orbital pz perpendicularly to the layer. These orbitals
bind strongly the carbon atoms in a hexagonal lattice and are responsible for the high binding energy
and for the elastic properties of the graphene. b)The width of the forbidden gap between bonding
band (valence band) and antibonding (conduction band) is ~12 eV, while the bonding and
antibonding states are situated in the neghbourhood of the Fermi level (EF).Consequently, the bonds
are frequently neglected when the electronic properties of the graphene around the Fermi level are
predicted. c) Dirac cones localized in the six corners of the Brillouin 2D zone [from J.-C. Charlier, P. C.
Eklund J. Zhu, A. C. Ferrari, Advanced Topics in the Synthesis, Structure, Properties and Applications,
A. Jorio, G. Dresselhaus, M. S. Dresselhaus (Eds.), Springer-Verlag Berlin Heidelberg 2008, Springer
Series: Topics in Applied Physics, Vol. 111, p. 675].
From the theoretical point of view, the graphene has been investigated well before 2004
[16-18]. Some scientists considered that graphene cannot exist in the free state and its
analysis was carried out only for academic purposes [19]. All other curved structures
(fullerenes, nanotubes) were viewed as unstable.
The hypothesis of the thermodynamical instability, and, therefore, of the physical
inexistence of the 2D crystals appeared already in the middle 30 of the last century [20,21].
The thermal fluctuations would lead to atomic shift comparable to the interatomic distances at
every finite temperature [22,23]. A lot of experimental observaions supported this hypothesis.
For example, the melting temperature of a thin film decreases rapidly with its thickness and
the film becomes unstable and separates in islands or decomposes at thickness of several
atomic layers [24,25]. That is why the monoatomic layers werev physically prepared only by
epitaxial growth on the surface of single crystals, with lattices approaching that of the
monoatomic layer. The people was convinced that without a 3D basis the 2D materials cannot
exist. After 2004 was obtained not only separated graphenes but also boron nitride layers
[26]. Good 2D crystals were obtained in the following configurations:
- on the surface of a non-crystalline substrate

- as suspended membrane
- as suspension in liquids
To reconcile the theory of instability of graphene with the experiment, the following
explanations were proposed:
-The interatomic bonds are enough strong for preventing the generation of dislocations or
other defects at room temperature.
-The graphene is quenched in a metastable state because it is extracted from a 3D
material.
-The graphene is weakly waved in three directions (Fig. 3), the deformations outside the
plane being of the order of nanometers [27]. Such ondulations increase the elastic energy of
the lattice, but compensates the thermal vibrations (very large in 2D), and above a given
temperature they can minimize the total free energy [28].
Figure 3. Illustration of the waved structure of graphene, observed experimentally by transmission

electron microscopy [27].
Investigations have been carried out on the variation of the graphene properties as a
function of the number of layers in a graphite packing. There as estsablished that the
electronic structure evoluates very rapidly with the layer number, and reaches the state
corresponding to av 3D crystal for a pack of ten graphenes. Nevertheless, only graphene and,
with a good approximation, the double layer exhibit a simple electronic spectrum. Both are
semiconductors with the width of the of the forbidden gap zero, having only one type of
electron and one type of hole. If the number of layers raises to three or more, the electronic
spectrum becomes more and more complicated. Several types of charge carriers appear and
the conduction and valence bands gradually superpose. This behaviour allows for
distinguishing between a graphene, di-layer and multilayer (from 3 to 10), as three types of
2D crystals.
Graphenes of high quality show an ambipolar filed effect (Fig. 4).
Figure 4. The effect of ambipolar field effect in the monolayer graphene. There are represented the E(k)
spectra of low energy (cones); it is indicated the change of Fermi level, EF, with the change of the gate
voltage, Vg. Positive, and, respectively, negative gate voltages induce electrons (holes) with the
concentration n=Vg, where the coefficient 7.21010 cm-2V-1 for field effect devices with a film of
300 nm thicknes of SiO2 as dielectric. The rapid decrease of the resistivity, , for increasing number of
charge carriers, speaks in favour of their high mobility (a value of 5,000 cm2V-1s-1 that does not
change significantly with temperature up to 300 K) [15].
In graphene was observed, also, the quantum Hall effect, even at room temperature [34].
The graphene attracted the attention of the researchers due to the peculiar nature of its
charge carriers. These behave similarly to the relativistic particles and, therefore, they are
described more simply by Dirac equation than Schrdinger one. The interaction of the
electrons with the periodic potential of the graphene, produces new quasi-particles, which, at
low energies are described accurately by a Dirac equation (2+1 dimensional). These quasi-
particles, called Dirac fermions without mass, could be regarded as electrons that lost their
mass, mo, or as neutrinos that acquired an electrical charge e.
3.2. Methods of Graphene Preparation
Along the time several method for graphene preparation have been used:
-chemical exfoliation: atoms or molecules are intercalated in-between the graphenes [29];
-epitaxial growth by vhemical vapour deposition of hydrocarbons on metallic supports;
-thermal decomposition of SiC;

-micromechanical cleavage of the graphite crystal.
-the method of the micromechanical cleavage allowed for the graphene separation and its
observation for the first time (Fig. 5) [26].
Figure 5. a. The graphene vizualized by atomic force microscopy [26]; b. Suspended graphene on
metallic grid of micrometer size (TEM image) [27]; c. Image obtained by electron microscopy; one
observes the zig-zag and chair-like edges [15].
After successive cleavage with the help of adhesive bands, the layer is pressed against a
substrate and is looked for the remaining fragments of graphenes.
The secrets of the method consist in the use of an optical microscope and in an
appropriate thickness of the SiO2 film on the Si wafer. Thus, the optimum contrast is
optimum and the graphene can be observed, with great effort and attention. It is enough to
shift the SiO2 thickness by around 5 % (e.g. 315 nm against 300 nm) and the graphene layer
becomes invisible.
Moreover, the graphite used for cleavage must be carefully selected (large crystallites are
needed), the cleavage must be fresh, and SiO2 must exhibit a very clean surface.
The graphene gives a very strong and peculiar signature in the Raman microscopy
measurements [30, 31], and this makes useful the Raman technique for rapid analysis of the
thickness of the graphenes identified by optical microscopy.
3.3. Applications
In spite of the optimistic opinions regarding the future of applications of graphenes in

electronics, the graphene microprocessor seems to be still a dream.
We must enumerate a series of nowadays applications:
-use of graphenes in composite materials.

-use of graphene powder in electrical batteries. The powder is cheaper than the
nanocarbon tube powder used now by NEC Company (Japan).
-source of electrons for TV screens.
-sensors
-hydrogen storage
3.4. Graphene Nanoribbon
There are many scientific papers that report the investigations of the nano-carbon
structures based on ribbon graphenes. The ribbon is considered as quasi-one-dimensional
(1D) due to its small width of several nanometers. As a function of the shape of the edges the
ribbons are assigned to three different configurations (Fig. 6).
Figure 6. The graphene edge in gaphene ribbons. a). Zig-zag edge (Z); b). Edges with chair-like shape
(A); c). Chiral edge (C).
The shape of the edges and the width of the ribbon determines the broadening of the
forbidden gap. The modelling has shown that the chair-like edge ribbon could exhibit a
metallic or semiconductor character, as a function of its width, while the zig-zag edge ribbon
is metallic.
3.5. Topological Defects in Graphene
Meyer et al. [35] from Berkeley Laboratories investigated a graphene monolayer with
high resolution microscopy (1 ) using low acceleration voltage (80 kV), in order to prevent
the graphene destruction during measurements. The graphene was obtained by mechanical
cleavage using the procedure presented in the section 3.2. Every atom from the visual field
was detected. One observes a very ordered crystalline lattice with very few defects (Fig. 7).
Figure 7 [35]. A). Direct image of a graphene monolayer; b). Transition from the monolayer (upper
part) to bi-layer (bottom part); c). The same figure as in b; additionally is shown the graphite AB
packing.
In Fig. 8 are presented the metastable defects in the 3-layers graphite lattice.
Figure 8 [35]. Metastable defects detected by electron microscopy (HREM) (the scale is 2): a. unperturbed
lattice before the appearance of the defect; b. Stone-Wales defect; c. the same image as in b, with superposed
atomic configuration (for the sake of clarity); d. relaxation of the unperturbed lattice (after 4 s). e.-g.
Elimination of a vacancy; e. initial image; f. image. + atom configuration with the indication of the pentagon;
g. lattice recovered after 4s; h., i. Image and atomic configuration of the defect consisting in 4 heptagons and
4 pentagons; one observes two adjacent pentagons; j., k. atomic configuration of the defect consisting in three
heptagons and three pentagons. This defect has been eliminated after 4s.
Figure 9. Nano-engineering of graphene defects: a. booble; b.crest; c. meta-crystal d. band [from M. T.

Lusk, L. D. Carr, Nanoengineering Defect Structures on Graphene, Physical Review Letters, 100,
175503 (2008)]
The graphene-type membranes are promising as support for materials to be used in

transmission electron microscope (TEM), because graphene ensures a crystalline very
transparent basis and its structure is accurately known.
It is a continuous interest in the modelling of the defects in graphenes with the purpose to
find new properties in the nanostructures. Irregular configuration of the defected graphenes
was clearly established (Fig. 9.).
3.6. Graphene-Based Structures
3.6.1. Ideal Graphene
Graphenes and nano-objects based on graphene configuration have been modelled in the
frame of the valence force field model [36]. Bond stretching and bond bending force
constants reported recently for fullerenes: kr=6.05 10-4 dyn/3 and kB = 7 10-5 dyn.,
have been used [37].
Figure 10. The modeling of a graphene sheet (150 carbon atoms). The total free energy per bond and
bonding angle = 3.14210-8 meV and s=2sin/.
The calculation of the free energy of every carbon configuration was carried out by the
Monte Carlo Metropolis method, with special computer programs developed in the National
Institute of Materials Physics, and run on powerful PC computers. For every configuration
there were performed 60 millions iterations, starting with the working step of 0.02 nm and
gradually reducing the iteration step in order to refine the structure [38-40].
Firstly we used a hand-built model of graphene (150 carbon atoms). The atomic
coordinates have been carefully measured and the table of atom interactions has been built.
The data strings were put in the computer and special program was run in order to find the
structure of minimum free energy (minimum bond stretching and bond bending distortion
energy. For graphene this calculation is trivial because the ideal structure must give zero free
energy and exact bond length and bond angle values.
Figure 10 shows the results after 60 millions iterative steps. The total free energy was
found: 3.142 10-8 meV. Fig. 10a shows the interatomic distance distribution in the model.
Fig. 10 b presents the X-ray diffraction pattern calculated for such structure. The elongated
and asymmetric shape of the diffraction peaks is characteristic to one-dimensional structures.
Fig. 10c illustrates the distribution of the angles between bonds. The bonding angles are very
close to ideal 120 oC. The calculation is important because it reveals the limits of the iteration
method to reproduce the exact structure of a given configuration of atoms in the frame of the
Monte-Carlo Metropolis method.
3.6.2. Nano-cones and Nanohorns
A carbon nanocone can be modelled by a cut and glued procedure, thus creating a
disclination defect. More precisely, a sector of 60 is cut and the remaining margins are glued
(Fig. 11). Thus, if the deviation from the plane surface is permitted, one obtains a cone whom
top angle is directly related to the disclination angle.
Figure 11. How to build a cone from a graphene [41]: 1) the sector is cut and one put together
and to create a cone with one pentagon at top(n=1); 2) the second sector is cut and the and is
glued, thus producing a cone with a lower angle at the top (n=2). The top ring made of 4 atoms is very
unstable; the true cones with the same angle at the top contain very probably two vicin pentagons.
Due to graphene symmetry, only five types of cones can be created from a graphene
sheet. The disclination angles are multiple of 60 (60, 120, 180, 240, 300), corresponding
to the presence of a given number of pentagons, n, at the top (respectively, n=1, 2, 3, 4, 5),
and the top angles are 113, 85, 60, 39, 19, values observed experimentally [42]. If n=6
one gets a closed nanotube at one end and n=0. This is a disc. Experimentally, there were
observed cones with the top angles: 30, 50 i 70 [43], but one considers that these
nanocones are opened at the top (Fig. 12). Another possibility is the creation of partial
disclinations in the structure.
Figure 12. The structure of an open nanocone (abat-jour-like configuration).
Figure 13. Electron microscope images (SEM) showing a carbon disk and three carbon nanocones of
one micrometer diameter [from http://www.complexphysics.org/Projects/Nanocarbon.html].
By using a laser ablation technique at room temperature and in the absence of the
catalysts there was obtained a new class of carbonic materials, called nanohorns. These
nanohorns exhibit a unique top angle: ~20 [44] (Fig. 14).
These top angle of ~20, correspons to a disclination of 5/3, and this fact implies that all
nanohorns contain exactly 5 top pentagons [45].
Figure 14. TEM images of the nanotubes(a) and nanohorns (b), (c). Additionally, it is presented the
schematic of such nanohorns (c, at bottom) [from Iijima Sumio, Yudasaka Masako, Nihey Fumiyuki,
Carbon Nanotube Technology, Nec Technical Journal, 2(1), (2007) p.52].
The modeling of the nano-cone objects has been carried out starting from hand-built
models followed by structural relaxation of the coordinates in the frame of the Monte-Carlo-
Metropolis method.
Three configurations have been constructed: broad cupola, narrow cupola and small cup.
After relaxation the nano-objects were characterized according to the total free energy
and distribution of the bond distortion energies.
Broad cupola has 80 atoms and is characterized by one five fold ring at the top, the
remaining rings being 6-fold rings of carbon atoms (Fig. 15). After relaxation, the free energy
per bond and angle is 0.322 meV. The top angle of the cone is 113.48o. The wall inclination
is 60o. The narrow cupola has 73 carbon atoms and the free energy per bond and angle is 1.1
meV (Fig. 16). The top angle of the cone is 60o. The inclination angle of the walls is around
30o. The small cup configuration contains 35 carbon atoms and exhibits a distortion energy
per bond and angle (free energy) of 4.79 meV. (Fig. 17).
As it easily observed the small cup configuration has the most distorted valence bonds,
and, therefore is least stable. The broad cupola that contains only one defect in the graphene
(one 5-fold ring) is less distorted, and seems to be a very stable structure which could be,
therefore, practically obtained.
As shown in Fig. 13 the nano-cones have been experimentally observed. It is interesting
that, mostly, narrow cupolae have been observed.
Figure 15. Broad cupola (one five fold ring at the top) - 80 carbon atoms a. Pair distance distribution b.
X-ray diffraction pattern c. Bonding angle distribution. Free energy/(bond and angle) = 0.332 meV.
Figure 16. Narrow cupola (3 five fold rings at the top) - 73 carbon atoms a. Pair distance distribution
b. X-ray diffraction pattern c. Bonding angle distribution. Free energy / (bond and angle) = 1.1 meV
Figure 17. Cup configuration (6 fivefold rings) - 35 carbon atoms. a. Pair distance distribution b. X-ray
diffraction pattern c. Bonding angle distribution. Free energy / (bond and angle) = 4.79 meV
Figure 17 bis. e1) One heptagon in graphene (175 atoms); e2) side view. Free energy / (bond and
angle) = 0.0152 meV.
A quite different type of configuration is induced by heptagons created in a rather perfect

graphene. Fig. 17-bis shows the butterfly configuration of the defected graphene having a
heptagon configuration of carbons in the centre.
3.7. Fullerene and Fullerene Based Nano-Objects
3.7.1. How the Fullerenes Are Formed
The exotic geometries of the carbon originate from the topological defects of the
graphenes. The following structures have been modelled: fullerenes, nanotubes, nanocones,
nanohorns, multilayer graphites, etc...
Fullerenes are ball configurations of pure carbon, and were discovered in 1985 by Kroto,
Smalley and Curl [46]. These scientists received the Nobel Prize for Chemistry for the year
1996. It must to remark that theoretical studies on the C60 molecule have been carried out as
early as 1970, but the nobelists were unaware of these studies. The concept of fullerene
comes from the name of the americain architect Richard Buckminster Fuller, who created the
geodesic dome with the structure similar to that of C60 configuration. (Fig. 18).
Figure 18. Geodesic dome created by Richard Buckminster Fuller.

[from http://commons.wikimedia.org/ wiki/File:Biosphere_in_Montreal.jpg].
Fullerenes have been obtained by self-assembling of the carbon atoms in a hot carbon
plasma, created by irradiating a graphite disk with focused laser pulses (YAG:Nd, = 532
nm, pulse duration: 5 ns) having the pulse energy of ~30 mJ (Fig. 19).
Figure 19. Mass spectra of the distribution of the carbon clusters produced in various working
conditions (a, b, c). One observes that in the case a. the stable carbon clusters, C60 i C70, these are
formed abundantly. This is a proof of the inexistence of free bonds (dangling bonds) in these clusters.
The clusters must be in closed configuration with every atom three-fold coordinated [46].
Because in specific working conditions (Fig. 19a), there were formed mainly C60 i C70
clusters, the Nobel Prize laureates proposed for C60 cluster a geometrical configuration based
on a cut icosahedron architecture (Fig. 20). The typical molecular fullerene C60, is composed
of 60 carbon atoms, that form an Archimedic polyhedron with 12 pentagons and 20 hexagons.
Every pentagon is surrounded by hexagons and every hexagon is surrounded by three
pentagons and three hexagons that alternate around.
Figure 20. The structure of a cut icosahedron, proposed for C60 molecule [from R. F. Curl and R. E.
Smalley, Probing C60, Science 242, 1017 (1988)].
An other way of fullerene synthesis consists in the self-assembling of the evaporated

carbon clusters in a very hot electric arc discharge (2800 C) between two graphite electrodes,
in a vessel filled by Helium at a pressure of 0.4 bar.
As well known, an euclidean plane can be covered by a hexagonal tri-coordinated lattice
with Nc=3 i Nl=6. Three hexagons that intersect at the top determine three angles of 3 120
= 360. If one hexagon is substituted by one pentagon, then the pentagon will be deformed, or
if the pentagon remain perfect, then the full structure will be strongly deformed and goes out
of the initial plane. Every pentagon creates a deficit of 12 in every corner. The heptagons
introduced in the structure compensates the deficit.
In the hot plasma that triggers the evaporation of the graphite, there is a large variety of
carbon clusters: C2, C3, C4,...C6 (benzene ring), C10 (two adjacent rings as in naphtalene) ande
even C12 clusters consisting of 3 rings: two hexagons and one pentagon (Fig. 21).
Figure 21. The C12 molecule consisting of two hexagons and one pentagon [from R. Kerner, Cap. 3
The Role of Topology in Growth and Agglomeration in Topology in Condensed Matter, M.I.
Monastyrsky (Ed.), (Springer-Verlag Berlin Heidelberg 2006, Springer Series in solid-state sciences vol
150), p.77].
The C12 molecule is enough large to become a center for nucleation of the fullerene. How
the growths proceed? We must take into account that in C60 fullerene all the corners are
equivalent. They are formed by two hexagons and one pentagon. Two pentagons must not
have a common edge or a common corner, nor do three hexagons have a common corner.
These conditions must be accomplished when a new ring is added to the molecule C12 (by
addition of C2 or C3 molecules) or when a larger molecule, e.g. C9 is added. What is built by
self-assembling of different clusters is only a waved surface, with dangling bonds.
Nevertheless, these additive processes are statistical and, therefore, the preference for
fullerene configurations cannot be explained. That is why we must admit a significant
difference between the energies of different added polygons.
The fullerene C60 can be regarded as the self-assembly of 12 pentagons, the hexagons
being a consequence of this assembling. To admit a high probability for the formation of
pentagons is very important.
In 1990 Krtschmer, Huffman et al. [47] discovered that C60 fullerene, produced in high
amount, can crystallize (Fig. 22).
Figure 22. a). The elementary cell of the cubic crystal (f. c. c.) of fullerite (C60) [47]; b). Fullerite
crystals [from http://en.wikipedia.org/wiki/Fullerene].
3.7.2. Multilayer (Onion-Like) Fullerenes
Nanocarbon structures of multilayer fullerenes built from concentric fullerenes (Fig. 23a,
b) have been prepared and investigated.
Of course, the diameters of these concentric fullerenes must stay in rigorous relation, so
that the van der Waals interaction energy between two layers be minimum. For that it is
necessary that the interlayer distance be not less than the distance between the atom planes in
graphite: 3.354 .
Let us suppose that, for getting more and more larger fullerenes, we must preserve the
pentagon number (12) and we must increase the number of hexagons (according to Euler
formula). The 20 triangular faces constituted from a given number of hexagons with three
pentagons at the corners (Fig. 20), become more and more plane and the fullerenes will
exhibit a more and more distinct icosahedral structure (Fig. 21). Every triangular face can be
parameterized, using the notation of Coxeter [48], by two integer numbers (p,q), which
represent the relative positions of the pentagons one to another in a hexagonal system of
coordinates (Fig. 24). Fig. 25 shows the family of icosahedral fullerenes having the same
number of hexagons and a variable number of hexagons.
Figure 23. a. Structure of a fullerene with three layers b. Electron microscope picture [see the reference
from F. Banhart, Structural transformations in carbon nanoparticles induced by electron irradiation,
Fizika dverdovo tela (ru), 44(3) (2002) p.388].
Figure 24. Possible triangular configurations, which, in the notation of Coxeter correspond to the
parameters (p,q): a: (2,2); b. (3.0); c. (4,2) [from R. Kerner, Cap. 3 The Role of Topology in Growth
and Agglomeration in Topology in Condensed Matter, M.I. Monastyrsky (Ed.), (Springer-Verlag
Berlin Heidelberg 2006, Springer Series in solid-state sciences vol 150), p.80.]
Figure 25. The family of icosahedral fullerenes C20(p2+pq+q2) (p1, q0, p=q), with the same number of
pentagons (12) and variable number of hexagons [60]. a. C240 : 20*(22+2*2+22); b. C540 :
20*(32+3*3+32); c. C60 : 20*(12+1*1+12); d. C960 : 20*(42+4*4+42); e. C1500 : 20*(52+5*5+52).
Figure 26. The fullerene family of quasi-spherical balls C60*n2 (n=3-5), that contain a variable number of
pentagons and heptagons [60]. a. C540 (60*32); b. C960 (60*42); c. C1500 (60*52).
The number of the carbon atoms in the icosahedral molecule built from triangles of the
type (p,q) is:
N = 20( p 2 + pq + q 2 )
In Fig. 26 are presented three quasi-spherical fullerenes built from a variable number of
pentagons, hexagons and heptagons.
3.7.3. Fullerene Modeling
We have modellled two types of fullerenes: the C60 fullerene ball, which is the first
fullerene discovered and investigated, and the small fullerene ball C35, in order to compare the
structures and investigate the free energy relation.
Figure 27 shows the fullerene configuration and its structural characterization: pair
distance distribution, X-ray diffraction pattern and bonding angle distribution. The full
relaxation gives the free energy (per bonding distance and bonding angle) of the fullerene ball
gives 4.33 meV, a value approaching that of the cup modeled in the previous section. The
smaller fullerene ball exhibits a much higher free energy (7.24 meV) that demonstrates low
stability of such nano-object. Thus, is not expected to find or to prepare easily such type of
fullerenes.
Figure 27. Fullerene (12 five fold rings, 60 carbon atoms). a. Pair distance distribution b. X-ray
diffraction pattern c. Bonding angle distribution. Free energy / (bond and angle) = 4.33 meV.
Figure 28. Small fullerene ball (12 five fold rings) - 36 carbon atoms a. Pair distance distribution
b. X-ray diffraction pattern c. Bonding angle distribution. Free energy / (bond and angle) = 7.24 meV.
3.8. Carbon Nanotubes
3.8.1. Atomic and Electronic Structure
In 1991, Iijima from the NEC Laboratory, Japan has reported the first observation of
some multiwall carbon nanotubes in the soot obtained by arc discharge between two graphite
electrodes [49]. After two years Iijima discovered the single wall carbon nanotubes [50].
The electrical and mechanical properties of the carbon nanotubes have attracted the
attention of the scientists, and the understanding of these properties was the motor which
propulsed the applications and the rapid development of the field of nano-carbons. A single
wall carbon nanotube (NTC) can be considered as a curved graphene sheet and closed bas a
cylinder, without any defect or free bond. All the polygons of this tube are hexagons [51]
(Fig. 29). A necessary condition for getting a cylinder without defects is: one node of the
graphene lattice (n1,n2) must coincide with the origin (0,0). In this condition, if a1 and a2 are
the lattice vecors of the graphenes, the circumference of the carbon nanotube is equal with the
length of the vector (n1a1+n2a2), while the chiral angle of the carbon nanotube, , is defined
as the angle between the vectors (n1a1+n2a2) and a1.
Figure 29. The structure of theb carbon nanotube. a) Graphene with the lattice vectors a1 and a2. The
Miller indices are indicated for several lattice sites (0,0), (1,0), (3,0), (5,0), (1,1), (2,2), (3,3). is the
chiral angle for a carbon naotube. (3,1). The dotted lines is the circumference of a possible chair-like
nanotube, and the discontinuous line is the circumference of the zig-zag nanotube [51]; b) is the carbon
chair-like nanotube (5,5) [51]; c) is the carbon zig-zag nanotube (9,0) [51]; d) Axial view of the chair-
like nanotube (10,10); e) Axial view of the chair-like nanotube (16,0); f)Axial view of the chair-like
nanotube (15,5) tip chiral.
The chiral angle of a chiral nanotube is given by:
and the corresponding diameter is given by:
In these two relations the parameter a is the lattice constant of the graphene.
The diameter and the chirality of a carbon nanotube, and, consequently, its atomic
geometry, is fully determined by the two Miller indices (n1,n2), which are called the chiral
indices of the nanotube. Due to the symmetry of the graphene lattice, the chiral indices can
take values in the range n1n20, and n1>0, while the chiral angle, , takes values in the range
(0,30). The theoretical calculations [31-34] have shown that the electronic properties of the
carbon nanotubes are very sensitive to their geometrical structure. Although the graphene is a
zero-gap semiconductor, the theory predicted that NTC can exhibit either metallic character,
or semiconductor with different widths of the forbidden gap, as a function of the diameter and
chiral indices of the tubes. Due to intimate correlation betwen the geometrical structure and
the electronic one, new special properties appear, especially at the junction of nanotubes with
different diameters (Fig. 30).
Figure 30. Carbon nanotube illustrating a metal-semiconductor junction [from http://www.nanotech-

now.com/nanotube-buckyball-sites.htm].
The general rules for the character of the electrical conduction are:
-chair-like nanotubes (n,n) (n1=n2=n) are metals

- nanotubes with n1-n2=3j, including those with (3j,0), part of the zig-zag ones, are very
narrow band semiconductors (~ 10 meV). This originates from the curvature effects (j>0 is an
integral number)
-nanotuburile with n1-n23j are semiconductors with wide forbidden gap.
Figure 31. a. Carbon nanotube with four walls; b. HRTEM images of a multiwall NTC prepared by arc
discharge, with well graphitized walls and bamboo structure [from http://www.nanotech-
now.com/nanotube-buckyball-sites.htm].
NTC (n,n) are metallic independently of their curvature, due to their symmetry. The
width of the forbidden gap for the other two types of nanocarbons decreases with the increase
of the tube diameter. The tubes of wide forbidden gap show gap variation proportional to 1/d
(d is the tube diameter), while those of very narrow gap show gap variation proportional to
1/d2.
The experimental measurements cannot distinguish between metallic and quasi-metallic
nanotubes due to the presence of the contact resistances and thermal effects.
Figure 31 shows the structure of a four-wall nanotube.
In the paper [40] are reported the computer modelling results for the nano-tube
nanotube connexion. These connexions are important for applications in electronic circuits,
because the nanotubes can play the role of conductors in nanotechnological devices.
3.8.2. Properties of the Carbon Nanotubes
The following outstanding properties must be mentioned:
-high mechanical resistance: Young modulus higher than 1.2 TPa, six times higher than
the value for steel.
-high thermal conductivity: 6103 W/(mK) for isolated tubes [56].
-high elasticity and no plasticity even for large deformations [37].
-The metallic NTC are quantum unidimensional conductors, where the electrons are
transported balistically. The heat dissipates only to contacts.
-The ratio length/diameter could be huge: 105 or higher. The elecron emission can be
induced through the end of long metallic NTS, by application of medium electrical fields.
-As a function of the chiral indices, the metallic NTC can transit in semiconductors if
they are stretched (by extension) or twisted.
-Atoms and molecles can be encapsulated within NTC (Fig. 32).
-They can be doped by p or n type elements.
Figure 32. TEM image of a NTC multilayer uniformly filled by leadv oxide.The filling was achieved by
capillarity [58].
The Haeckelites. As well known, a plane can be covered by pentagons, hexagons and
heptagons. Therefore, it is possible to imagine a graphene built by such polygons, where the
number of pentagons and heptagons must be equal in order to compensate the negative
curvature of the heptagons and the positive curvature of the pentagons [59,60] (Fig. 33).
These lattices have been called haeckelites in the honor of Ernst Haeckel who produced very
beautiful drawings where all these types of rings could be seen [61].
The haeckelite nanotubes are conductors independently of their diameter and chirality.
They are very rigid and their Young modulus is ~1.0 TPa.
Figure 33. Haeckelites [60]: a). Rectangular lattice (R); b). Hexagonal lattice (H); c). Oblic lattice (O);
d)-f). Nanotubes corresponding to left side lattices; g). Waved oblic nanotube of haeckelite.
3.8.3. Modelling the Combination Fullerene Nanotube (nanoBuds)

and Nanotube-Nanotube
In nanotehnology, the combination NTC-fullerene represents a new material which

presents both properties of NTC and fullerene. Thus, the mechanical properties and the
electrical conductivity are similars to those of NTC, while, due to high reactivity of the
attached fullerene molecules, the hybrid material can be functionalized by the well known
chemistry of fullerenes. Moreover, the fullerene molecules can be used as anchor molecules
to prevent the gliding of the nanotubes in different composite materials, thus improving their
mechanical properties. In such a new type of material the fullerenes arev bonded covalently to
the external face orf the nanotube wall (Fig. 34).
Due to high curvature of the fullerene surface, this nanoobject acts as an electron emitter
on the carbon nanotube conductor. Thus a thin film of such hibrid materials presents a very
low extraction work for the electrons (0.65 V/m) as compared to the value of 2 V/m for
single wall unfunctionalized NTC. Therefore, these materials are ideal candidates for electron
sources in TV screens.
We have modeled several special configurations including the attachment of a fullerene
molecule to the wall of a nanotube and the coupling of two nanotubes linked perpendicularly.
We tried to demonstrate that such configurations are possible from the crystallo-chemistry
point of view [38].
Figure 34. Various nanotube-fullerene structures [from http://en.wikipedia.org/wiki/Carbon_nanobud].
Figure 35. Carbon Nanotube (14 five fold rings + 2 seven fold rings) - closed ends (154 carbon atoms)
a. Pair distance distribution b. X-ray diffraction pattern; c. Bonding angle distribution. Free energy /
(bond and angle) = 2.41 meV
Figure 36. Nanotube-Fullerene (214 carbon atoms) Free energy/(bond and angle) = 2.99 meV.
The results allow to conclude that the change in the free energy during the attachment of
the fullerene to nanotube and the coupling of two (open) nanotubes is enough small to
guarantee high stability to the complex configurations. In the same time the modeling
suggests one new mechanism for the formation of fullerene: the nucleation at the nanotube
wall. This is achieved with the help of pentagonal rings accidentally introduced during
growth. Another result is the possibility to grow new nanotubes directly on the external part
of a nanotube wall by protruding the wall with the help of hexagonal rings of atoms (Fig. 35).
Last but not least, we must remark a special aspect of the growth of nanotubes, one
perpendicular to another: the nanotube, on which is nucleated another nanotube at right angle
becomes curved, elliptical in cross-section and twisted (Fig. 36).
Furthermore, we have investigated the dihedral angle distribution in the three models of
nanocarbon species (Fig. 37). The distribution of the dihedral angles in fullerene (C60) is: 180
angles with 0 , 60 angles with 138 and 120 angles with 142. For the nanotube the dihedral
angles show a larger dispersion due to the closed ends: 126 angles with 0. and 224 angles
with 26. New angles appear at 4 (28 angles) at 6 (56 angles) and at 10 (28 angles). In the
fullerene-nanotubule complex the dihedral angles are distributed on a larger range with
maxims at 0, 2, 6, 10, 26, 128, 138 and 180. This means that the complex
configuration is subjected to inhomogeneous stresses. The identification of these stresses is
important. The preliminary determinations have shown that the junction fullerene-nanotubule
is the most distorted one: the stresses are the largest.
Figure 37.A. Carbon nanotube-nanotube interconnection (246 carbon atoms). Free energy/(bond and
angle) = 0.682 meV.
Figure 37.B. Dihedral angle distribution in the three relaxed models of nano-carbon configurations.
Figure 37.C. Void distribution in the three relaxed models of nano-carbon configurations.
Finally, the void structure of the carbon configurations has been studied. In the normal
fullerene (C60) the unique void radius is 0.2925 nm. The nanotubule contains a void of
diameter 0.2275 nm, while the complex fullerene-nanotubule contains a distribution of voids
situated between 0.2125 and 0.2275 nm.
The conclusions of the modelling studies are: a. the nanometric structure of the
combination fullerene-nanotube is physically realistic b) the bonding distortion at the junction
fullerenenanotube is enough low to permit the coupling of the fullerene molecule to
nanotubule, c). the structural voids in the complex are enough large to permit the introduction
of the metallic atoms (Fe, Co, Ni with radii ~0.123 nm) to form compact rows, or small
clusters, thus giving rise to metallic conduction; this could be used in the integrated systems
based on nano-devices, in the future optoelectronics d). modelling of the carbon
nanostructures is a simple and cheap method and can be easily extended to other systems
as e.g. silicon, in order to demonstrate the feasibility of nano-wires for applications in nano-
electronics and spintronics.
3.9. Exotic Nano-Configurations
We can imagine a lot of nanometric structures based on graphite carbon. Here we present
several examples: Toroidal structure (Fig. 38); Zeolite-like structure (Fig. 39) [60,67];
Giroidal sructure (Fig. 40); Elicoidal nanotube (Fig. 41); Fullerene with holes, without
pentagons (Fig. 42); Nanotube with holes, without heptagons (Fig. 43).
All the carbon nano-objects presented above have been not produced experimentally but
the crystallochemical parameters, especially the bond distortion, seems to be so reasonable,
that the work for discovering new carbon objects will be, surely, fully rewarded.
Figure 38. Toroidal nanocarbon structures [from A. Lrinczi, M. Popescu, F. Sava, A. Anghel,
Modelling of the the complex carbon structure: fullerene nanotubule, J. Optoelectron. Adv. Mater.,
6(1), 349 (2004)]. a) nanotorus formed only by hexagons. A ring built by iron atoms can be observed;
b) Twisted nanotorus; c) Nanotorus formed by hexagons, pentagons and heptagons. One observes a
more waved surface than in a; d) nanotorus with small diameter; e) Fullerene C60 for comparison.
Figure 39 a). Four cubic cells decorated by graphenes built by hexagons and octogons (192 atoms per
cell); b). Triple periodic primitive surface [from A. Lrinczi, M. Popescu, F. Sava, A. Anghel,
Modelling of the the complex carbon structure: fullerene nanotubule, J. Optoelectron. Adv. Mater.,
6(1), 349 (2004)].
Figure 40. Giroidal triple periodic primitive surfaces [from M. T. Lusk and N. Hamm, Ab initio study of
toroidal carbon nanotubes with encapsulated atomic metal loops, PRB 76, 125422 (2007)].
Figure 41. Elicoidal nanotube (with pentagons, heptagons and hexagons) [60].
Figure 42. Structures of pierced fullerenes (with heptagons and hexagons, but without pentagons) [60].
Figure 43. Pierced nanotube (with heptagons and hexagons but without pentagons) [60].
3.10. Complex Nano-Configurations: Carbon-Chalcogenides
We have developed a more complex configuration of nanostructure based on carbon

nanotube network and arsenic sulphide network of atoms, known to have a nanotube structure
[4].
Figure 44. Carbon nanotube with zig-zag configuration (15, 0), having at the coupling end 2
pentagonal rings of atoms linked to a zig-zag arsenic sulphide nanotube. At the other end of the zig-zag
arsenic sulphide tube a fullerene molecule is attached. For attaching one 5-fold rings of atoms was
eliminated [60].
Figure 45. The distortion energy distribution in the complex nanostructure based on the combination of
a carbon nanotube, As2S3 chalcogenide tube and a fullerene C60 molecule.
We have built by computer (HyperChem soft) an As2S3 nanotube. This nanotube was
capped at one end by a carbon nanotube and at the other end by a fullerene molecule. Fig. 44
shows the final configuration after energy relaxation. Fig. 45 illustrates the variation of the
free energy of the configuration along the nanotube axis. In the region of connection carbon
nanotube-arsenic sulphide tube the distortion energy is very high. In the connecting region
nanotube-fullerene the distortion energy variation is low.
3.11. Prospective of the Wealth of Nano-Objects as Revealed by Atomic-Scale

Modelling
If the free energy of the models of nano-objects are compared one can get important
conclusions on the stability and probability of formation of a huge number of carbon
configurations and even complex carbon-chalcogenide configuration.
Figure 46. The free energy per bond and angle for various nano-objects based on carbon.
Fig. 46 shows how the different nano-objects based on graphene configurations are
compared when the average free energy per atom is considered. Objects as nanocupolae and
nanotubes with closed end exhibit lower distortion energy, and, therefore, higher stability.
The modeling studies can speak in favour of one or another configuration, to be
reproduced experimentally.
It is also a challenge for chemists and physicists to prepare new materials at the nano-
scale, based on low coordinated elements as e.g. P, As, S, Se , Te, etc
The new materials could be a reservoir of new properties and applications in nano-
technology.
Acknowledgment
The support of the CNCSIS in the frame of the "Exploratory research project" ID 1356
is acknowledged with thanks.
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Chapter 17
NANOSTRUCTURE DESIGNBETWEEN SCIENCE

AND ART
Mircea V. Diudea*
Faculty of Chemistry and Chemical Engineering Babes-Bolyai University A. Janos
Street No. 11, 400028 Cluj-Napoca, ROMANIA
1. Covering/Tiling
1.1. Introduction
Covering a surface by various polygonal or curved regions is an ancient human activity.

It occurred in house building, particularly in floor, windows and ceiling decoration. There
were well known three regular Platonic tessellations (i.e., coverings by a single type face and
a single vertex degree): (4,4), (6,3) and (3,6), written here as Schlfli symbols [Schlfli,
1901]. The Greek and Roman mosaics were very appreciated in this respect (Figure 1).
It is well established that covering/tessellating of fullerenes (nanostructures, in general)
dictates the stability and reactivity of these molecules. Coverings and their modification
enable understanding of chemical reactions (their regioselectivity) occurring in
nanostructures, particularly in carbon allotropes.
Modeling molecules, particularly nanostructures, scientists often use the embedding of a
polygonal lattice in a given 3D surface S. Such a combinatorial (discretized) surface is
called a map (Pisanski and Randi, 2000). Analytical formulas, for generating a smooth
surface, can be found in Mathematical recipes, available on the Internet. The coordinates of
the lattice points are obtained by partitioning S, either by dedicated algorithms or by simply
drawing vertices and edges on display, with the aid of some builders to switch from 2D to 3D.
Another way uses templates, or unit blocks with a prescribed spatial arrangement. This last
technique is also used (or naturally happens) in self assembling reactions, in experiments (or
occurring in vivo).
*
E-mail addresses: diudea@chem.ubbcluj.ro, diudea@gmail.com
426 Mircea V. Diudea
Crystallography is another domain of great importance which searches infinite polyhedral

tilings appearing in the crystalline state of matter.
Covering is nowadays a mathematically founded science. It makes use of the Graph and
Set Theory and is often inspired by, or inspires itself, the Arts and Architecture (see the recent
books of Diudea, Ed., 2005; and Diudea and Nagy, 2007). In this respect, researcher groups
in the U.S.A. (B. Grunbaum, M. Terrones, M. OKeefee, J. D. Klein, G. Heart), Australia (S.
T. Hyde, S. Ramsden), Brazil (J.-G. Eon), Italy (D. M. Proserpio, L. Carlucci), the UK (P. W.
Fowler, J. Klinowski), Germany (P. E. John), Slovenia (T. Pisanski), Hungary (I. Laszlo),
Russia (V. A. Blatov) and Romania (M. V. Diudea) have developed methods of generation
and classification of covering/filling the 2D/3D space, with applications in Mathematics,
Chemistry and Arts. There exist databases with beautiful galleries (HSAKA, EPINET) of
mathematical coverings (RCSR Center of Reticular Structure Resources, Epinet, ESMC-SG
European Society of Mathematical Chemistry-Structure Gallery) including online software
programs working for generation and classification of known and novel molecular or
crystalline architectures.
Figure 1. Ancient and modern mosaics in Milan, Italy.
It was our goal to develop and present some mathematical methods enabling discrete or
periodic coverings/tilings. Although some simple tessellations can be drown by hand, the
more elaborate ones need the aid of a computer. In this respect, the TOPO GROUP Cluj has
developed some software programs, based on either well-known or original map operations,
which will be presented in Section 1.2.
Changing the square tiling (4,4) to polyhex (6,3) or [(4,8)3] or even [(5,7)3] patterns,
appearing in modeling tubular nanostructures, by some cutting procedures is given in detail in
Section 2. Then, Section 3 presents a transformation/isomerization known as the Stone-Wales
edge rotation. Section 4 introduces map operations, from simple to composite operations or
generalized ones. Extension of map operations to 3D nets is presented in Section 5.
1.2. Cluj Covering Software
Nanostructure modeling necessarily involves the embedding of a polygonal lattice in a

given 3D surface S. Analytical formulas, for generating a smooth surface, can be found in
Mathematical recipes, available on the Internet. The coordinates of the lattice points are
obtained by partitioning S, either by dedicated algorithms or by simply drawing vertices and
Nanostructure Designbetween Science and Art 427
edges on display, with the aid of some builders to switch from 2D to 3D. Another way uses
templates, e.g., unit blocks with a prescribed spatial arrangement.
TOPO GROUP CLUJ has developed four main software programs dedicated to
polyhedral tessellation and embedment in surfaces of various genera, either as finite or
infinite lattices: TORUS (2003), CageVersatile_CVNET (2005), JSCHEM (2005), OMEGA
(2006) counter and NANO-Studio (2009).
1.2.1. TORUS
The program called TORUS (2003) is written in Delphi and works as a generator of
coordinates for tori of various covering. It generates tori and tubes, tessellated according to
selected type of cycles (C6 for (6,3), C8 for [(4,8)3] and C7 for [(5,7)3]. The dimensions of
objects: "c" (meaning the number of atoms in the cross-section of the torus or tube (if "tube"
is selected) and "n" (counting the number of cross-sections along the large hollow of the
torus) are at choice. Twisted tori/tubes can be obtained by using the "twist" window and no.
of twisted faces (even, integer). TORUSN-version also generates phenylenic C4C6C4C6
objects. H/V means Zigzag/Armchair objects. TORUSP-version allows Wiener number (of
total distances in graph) and Hosoya polynomial calculation. To see the HIN files generated
by the Torus program one needs the HyperChem Program.
1.2.2. CageVersatile, CVNET
CageVersatile (Net) CVNET (2005) software package, written in C, is a program, created

on the ground of map operations, as described by Diudea (2004), Diudea and John (2003),
Diudea et al. (2003, 2006b), Stefu et al. (2005), as a theoretical support, for generating
coordinates of closed or open lattices covering nanostructures. The program works in four
levels of complexity: (1) Simple map operations (medial Med, dual Du, polygonal k-
mapping Pk (k=3,4,5), truncation Tr (all or only selected atoms), rotate RO (Stone-Wales,
1986, operation) and split (bisect) edge SP); (2) Complex map operations (Leapfrog Le1,1,
Chamfering/Quadrupling Q2,0, Capra/Septupling Ca2,1 (or S1), Septupling 2 and Flower
disjunction); (3) Generalized map operations Leapfrog Le2,2(and Le2,2C), Quadrupling Q3,0,
Quadrupling Q4,0, Capra Ca3,2 (and Ca3,2C) and Flower disjunction) and (4) Net operations
(operated by the button take all cycles which allow us to perform operations on nets, by
considering all the hard rings in a structure. The operations working on this button are: dual,
medial, stellation, truncation, leapfrog, quadrupling and capra.
1.2.3. JSChem
JSChem software package (2005), is written in Java Script, and works as an assistant
program (generates script input and/or collects the output files for other programs) in the field
of molecular topology, crystallography and quantum chemistry. The program was developed
in four directions: (1) HyperChem (Script general (provides script list for HyperChem);
Homo-Lumo Gap (extracts info from the semiempirical log files); All Aromatic (makes all
atoms C of C A typeputs the baricentre of molecule); MolColor (put colors by changing
C with heteroatoms); Hin2Pdb (converts .hin file into .ent=.pdb format with preserving
connectivity); (2) NanoUtils (POAV1 (calculates the strain, of sp2 C, in kcal/mol, per atom,
for all or for eventually marked atoms in a molecule); HOMA (computes aromaticity from
actual (optimised or crystallographic) geometryboth as global and local data); Stone-Wales
(rotation of marked edges); Kekule-Clar (depictes double bonds at selected threshold and
disjoint hexagons when a structure shows perfect CLAR PC structure) and Schlegel (draws
plane projections of polyhedra/fullerenes according to the marked face); (3) Topology
(Homeomorf (put k points on the marked edges, either C or heteroatom); Medial (operates
Medial on a trivalent map); Truncation (operates Truncation on a trivalent map); Dual
(operates Dual on a trivalent map); MolConnect (connects points by joining and faces by
identification in assembling repeat units in molecular architectures)) and (4) NanoGen
(TubeGen (generates nanotubes or series of nanotubes cf. (n,m) nomenclature). Input and
output of this program is also in HIN format of HyperChem Program.
1.2.4. Omega Counter
The program called OMEGA (2006) counter is written in Visual J#. It is used for
generating the Omega polynomial (the opposite edge strips).
The program works with .hin files of HyperChem. You can download the HyperChem
program as an Evaluation version. The input files are stored in a subfolder named hin of
Omega program main folder. All the HyperChem files from .hin folder will be input files. To
use this program one sets: the maximum length cycle; the maximum vertex degree and the
structure type (Planar structures, Fullerenes, Net, Torus with 5-7 covering, Torus with 6
covering, Torus with 4-8 covering). The program was developed on the ground of our original
Omega polynomial, presented in Diudea (2006, 2009), Diudea et al. (2006a, 2009), Vizitiu et
al. (2006).
1.2.5. NANO-Studio
This program (2009) is written in C Sharp and can be seen as a new version of JSChem.
In addition to the old version, it provides complete topological characterization of a graph
(number of vertices, edges, faces and equivalence classes of the above ones), aromaticity
index calculation and Omega polynomial calculation on cages and nets.
There exist other sotware programs, e.g., SYSTRE, TOPOS, EPINET, or that used by G.
HART, the readers can use in performing various tessellations and tilings.
2. Cutting Procedures on (4,4) Tessellation

Covering the cylinder or the torus by hexagons is most often achieved by the graphite
zone-folding procedure, as presented in Bovin et al. (2001), Ceulemans et al. (1998), Kirby et
al. (1993), Marusic and Pisanski (2000). The method defines an equivalent planar
parallelogram on the graphite sheet and identifies a pair of opposite sides to form a tube.
Finally the two ends of the tube are glued in order to form a torus.
A second procedure uses the so-called topological coordinates, extracted from the
adjacency matrix eigenvectors, Graovac et al. (2000), Laszlo and Rassat (2001, 2003),
Pisanski and Shawe-Taylor (2000).
Construction of polyhex (6,3) nanotubes and tori from square tiled (4,4) objects, as
developed by Diudea (2002a, 2002b, 2005), Diudea and Nagy (2007), at TOPO GROUP
Cluj, is a third main route.
S. Iijima (1991) firstly reported graphitic carbon nanotubes (see also Endo et al., 1996).
Next, clear distinction between single walled nanotubes SWNT and multi walled ones was
made. Function of their diameter and chirality, the nanotubes can be metallic or
semiconductors. Nowadays, nanotubes found the most important applications (among the
newly discovered nanocarbon allortopes) in nanoelectronics and materials science.
Circle crops structures have firstly been observed by Liu et at. (1997) and then by other
groups, see Ahlskog et a. (1999), Martel at al. (1999a, 1999b). Martel et al. (1999b) argued
that the observed rings were coils rather than perfect tori, but these structures have continued
to attract a multitude of theoretical studies, dealing with construction, mathematical and
physical properties of graphitic tori, see Babic et al. (2001), Johnson et al. (1994), Kirby
(1993), Lin and Chu (1998), Meunier (1998).
We implemented the cutting and graphite zone-folding procedures in our TORUS and
JSCHEM original programs.
2.1. Square (4,4) Lattice
The embedding of the (4,4) net is made by circulating a c-fold cycle, circumscribed to the
toroidal tube cross-section of radius r, along the cylinder or around the large hollow of the
torus, of radius R > r (Figure 2). The subsequent n images of c-fold cycle, equally spaced are
joined with edges, point by point, to form a polyhedral cylinder or torus tiled by a tetragonal
pattern. In case of the torus, the position of each of the n images of the circulant around the
central hollow is characterized by angle while angle locates the c points across the tube.
In all, cn points are generated.
Toroidal parameters The (4,4) covering
Figure 2. Embedding of the (4,4) net in the torus.
The parameters R and r are not directly involved in the topological characterization of the
lattice embedded in the torus (see our books: Diudea, Ed., 2005; and Diudea and Nagy, 2007).
The formulas for drawing the smooth toroidal surface were:
P ( x, y , z ) :
x = cos()( R + r cos )
y = sin()( R + r cos )
z = r sin
2
i = i ; i = 0,..., n 1
n
2 (1)
j = j ; j = 0,..., c 1
c
For the cylinder, the procedure is similar.

The squares can be changed to hexagons (or other tiling patterns, suitable from chemical
point of view) by appropriate edge-cutting, as described in Diudea (2002a-c), Diudea and
Kirby (2001), Diudea et al. (2003), or by performing some map operations (see below).
2.2. Polyhex (6,3) Covering
To obtain the (6,3) tessellation, each second edge of the (4,4) net has to be cut off. Two
isomeric embeddings can be defined in the torus T (Figure 3):
(i) The H-embedding (Figure 3 -a) when the cut edges lye horizontally (i.e.,
perpendicular to the Z axis of the torus). It is also called zigzag Z, by the tube
cross-section shape.
(ii) The V-embedding (Figure 3 -b) when the cut edges lye vertically (i.e., parallel to the
Z axis of the torus). It is also called armchair A, by the tube cross-section aspect.
(a) T(6,3)H/Z-embedding (b) T(6,3)V/A- embedding
Figure 3. The (6,3) covering by H/Z (a) and V/A (b) cutting of the (4,4) net. To obtain a torus, the two
pairs of opposite edges have to be identified.
Twisted, chiral, (4,4) tori can be generated by the following two procedures: (1) twisting
the horizontal layer connections (Figure 5 -a and Figure 6) and (2) twisting the vertical layer
(offset) connections (Figure 5 -b).
Accordingly, two topologically distinct tori are obtained by the TORUS program:
T(6,3)H/Z[c,n] and T(6,3)V/A[c,n] and they correspond to two different classes of aromatic
chemical compounds, phenacenes and acenes, respectively. The name of such tori is a string
of characters including the tiling, type of embedding and the tube dimensions [c,n]. Note that
each hexagon consumes exactly two squares in the (4,4) net. By construction, the number of
hexagons in the (6,3)H/Z isomer is half the number of squares on dimension c of the (4,4)
torus. The same is true for the (6,3)V/A isomer, but on dimension n. Thus, T(6,3)H[2c,n] has
the same number of hexes as its embedding isomer T(6,3)V[c,2n]. We focused here on the
procedure concerning the toroidal embedding because of its higher complexity. The
procedure for cylindrical embedding is immediate; another reason is the corresponding
nanotubes can be generated by simply cross-cutting of the toroidal tube.
(a) T(4,4)H2[8,24] (b) T(4,4)V2[8,24]
Figure 4. An H-twisted (a) and a V-twisted (offset - b) (4,4) net.
(a) (4,4) net (b) (6,3) net
Figure 5. Twisted (4,4) pattern (a) and its (6,3) derivative (b).
(a) Tu(6,3)V/A[12,12]; v = 144 (b) T(6,3)H/Z[12,50]; v = 600
Figure 6. The (6,3) covering in the cylindrical (a) and toroidal (b) embedding, respectively.
After optimization, by a Molecular Mechanics procedure, the generated polyhex tubes

and tori look like in Figure 6. The objects in these examples represent non-chiral structures.
2.2.1. Topology of Polyhex Tori
Each of the above twisting superimposes on the two basic cuttings, thus resulting four
classes (Diudea Ed. 2005) of twisted tori: (i) H-twist, H-cut HHt[c,n]; (ii) H-twist, V-cut,
HVt[c,n]; (iii) V-twist, H-cut, VHt[c,n]; and (iv) V-twist, V-cut, VVt[c,n]. The type of cutting
will dictate the type of embedding and, ultimately, the shape of objects. Conversely, the type
of twisting is involved in the -electron structure of polyhex tori. Figure 7 illustrates some
(non-optimized) twisted polyhex tori.
The twist number t is just the deviation (in number of hexagons) of the chiral (i.e.,
rolling-up) vector to the zigzag line, in the graphite sheet representation (Hamada et al. 1992).
Accordingly, a torus can be drawn as an equivalent planar parallelogram, involving two
tubes: one tube is built on the rolling-up vector R (Figure 8), which, in terms of the primitive
graphite lattice vectors, is written as:
R = ka1 + la 2 (2)
The second tube is formally defined on the translating vector T:
T = pa1 + qa 2 (3)
T(6,3)HH2[8,24] T(6,3)VH2[8,24] (offset)
T(6,3)HV2[8,24] T(6,3)VV2[8,24] (offset)
Figure 7. The four classes of twisted polyhex tori (non-optimized geometry).
For a given torus, the first tube can be identified by cutting the object across the tube
while the second one results by cutting it around the large hollow. Anyway, a four integer
parameter description (k,l,p,q) can be written. The coordinates of THH4[14,6] torus depicted
in Figure 8 are (Diudea, Ed., 2005): (5, -4, 3, 3). Note that this representation is not unique
and is reducible to three parameter notation, theorized by Kirby et al. (1993, 1998).
Correspondence between our notation for tubes (TUXt[c,n]) and tori (TXt[c,n]) and that
in two (k,l) and four (k,l,p,q) integers notation are given in Tables 1 and 2, respectively.
(3,3)
a2 a1
(5,-4)
Figure 8. Representation of the torus THH4[14,6] by an equivalent parallelogram defining two tubes:
one defined on the rolling-up vector R (with integer coordinates (k,l)) and the other on the translating
vector T (given by the pair (p,q)). The four parameter specification of the depicted torus is (5, -4, 3, 3).
Table 1. Correspondence between the TUXt[c,n] and (k,l) notation in nanotubes
Tube Tube
(c,t); (k,l)
Xt (k,l)
1 H c=2k; t=l=0 (c/2,0); Z
2 HHt c=k+2l; t=k; l=(c-t)/2 [t,(c-t)/2]
3 HVt c=k+l; t=k; l=c-t [t,(c-t)]
4 V c=2k; t=l=0 (c/2,c/2); A
Table 2. Correspondence between the TXt[c,n] and (k,l,p,q) notation in tori
Torus Xt Tube R Tube T Torus (k,l,p,q)* v

1 H H/Z V/A (c / 2,c / 2, n / 2, n / 2) 2(kq lp) = cn
2 V V/A H/Z (c / 2, c / 2, n / 2,n / 2 ) 2(lp kq ) = cn
3 HHt HH (tw) V/A [(c t ) / 2,t , n / 2, n / 2] 2( 2kq lp ) = cn
4 HVt HV (tw) H/Z [(c + t ) / 2, (c t ) / 2, n / 2, n / 2] 2(lp kq) = cn
5 VHt H/Z HV (tw) [c / 2,c / 2, (n + t ) / 2, (n t ) / 2] 2(kq lp ) = cn
(offset)
6 VVt V/A HH (tw) [c / 2, c / 2, (n t ) / 2,t )] 2( 2lp kq) = cn
(offset)
*First pair (k,l) denotes the rolling-up vector R while last pair (p,q) specifies the translating vector T. The
representation (m,-m) = (m,0), is an H/Z-tube while (m,m) is a V/A-tube (see Figure 7).
Encoding the type of tessellation can be done, for example, by the -spiral ring code,
which was first proposed for coding and constructing spherical fullerenes (Manolopoulos et
al. 1991; Brinkmann and Fowler 1998). We adapted the spiral ring code for tubular structures
(Diudea, 2002c). In a periodic tubular net, the ring code brings information on size and
sequence of faces (i.e., repeat units) and embedding of the actual net on the parent (4,4)[c,n]
lattice. The ring code for the polyhex tori is given in Table 3.
Table 3. Ring code of polyhex tori
Torus Ring code

1 H/Z[c,n] [ 6 c / 2 ]n
2 HH[c,n] [ (6 c / 2 ) t ] n / t
3 HV[c,n] [ ( 6 c ) t ] n / 2t
4 VH[c,n] [ ( 6 n ) t ] c / 2t
5 VV[c,n] [ (6 n / 2 ) t ] c / t
6 V/A[c,n] [ 6 c ]n / 2
The number t inside the brackets equals the helicity while the number out the brackets
gives the steps of a helix. Note that the helicity could be less than t, if an integer number of
steps appear.
A different topological description of polyhex tori is possible by means of the Omega
polynomial (Diudea 2006, 2009; Diudea et al. 2006a, 2009; Vizitiu et al. 2007).
2.2.2. -Electronic Structure of Polyhex Tori
In the Spectral Theory, at the simple -only Hckel (1931) level of theory, the energy of
the ith molecular orbital Ei = + xi is evaluated by calculating the solutions xi of the
characteristic polynomial Ch(G,x) or the eigenvalues of the adjacency matrix associated to
the molecular hydrogen depleted graph.
Table 4. Covering criteria for metallic character in polyhex tori
Torus Metallic
Non-wisted
1 H/Z[c,n] 0 mod (c,6)
2 V/A[c,n] 0 mod (n,6)
H-Twisted
3 HHt[c,n] 0 mod (c,6)
4 HVt[c,n] 0 mod (n,6)
0 mod(t,6)
V-Twisted
5 VHt[c,n] 0 mod (c,6)
0 mod (t,6)
6 VVt[c,n] 0 mod (n,6)
The -electronic shells of neutral graphitic objects are classified (Fowler 1990, 1997),
function of their eigenvalue spectra, as closed, when xv / 2 > 0 xv / 2 +1 or open, when the
HOMO and LUMO molecular orbitals are degenerate, xv / 2 = xv / 2 +1 .
The metallic character involves the existence of a zero HOMO-LUMO gap (a particular
case of the open shell) and the degeneracy of some non-bonding orbitals (Yoshida et al. 1997)
(NBOs) favoring the spin multiplicity, cf. the Hund rule. In polyhex tori, the metallic
behavior is ensured by four NBOs, also present in the graphite sheet. The gap (in units) is
taken as the absolute value of the difference EHOMO - ELUMO. Table 4 gives the lattice [c,n]
criteria (in terms of our notation) for metallic shell in (6,3) tori of various types.
2.2.3. Identical Polyhex Tori by the Cutting Procedure
Toroidal objects generated by the TORUS software, even correctly named to reflect
different embeddings, could represent one and the same graph.
Let consider normal tori (i.e., those with c < n). Their net dimensions can be written as:
n=c+r; r = 0,2,..c 2, c,.. and t = 0,2,.., c,.. .Investigating the spectra of the
characteristic polynomial of families of polyhex tori led to the following:
Rules of Valencia (see the book of Diudea and Nagy, 2007)
(i) The maximum value of t to provide distinct topological objects, in a family of H-

twisted polyhex tori, equals n / 2 .
(ii) The maximum value of t to provide distinct topological objects, in a family of V-
twisted polyhex tori, equals
Table 5. Identical graphs in families of twisted polyhex tori according to the

Rules of Valencia
Case Characters
1 General n = c + r; r = 0, (2,..c 2), c,.. ; t = 0,2,.., c,..
2 H-twist t = 0,2,.., n / 2; distinct objects
2a H-twist n = 2c t max = c; all distinct objects
Case: r = c
2b H-twist n = c V twist
Case: r = 0
2c H-twist t = 0,2,..(r 2); distinct objects
Case: t = r + 0,2,4,.., (c r ) / 2 c 0,2,4,..( c r ) / 2 ; distinct pairs
0<r<c
3 V-twist t = 0,2,.., c / 2; distinct objects
3a V-twist t = 0 + 0,2,4,.., c / 2 c 0,2,4,..c / 2 ; distinct pairs
Any case:
note When c/2 or n/2 are odd, then t max = t 1
As, by construction of the H-twisted polyhex tori, the maximum possible t-value is
t max = c , the immediate consequence of Rule (i) is that n must be at most twice higher than c
for having all distinct topological objects. Higher values for n will only repeat the already
generated structures. When n / 2 < c , some duplicate objects appear, as indicated in Table
3.4.
In case of V-twisted polyhex tori, t does not depend of the ratio c / n ; since t can take
values up to n (by construction), with periodicity at k (c / 2) , k=1, 2,.., the Rule (ii) was
formulated for t = c at most. Details are given in Table 5.
In non-twisted tori, the HOMO-LUMO gap remains constant, at a given c- (in H/Z[c,n]
series) and n- (in V/A[c,n]) values, respectively. The same is true for the twisted tori,
according to the second capital letter in their name.
Note the identity of graphs H[c,n] = V[ n,c] but having different embedding.
At c = n, H[c,c] = V[c,c] and HVt[c,c] = VHt[c,c].
2.3. Other Coverings by the Cutting Procedure
2.3.1. Bathroom Floor and Pentaheptite Tessellations
A ((4,8)3)S (bathroom floor) covering can be derived from the tetragonal (4,4) covering
by deleting appropriate edges (Figure 9). The cut edge lay either horizontally or vertically,
which results in two embedding isomers; however, the net is isotropic (see Diudea, Ed.,
2005). Letter S comes from the square shape of the tetragon, in the optimized objects
(Figure 10).
((4,8)3)S-pattern ((5,7)3)SP-pattern
Figure 9. Non-graphitic coverings in the toroidal embedding.
According to the building procedure, the following relations account for the involved
toroidal embedding isomers:
((4,8)3)HS[c, n] = ((4,8)3)VS[c / 2,2n] (4)
((4,8)3) VS[c, n] = ((4,8)3)HS[2c, n / 2] = ((4,8)3)VS[n / 2,2c] (5)
Construction of a ((5,7)3)SP pattern (SP comes from spiral ) needs, in our procedure,
four vertex rows (i.e., a 0 mod(c,4) lattice). It is called the pentaheptite tessellation and shows
a local (t5, t7) signature of (1,3) type. Several ((5,7)3) lattices with various local signatures
have been proposed, see Deza et al. 2000, Diudea et al. 2003, Kirby 1994.
((4,8)3)SH[20,64]; N = 1280 ((5,7)3)SPH[20,64]; N = 1280
Figure 10. Non-graphitic optimized tori.
Table 6. Ring Code in Pentaheptite Tori
Torus Ring code

1 ((5,7)3)SPH [(5 7)c/4 , (7 5)c/4 ] ( n / 4)
2 ((5,7)3)SPV [(5 7)c/2 , (7 5)c/2 ] ( n /8)
Rings of size 5 and 7 were also used for curvature matching and strain relief in polyhex
tori, see Babic et al. 2001, Iijima et al. 1992, Itoh and Ihara 1993, Itoh et al. 1993. Such
coverings can also be drawn by the Stone-Wales transformation of a (6,3) net, see Deza et al.
2000, Diudea et al. 2003. The ring code in pentaheptite tori is given in Table 6.
2.3.2. Phenylenic and Naphthylenic Covering
Phenylenic patterns: ((4,6,8)3)H/V and ((4,6,8)3)HX/VX can be derived from the

tetragonal (4,4) net (Figure 11 Diudea 2002b). Their local signature is: t4j(0, 2, 2); t6j(2, 0,
4); and t8j(2, 4, 2), j = 4, 6, 8. The resulting toroidal objects differ in orientation and number
of the (4,6,8) repeat units. Figure 12 illustrates some phenylenic tori, as optimized objects.
. .
. .
.
.
((4,6,8)3)H-net ((4,6,8)3)HX-net
Figure 11. Phenylenic covering in the toroidal embedding.
Phenylenic chemical structures have been synthesized by the group of Vollhardt, see
Berris et al. 1985, Vollhardt 1993, Vollhardt and Mohler 1966. Some of the phenylenic tori
were predicted to have metallic character (Diudea 2002b).
((4,6,8)3)H[12,96]; N =1152 ((4,6,8)3)HX[12,96]; N =1152
Figure 12. Optimized phenylenic tori.
.
.
((4,6,8)3)HN-pattern ((4,6,8)3)HNX-pattern
Figure 13. Naphthylenic covering in toroidal embedding.
In close analogy to the phenylenic net, we proposed (Diudea 2002b) the naphthylenic net,
with the sequence: C6, C6, C4,..., C6, C6, C4. The HN/VN lattice has the local signature:
((4,6,8)3)HN, t4j(0, 2, 2); t6j(1, 3, 2); and t8j(2, 4, 0), while the net HNX/VNX has the
signature: t4j(0, 4, 0); t6j(1, 3, 2); and t8j(0, 8, 0), with j = 4, 6, 8 (Figure 13). This last net can
be obtained from the square (4,4) lattice by a double leapfrog operation. Figure 14 illustrates
two optimized naphthylenic tori.
((4,6,8)3)HN[25,80]; v =2000 ((4,6,8)3)HNX[16,90]; v =1440
Figure 14. Optimized naphthylenic tori.
Insulating is the major trend of the -electronic shell of naphthylenic toroidal

nanostructures, in case of even-dimensional objects. On the contrary, odd-dimensional objects
show open-shell structure. The X-net embedded in the torus shows a properly closed-shell
(Diudea 2002c).
The ring code of phenylenic and naphthylenic tori are given in Table 7.
Table 7. Ring Code in Phenylenic Tori
Torus Ring Code

1 HPH [(4 6 8) c / 3 ]n / 2
2 VPH [(4 8 6) c / 2 ]n / 3
3 HPHX [(4 8 6) c / 3 ]n / 2
4 VPHX [( 4 6 8) c / 2 ] n / 3
5 HNP [(4 6 6 6 8) c / 5 ] n / 2
6 VNP [(4 8 6) c / 2 6 c ]n / 5
7 HNPX & VNPX [(4 6 3 ) c / 3 (8 6) c / 3 ]n / 4
3. Stone-Wales Isomerization in Nanostructures

A given tessellation, embedded either in the sphere, torus or cylinder, can be modified
such that the number of points (i.e., atoms) is preserved; the only allowed changing, in the
following, is the connectivity.
There is a well-known edge rotation procedure, patterned by Stone and Wales (1986).
The bold edge (Figure 15) shares two cycles of size (sm, sn) to be reduced, after rotation, to
(sm-1, sn-1). Correspondingly, the two cycles joined by this edge will increase in size from (sp,
sr) to (sp+1, sr+1) in the Stone-Wales SW isomerization (Diudea, 2003b). Often, the edge
flipping runs as a cascade SW transformation.
(a) (b)
Figure 15. Stone-Wales edge rotation can change: the position (a) or the size (b) of polygons.
This section presents several SW examples, possible isomerization routes in real

experiments.
3.1. The Coalescence Process
Recently, a hybrid structure consisting of fullerene molecules encapsulated in single-

walled nanotubes and called nanopeapods, have been experimentaly proved by high-
resolution transmission electron microscopy HRTEM. The symbol for such structures is
inspired from the endohedral metal doped fullerenes (Singh et al. 2004): for example
(C60)n@SWNT is the name of C60-nanopeapod.
By exposure at an electron beam, fullerenes inside the nanotube coalesce into larger
capsules, capped by C60 halves. The length of such capsules corresponds to three-four
fullerene units, and the diameter is constrained by the outer nanotube dimensions (see Diudea
and Nagy 2007, Fang et al. 1998).
(a) (b)
(c) (d)
Figure 16. From the [2+2] cycloadduct of C60, to peapods and double walled nanotube DWNT.
Topological analysis suggests that the merging process of two fullerene molecules can be
achieved by a sequence of SW bond rotations. The first step in the C60 coalescence is the
formation of a [2+2] (sp3-joined) cycloadduct Figure 16 -a. An intermediate step is the
formation of all sp2 peanut shaped structure Figure 16 -b; subsequent SW bond flipping, in a
circumferential order, transforms the heptagon-pentagon junction into a hexagonal (6,3)
covering (Figure 16 -c). Finally, the coalescence process leads to a double walled nanotube
DWNT (Figure 16 -d).
3.2. Isomerization of Peanut Tubulenes
By cutting off the polar ring k of a spherical fullerene, a fullerene-like cap is obtained.
Such a cap fits to a Z nanotube. Figure 17 illustrates two peanut-shaped fullerenes with
different nanotubes (observe the complete description of tube covering) distancing the two
caps.
(a) C168( 6 66 (5 6)6 ( 6 5)6 76 66 66 76 ) (D6d)(b) C168( 6 66 (5 6) 6 ( 6 5)6 7 6 (5 7 )3 ( 7 5)3 7 6 ) (S6)
Figure 17. Peanut-shaped kf -tubulenes.

C 72( 76 66 66 76 ) C 72( 76 5 64 7 7 64 5 76 ) C 72( 76 5 62 7 5 7 2 62 5 7 5 76 ) C 72( 76 (5 7 )3 ( 7 5)3 76 )
Figure 18. SW isomerization of the necks of a peanut cages, from polyhex C 72( 7 6 66 66 7 6 ) to azulenic
C 72( 76 (5 7 )3 ( 7 5)3 76 ) covering and the corresponding geodesic projections.
The peanut in Figure 17 -a, C168( 6 66 (5 6)6 ( 6 5)6 7 6 66 66 7 6 ) (D6d), isomerizes to the peanut
C168( 6 66 (5 6)6 ( 6 5)6 76 (5 7 )3 ( 7 5)3 76 ) (S6), Figure 17 -b, with azulenic covering on the distancing tube,
achived by (three) Stone-Walls SW edge rotations (Diudea et al. 2005) (see the necks and
their geodesic projections in Figure 18).
The azulenic ((5,7)3) covering, well-known being the aromatic conjugation in such
systems (Diudea Ed. 2005, Diudea and Nagy 2007), appears (from semiempirical PM3
calculations) as a stabilizing factor, even competing the polyhex covering.
The cages in Figure 19 have even shorter distancing tube (one atom (a) and zero atom (b)
rows, respectively) between the two caps. The name of such tubulenes includes the code for
the cap and distancing zone up to the second cap, if the two caps are identical, or full
description, if they are different. The cage C108 has been observed experimentally as a peapod
(Hernandez et al. 2003).
At moderate temperature and pressure (300C and 1 GPa) spherical fullerenes arrange in
one dimensional assemblies (Lebedkin et al. 2000). This suggested the existence of periodic
fullerenes, like that presented in Figure 20. Recall that the phantasmagorical fullerene
designed by the groups of Fowler and Dress, see Dress and Brinkmann 1996, respectively,
also have 260 points and f 5 = f 7 + 12; f 7 = 60 , as Diudeas C260 ((5,7)3) cage (Diudea Ed.
2005).
(a) C120 (5 65 ( 5 6 )5 ( 6 5)5 75 75 Z (10,1]) (b) C108( 6 (5 6)3 ( 6 6 5)3 ( 6 5 6)3 7 6 Z (12,0 ])
Figure 19. Peanut-shaped kf tubulenes with the shortest distancing tube.

C 260 ( k 5k ( 7 k 52 k 7 k ) r 5k k ); k = 5; r =6
Figure 20. Diudeas C260 ((5,7)3) cage.
Table 8. Periodic ((5,7)3) cages: net counting
Formulas for k = 5; 7
f 5k = 2k ( r + 1) + 2t 5 ; f 7 k = 2kr + 2t 7
e5,5 k = 2 k ( r + 1 + t5 ) ; e5,7 k = 2k (3r + 2 + t 7 ) ; e7,7 k = 2k ( 2r 1)
v5,5,5k = 2kt 5 ; v5,5,7 k = 2k (2r + 1 + t 7 ) ; v5,7,7 k = 2k (r + 1) ; v 7,7,7 k = 2k ( r 1)
vk = 4k (2r + 1)
* t s = 1 if s = k , and zero otherwise .
For a periodic ((5,7)3) cage, the number of faces, edges, and vertices of various types can
be counted function of the repeat unit r and the polar ring size k (Table 8).
3.3. Isomerization of Tubercular Fullerenes
The SW isomerization of tubercular cages of general formula C12 k ( k 5k 7 k 52 k 7 k 5k k )
(Figure 21 -a) leads to the classical C12 k ( k 6k ( 5 6 ) k ( 6 5) k 6k k ) fullerenes (Figure 21 -b). Routes of
SW isomerization of spherical fullerenes to each other are given in The Atlas of Fullerenes
(Fowler and Manolopoulos 1995).
(a) C 60( 5 557 55107 5555) (Ci) (b) C 60 (5 65 ( 5 6)5 ( 6 5)5 655) (Ih)
Figure 21. Isomerization of all ((5,7)3) cages leading to the classical C12k fullerenes.
(a) C100 ( k 5k ( 7k 52 k 7k ) r 5k k ); k =5; r =2

(b) C100 (5 65 (5 6 )5 A[10, 2])
(c) C 100 ( k 5k 7 k 52 k 8k ( 5 6 ) k ( 5 7 ) k 5k k ); k =5
(d) C100 ( 5 5575 (5 6)5 ( 6 6 )5 ( 6 5)5 75555)
(e) C100 ( k 6 k (5 6 ) k ( 5 7 ) k 7 k (5 6) k ( 5 6 ) k k ); k =5
(f) C100 (5 65 ( 5 6 )5 ( 5 8)5 ( 5 6 )5 ( 6 5)5 655)
Figure 22. Ways of the Stone-Wales isomerization.
Isomerization of the peanut C100 ( 5 55 ( 75510 75 ) 2 555) tubercular cage (Figure 22 -a) to the
corresponding tubulene C100 ( 5 65 ( 5 6 )5 A[10, 2 ]) (Figure 22 -b) could follow two ways, as the
SW rotation process starts: (i) by the red bonds sharing two heptagons in the zone of
joining the two repeat units and (ii) the blue bonds at the cap zone. The stepwise process is
given in Figure 22 (c to f); Quantum calculations proved the blue route is energetically more
favored (Diudea Ed. 2005).
3.4. Isomerization of the (6,3) Net
Let (6,3) net be embedded in the cylinder, as Tu(6,3)H/Z[c,n] and Tu(6,3)V/A[c,n] in our
notation or in the (k,l) notation (Hamada et al. 1992), zigzag (c/2,0) and armchair
(c/2,c/2) nanotubes (Figure 23).
Let denote by H(i,j),(p,r) the edges lying parallel to the horizontally oriented tube generator,
in the schematic lattice representation; the first subscript bracket encodes the relative location
of the start-point of rotating edges along the tube while the second one the location of edges
around the tube. Mark V(i,j),(p,r) the edges lying perpendicular to the tube generator. The
marked edges will be rotated in the following isomerization and the above symbols play the
role of a true rotational operator (Diudea 2003b, 2004).
The hexagonal (6,3) covering is transformed into the rhomboidal-bathroom-floor tiling
((4, 8)3)R, by the operations (Diudea 2003b):
H(1,3),(1,3)((6,3)H/Z) = ((4, 8)3)R = V(1,3),(1,3)((6,3)V/A) (6)

which illustrated in Figure 23.
(a) H(1,3),(1,3) ((6,3)H/Z) (b) ((4,8)3)R
Figure 23. SW rotation of the marked bonds of the (6,3) covering (a) leads to the ((4,8)3)R pattern.
V(1,5),(1,5)((6,3)H/Z) ((4,8)3)S
Figure 24. A spiral path of SW edge rotation and its transform.
The operation can be written as:
V(1,5),(1,5)((6,3)Z) = ((4, 8)3)S (7)
Similarly, the operation:
V(1,5),(1,5),1a ((6,3)Z) = ((5, 7)3)SP (8)
leads to a spiral ((5,7)3)SP net (Diudea et al. 2003), Figure 25. Note the combination
V/A&H/Z, for describing a spiral path and the subscript 1a for a leave one row/column out
way in getting an alternating spiral net.
V(1,5),(1,5),1a ((6,3)H/Z ((5,7)3)SP
Figure 25. A spiral path of SW edge rotation and its spiral net product.
The same operations can be done on the (6,3)A net thus resulting the corresponding pair
embedding isomers. Different pentaheptite ((5,7)3) lattices (Deza et al., 2000) can be
obtained by the following operations:
H(1,5),(1,5)((6,3)Z) = ((5,7)3)V (9)

V(1,5),(1,5)((6,3)A) = ((5,7)3)H (10)
These coverings will be illustrated in the Figures 26 and 27.
3.5. Isomerizations on the ((4,8)3) Net
The ((4,8)3) covering, particularly ((4,8)3)R, transforms to either (6,3)V/A or (6,3)H/Z

net by operations:
H(1,4),(1,4)(((4,8)3)R) = (6,3)V/A (11)
V(1,4),(1,4)(((4,8)3)R) = (6,3)H/Z (12)
as a unique intermediate of the (6,3) net isomerization. Other transformations of this covering
are:
H(1,7),(1,7) (((4,8)3)R) = ((5, 7)3)H (13)
V(1,7),(1,7) (((4,8)3)R) = ((5, 7)3)V (14)
the corresponding objects being illustrated in Figures 26 and 27.
H(1,3),(1,3)(((4,8)3)R) ((5, 7)3)H
Figure 26. SW isomerization of ((4,8)3)R to ((5,7)3)H lattice.
V(1,7),(1,7) (((4,8)3)R) ((5, 7)3)V
Figure 27. SW isomerization of ((4,8)3)R to ((5,7)3)V lattice.
Note that the pentaheptite H/V((5,7)3) lattice is encountered in the chemical net of
ThMoB4. It is a 2-isohedral tiling (Grnbaum et al., 1985), i.e., it has only two face orbits,
with the local signature (t5, t7) = (1, 3).
Other isomerizations are as follows:
H(1,6),(1,5) (V(1,7),(1,4)(((4,8)3)R) = ((5,6,7)3)HA (15)
V(1,5),(1,6) (H(1,4),(1,7)(((4,8)3)R) = ((5,6,7)3)VA (16)
V(1,7),(1,4) (((4,8)3)R) H(1,6),(1,5) (V(1,7),(1,4) (((4,8)3)R))
((5,6,7)3)VA Geodesic projection
Figure 28. The route to ((5,6,7)3)VA lattice.
(a)
(b)
Figure 29. Possible molecular mechanisms for the SW isomerization
This novel lattice has the local signature: t5j(0, 4, 1); t6j(2, 2, 2); and t7j(1, 4, 2), j = 5, 6, 7.
We limit here to present only the VA embedding (Figure 28), which is deducible from C60 by
cutting off two hexagonal parallel rings. It was described as a capped tubulene elsewhere
(Diudea et al. 2005).
Note that the ((4,8)3) lattices are deductible from the square (4,4) covering, by some
basic operations on maps (Diudea 2004).
It is worthy noted that Stone-Wales rotation attracted attention of chemists who proposed
an isomerization model involving reactive species such as free radicals (Figure 29 -a) or
carbenes (Bettinger et al. 2003 - Figure 29 -b). By quantum chemical calculations, an
activation energy for defect formation (in a (6,3) graphitic tube) in the range of 5-7 eV (or
about 115-160 kcal/mol), at a strain above 6%, was estimated.
Segments of a tube, with an altered helicity due to a SW isomerization, could appear,
with consequently forming different metal/metal, semiconductor/semiconductor, and/or
semiconductor/metal hetero-junctions, possibly leading to all-nanotube-based quantum dot
structures (Orlikowski et al. 2000). Such defects have been examined experimentally by
scanning tunneling microscopy STM (Zhao et al. 2000).The above SW edge rotations have
been performed by the CageVersatile original program.
4. Operations on Maps
Modifying a covering is a challenge and also a way to understand chemical reactions
occurring in nanostructures, particularly in carbon allotropes, see Deza et al. 2000, Fowler
and Pisanski 1994, Klein and Zhu 1997, de La Vaissire et al. 2001.
Some geometrical-topological transformations, called operations on maps, are used to
generate and/or modify the associate graphs of fullerenes (in general, nanostructures). Our
original software CageVersatile (CVNET), enables such operations.
A map M is a combinatorial representation of a (closed) surface (Pisanski and Randi,
2000). Let us denote in a map: v the number of vertices, e - the number of edges, f the
number of faces and d the vertex degree. A subscript 0 will mark the corresponding
parameters in the parent map.
Some basic relations in a map come form the very begin of Graph Theory (Euler, 1736):
d vd = 2e (17)
s f s = 2e (18)
where vd and fs are the number of vertices of degree d and number of s-gonal faces,
respectively. The two relations are joined in the famous EULER (1758) formula:
v e + f = ( M ) = 2(1 g ) (19)
with being the Euler characteristic and g the genus (Harary, 1969) of a graph (i.e., the
number of handles attached to the sphere to make it homeomorphic to the surface on which
the given graph is embedded; g=0 for a planar graph and 1 for a toroidal graph).
Positive/negative values indicate positive/negative curvature of a lattice. This formula is
useful for checking the consistency of an assumed structure.
4.1. Simple Operations on Maps
4.1.1. Dualization
Du. Dualization of a map starts by locating a point in the center of each face. Next, two
such points are joined if their corresponding faces share a common edge. It is the (Poincar)
dual Du(M). The vertices of Du(M) represent the faces of M and vice-versa(Pisanski and
Randi 2000). The parent and transformed map are related by the parameters:
Du(M): v = f 0 ; e = e 0 ; f = v0 (20)
Tetrahedron T Cube C Octahedron O Dodecahedron D Icosahedron I
Figure 30. The five Platonic polyhedra.
Dual of the dual returns the original map: Du(Du(M)) = M. Tetrahedron is self dual while
the other Platonic polyhedra form pairs: Du(Cube) = Octahedron; Du(Dodecahedron) =
Icosahedron. Figure 30 illustrates the five Platonic solids and symbols hereafter used. A
Petrie dual is also known.
4.1.2. Medial Med.
To achieve the medial, put new vertices in the middle of the original edges (Pisanski and
Randi 2000). Join two vertices if the edges span an angle (and are consecutive within a
rotation path around their common vertex in M). Medial is a 4-valent graph and
Med(M)=Med(Du(M)), as illustrated in Figure 31 -a. The transformed map parameters are:
Med(M): v = e0 ; e = 2e0 ; f = f 0 + v 0 (21)
(a) Med(C) = Cuboctahedron (b) Tr(O) = Truncated Octahedron
Figure 31. Medial and Truncated objects.
The medial operation rotates parent s-gonal faces by /s. Points in the medial map
represent original edges; this property can be used in topological analysis of edges in the
parent polyhedron. Similarly, the points in the dual map give information on the topology of
parent faces.
4.1.3. Truncation
Tr. Truncation is achieved by cutting off the neighborhood of each vertex by a plane
close to the vertex, such that it intersects each edge incident to the vertex. Truncation is
similar to the medial, the transformed map parameters being:
Tr(M): v = 2e0 = d 0 v 0 ; e = 3e0 ; f = f 0 + v 0 (22)
This was the main operation used by Archimedes in building its well-known 13 solids.
Figure 31 -b illustrates a truncated object.
4.1.4. Polygonal Pn Mapping (Diudea 2004)
To cover a map by all n-folded polygons (n= 3, 4, 5) add a new vertex in the center of
each face. Put n-3 points on the boundary edges. Connect the central point with one vertex on
each edge (the end points included). Thus, the parent map is entirely covered by triangles (n =
3), quadrilaterals (n = 4) or pentagons (n = 5). The P3 operation is also called stellation or
triangulation. The transformed map parameters are:
Pn(M): v = v0 + (n 3) e0 + f 0 ; e = ne0 ; f = s 0 f 0 (23)
so that the Eulers relation holds. Maps transformed by the above operations form dual pairs:
Du ( P3 ( M )) = Le( M ) ; Du ( P4 ( M )) = Me( Me( M )) ; Du ( P5 ( M )) = Sn( M ) .
Truncation was the main operation in construction of Archimedean objects, when applied
on the Platonic solids, see de La Vaissire et al. 2001, Pisanski and Randi, 2000. Their duals
are known as the Catalan objects. Note that all the net parameters refer to regular maps (i.e.,
having all vertices and faces of the same valence/size). Figure 32 illustrates the Pn operations;
the symbols in the brackets are identical to those used by de La Vaissire et al. 2001, for
Catalan objects (i.e., duals of the Archimedean solids). For other names of these operations
see HART.
(a) P3(D) (b) P4(D) = (C10)a (c) P5(D) = (C9)a
Figure 32. Polygonal Pn mapping of the Dodecahedron D.

4.1.5. Snub Sn.
Snub is a composite operation (Diudea 2004) that can be written as:
Sn( M ) = Du ( P5 ( M )) (24)
Sn(D) = (A9)a C60 = (A12)a
Figure 33. Snub of Dodecahedron; a Symbols in the brackets are identical to those used by de La
Vaissire et al. (2001) for the Archimedean solids. Note the insulated pentagons in C60.
Correspondingly, the dual of the snub is P5(M): Du(Sn(M)) = P5(M). Similar to the
medial, Sn(M) = Sn(Du(M)). In case of M = T, the snub is just the icosahedron I. Of chemical
interest is the easy transformation of the snub (a regular pentavalent graph) into the leapfrog
transform (a regular trivalent graph - see below), by deleting the edges of the triangle joining
any three parent faces (Figure 33, in black).
The transformed map parameters are:
Sn(M): v = s 0 f 0 = d 0 v 0 ; e = 5e 0 ; f = v0 + 2e0 + f 0 (25)
The multiplication ratio is v/v0 = d0, the same as for Le(M), both of them involving the
dualization.
4.2. Complex Operations on Maps
4.2.1. Leapfrog Le.
Leapfrog (tripling) is a composite operation (Eberhard 1891, Fowler 1986, 1990, 1997;
Fowler et al. 1998a&b, Fowler and Steer 1987, Diudea and John 2001, Diudea et al. 2003)
that can be written as:
Le( M ) = Du ( P3 ( M )) = Tr ( Du ( M )) (26)
A sequence of stellation-dualization rotates the parent s-gonal faces by /s. Leapfrog

operation is illustrated, on a pentagonal face, in Figure 34.
A bounding polygon, of size 2d0, is formed around each original vertex. In the most
frequent cases of 4- and 3-valent maps, the bounding polygon is an octagon and a hexagon,
respectively.
P3 Du
Figure 34. The Leapfrog Le operation on a pentagonal face.
If the map is a d0 regular graph, the following theorem holds, see Diudea and John 2001,
Diudea et al. 2003:
Theorem 4.1. The number of vertices in Le(M) is d0 times larger than in the original map
M, irrespective of the tessellation type.
The demonstration follows from the observation that, for each vertex of M, d0 new
vertices result in Le(M): v / v 0 = d 0 v 0 / v 0 = d 0 . The complete transformed map parameters
are:
Le(M): v = s 0 f 0 = d 0 v 0 ; e = 3e0 ; f = v 0 + f 0 (27)
Note that in Le(M) the vertex degree is always 3, as a consequence of the involved
triangulation P3. In other words, the dual of a triangulation is a cubic net (Pisanski and Randi
2000). It is also true that truncation always provides a trivalent net. A nice example of using
Le operation is: Le(Dodecahedron) = Fullerene C60 (Figure 35). The leapfrog operation can be
used to insulate the parent faces by surrounding bounding polygons.
Dodecahedron D; v = 20 Fullerene C60 ; v = 60
Figure 35. Realization of Le operation.
A retro-leapfrog (Vizitiu et al. 2006)RLe operation (Figure 36) can be written as:
RLe( M ) = RP3 ( Du ( Le( M ))) (28)
To perform this operation, suppose the actual map is Le(M); make its dual and then cut-
off all the vertices with degree lower than the maximal one.
Du RP3
Figure 36. The Retro-Leapfrog RLe operation on a pentagonal face.
4.2.2. Chamfering Q.
Chamfering (quadrupling - Diudea and John 2001, Diudea et al. 2003, Vizitiu et al.
2006, Goldberg 1937) is another composite operation, written as the sequence:
Q( M ) = RE (TrP3 ( P3 ( M ))) (29)
where RE denotes the (old) edge deletion (dashed lines, in Figure 37) in the truncation TrP3 of
each central vertex of the P3 mapping. The Q operation leaves unchanged the initial
orientation of the polygonal faces.
P3 TrP3
Figure 37. The Quadrupling Q operation on a pentagonal face.
Theorem 4.2. The vertex multiplication ratio in a Q transform is d0 + 1 irrespective of the

parent map tessellation.
With the observation that, for each vertex of M, d0 new vertices appear in Q(M) and the
old vertex is preserved, the demonstration is immediate, see Diudea and John 2001, Diudea et
al. 2003: v = d 0 v 0 + v 0 ; v / v 0 = d 0 + 1 . The complete transformed parameters are:
Q(M): v = (d 0 + 1)v 0 ; e = 4e0 ; f = f 0 + e0 (30)
Q operation involves two /s rotations, so that the initial orientation of the polygonal
faces is preserved. Note that, because of preserving the old vertices, Q(M) is, in general, non-
regular; only in case of a 3-valent M, Q(M) is a 3-regular graph and vertex multiplication is 4
(from which the name quadrupling is derived). Also note that edge chamfering is equivalent
to vertex truncation.
Q insulates the parent faces always by hexagons. An example of this operation is: Q
(Dodecahedron) = Fullerene C80 (Figure 38).
Dodecahedron D; v = 20 Fullerene C80 ; v = 80
Figure 38. Realization of Q operation.
The retro-quadrupling RQ operation, see Vizitiu et al. 2006 (Figure 39) is based on the
sequence:
RQ( M ) = E ( RTrP3 ( P3 ( M ))) (31)
and can be performed by adding new edges parallel to the boundary edges of the parent faces
followed by the deletion of these faces.
E RTrP3
Figure 39. The Retro-Quadrupling RQ operation on a pentagonal face.
4.2.3. Septupling Operations on Maps
Two main operations on maps, leading to Platonic tessellations in open lattices, are
known: the septupling S1 and S2 operations (Diudea 2003a, 2004, 2005; King and Diudea
2005, 2006).
The S1 operation is a composite operation that can be written as a sequence of simple
operations:
S1 ( M ) = TrP5 ( P5 ( M )) (32)
with TrP5 meaning the truncation of new, face centered, vertices introduced by P5 pentagonal
mapping, which involves an E2 (i.e., two new points put on each edge) operation.
S1 operation was also called (Diudea 2003a) Capra Ca - the goat, by the Romanian name
of the English leapfrog children game. Within this work, the two names are interchangeable.
The nuclearity of the Goldberg (1937) polyhedra (related to the fullerenes) is given by the
parameter:
m = (a 2 + ab + b 2 ); a b; a + b > 0 (33)
which is the multiplication factor m = v/v0: in a 3-valent map, Le ((1,1); m = 3; Q ((2,0); m = 4

and Ca((2,1); m = 7. The m factor was used since the ancient Egypt for calculating the
volume of truncated pyramid, of height h: V = mh/3.
P5(M) S1(M) Op(S1(M))
Figure 40. Septupling S1 operation on a square face, up to the open structure.
S1 insulates any face of M by its own hexagons, which are not shared with any old face. It
is an intrinsic chiral operation (King and Diudea 2006); it rotates the parent edges by /(3/2)s
and was extensively illustrated in our books (Diudea Ed. 2005, Diudea and Nagy 2007). Since
pentangulation of a face can be done either clockwise or counter-clockwise, it results in an
enantiomeric pair of objects: S1S(M) and S1R(M), with the subscript S and R given in terms of
the sinister/rectus stereochemical isomerism.
Si can continue with the opening operation: Op k ( S i ( M )) , where k represents the number
of points added on the boundary of the parent faces, that become the open faces. The resulting
open objects have all the polygons of the same (6+k) size. The above operation sequence
enables the construction of negatively curved networks. Figure 40 gives the steps of S1
realization on a square face in a trivalent lattice, up to the open structure.
Theorem 4.3. The vertex multiplication ratio in an S transformation is 2d0 + 1

irrespective of the original map tiling.
For demonstration, observe that, for each old vertex, 2d0 new vertices (Figure 40) appear
and the old vertex is preserved in the transformed map. Thus, v = 2d 0 v 0 + v 0 and
v / v 0 = 2d 0 + 1 .
The S2 operation (Diudea 2004, 2005 - Figure 41) is a simpler one; it can be achieved by
putting four vertices on each edge of the parent map M (E4 operation) and next join these new
vertices in order (-1, +3):
S 2 = J ( 1, +3) ( E 4 ( M )) (34)
It insulates the double sized parent faces by pentagons and parent vertices by pentagon
d0-multiples; the transformed objects are non-chiral.
Chirality in S2 is brought by the Op operation Op2a, achieved by putting two points on
alternative edges of the double sized parent face boundary (Figure 41). Note that both the
septupling operations keep the parent.
E4(M) S2(M) Op2a(S2(M))
Figure 41. Septupling S2 operation on a square face, up to the open structure.
The transformed map parameters are shown in the following relations:
S1 ( M ) & S 2 ( M ) : v = v 0 (2d 0 + 1) ; e = 7e0 ; f = f0 (s0 + 1) = 2e0 + f0 (35)
Op ( S 1 ( M )) : vOp = v 0 (3d 0 + 1) ; eOp = 9e0 ; fOp = f 0 s0 (36)
Op 2 a ( S 2 ( M )) : vOp = v0 (4d 0 + 1) ; eOp = 11e0 ; fOp = f 0 s0 (37)
where d and s are the vertex degree and face size, respectively; the subscript zero refers to the
original map M.
The iterative n-time operating (on maps with any vertex degree, d 0 3 ) leads to the
following lattice parameters, transformed by both S1 and S2 (Diudea and Nagy 2007):
vn = v0 q n (38)
e n = e0 m n
f n = f 0 ( s 0 p n + 1)
q n = 2d 0 p n + 1; n 2 (39)
n 1
p n = m i = ( m n 1) /( m 1) = m( m...( m + 1)... + 1) n 2 + 1 (40)
i =0
The parameter m is that defined in relation (33). From (39), it is obvious that:
p n = (q n 1) / 2d 0 (41)
For trivalent maps (i.e., those with d0 =3), the above parameters become:
qn = m n (42)
p n = ( m n 1) / 6 (43)
vn = v0 m n
e n = e0 m n
f n = f 0 ( s 0 (m n 1) / 6 + 1) (44)
For S1 and S2 the transformed lattice parameters will be:
v n = 7 n v 0 ; en = 7 n e0 ; f n = f 0 ( s 0 (7 n 1) / 6 + 1) (45)
In case of a cage opening after the nth iteration, the lattice parameters are as follows:
v n , Op ( S1 ) = v 0 q n + f 0 s 0 = v 0 ( d 0 + q n ) (46)
en ,Op ( S1 ) = e0 m n + f 0 s 0 = e0 (m n + 2)
f n ,Op ( S1 ) = f 0 ( s 0 p n + 1) f 0 = f 0 s 0 p n
v n , Op 2 a ( S 2 ) = v 0 q n + 2 f 0 s 0 = v 0 (2d 0 + q n )
en ,Op 2 a ( S 2 ) = e0 m n + 2 f 0 s 0 = e0 ( m n + 4)
f n ,Op 2 a ( S 2 ) = f 0 (s 0 p n + 1) f 0 = f 0 s 0 p n (47)
S1S(S1S (O)) (top) S1R(S1S (O)) (top)
Figure 42. Sequence of S1 pro-chiral operations on Octahedron: S1S,S1S transform is still twisted while
S1R,S1S one is no more chiral.
As above mentioned, S1 rotates the parent bonds, so that it provides chiral transforms.
The iterative application of S1 may lead to either chiral/twisted or non-chiral/non-twisted
transforms: for example, the sequence S1S(S1S(M)) results in a twisted structure while
S1R(S1S(M)) provides a non-twisted object (Figure 42).
In the opposite, S2 applied to closed cages, leads to non-twisted objects. Its iterative
application reveals the fractal fashion of the covering (Figure 43). The fractal characteristic
(El-Basil 1996, Klein et al. 1993, Diudea 2005) can be seen even in the algebraic form of pn
parameter, eq. (40).
The only classical fullerene constructible by S2 is C28 (from the Tetrahedron).
(a) S2(D); I; v = 140 (two-fold axis) (b) (S2)3(D); I; v = 6860 (five-fold axis)
Figure 43. Iterative S2 operation on Dodecahedron: observe the fractal covering in case of 3-time
repetition (b).
RTrP5 RE2
Figure 44. The Retro-Capra RCa operation on a pentagonal face.
C140 RTrP5 (D); v = 80
Figure 45. Realization of the Retro-Capra RCa operation.
Retro-capra RCa operation (Figure 44, Vizitiu et al. 2006) can be written as the
sequence:
RCa( M ) = RE 2 ( RTrP5 ( M )) (48)
To achieve this operation, delete the smallest faces of the actual map and continue with
RE2. A 3D realization of RCa is illustrated in Figure 45.
4.3. Generalized Operations on Maps
Recently, Peter E. John (see Diudea et al. 2006b, Stefu et al. 2005) has proposed a
generalization of operations on maps, inspired from the work of Goldberg (1937), and its
representation of polyhedra in the (a,b) inclined coordinates (60o between axes). The
multiplication factor m for trivalent maps is given by eq. (33). A similar procedure was used
by Coxeter (1973), who built up icosahedral polyhedra/fullerenes as dual master triangular
patches, represented by pairs of integers.
(2,2) (4,0)
G G
y G y G
x x
(2,2) (4,0)
Figure 46. Examples of the generalized (a, a) and (a, 0) operations.
G G
y G (3,2) y G (3,2)
x x
(a) (3,2); m =19 (b) C(3,2); m =13
Figure 47. Examples of the generalized (a, b) operation: a = b + 1 (a) and (central face and first
connected atoms) cut C(a,b) (b), the last one corresponding to m(3,1) =13 factor.
Figures 46 and 47 illustrate the method on the hexagonal face. The points of the master
hexagon must lie either in the center of a lattice hexagon or on a lattice vertex. so that in the
center of the parent hexagon must be a new hexagon. The edge length of the parent hexagon
is counted by the primitive lattice vectors (x,y).
For the (3,2) Cut operation - Figure 47 -b, the central face and first connected atoms
were cut off.
Some of the generalized composite operations, corresponding to non-prime m, can be
expressed as sequences of operations, as shown in Table 9. It is obvious that the operations
(a,a) also denoted Lea,a and (a,0) or Qa,0 provide achiral transforms (e.g., fullerenes of the full
Ih point group symmetry) while the operations (a,b), a b, (also noted Caab) result in chiral
transformed maps (e.g., fullerenes of the rotational I point group symmetry King and
Diudea 2006). The (a,0) operations produce non-rotated maps. The above generalized
operations, as implemented in the software package CageVersatile, work on any face and any
vertex-degree maps.
Table 9. Inclined coordinates (a, b), multiplication factor m = (a2 + ab + b2), number of
atoms v and operation symbols ( running on Dodecahedron, C20)
(a, b) m v Operation Obs.

1 (1, 0) 1 20 I Identity
2 (1, 1) 3 60 Le1,1 Rotated by / s; achiral
3 (2, 0) 4 80 Q2,0 Non-rotated; achiral
4 (2, 1) 7 140 Ca2,1 Rotated by / (3/2)s;
chiral
5 (2, 2) 12 240 Le1,1, Q2,0 Rotated by / s; achiral
6 (3, 0) 9 180 Le1,1, Le1,1 Non-rotated; achiral
7 (3, 1) 13 260 - Rotated; chiral
8 (3, 2) 19 380 - Rotated; chiral
8' (3, 2)c* 13 260 - Rotated; chiral
9 (3, 3) 27 540 Le1,1, Le1,1, Le1,1 Rotated by / s; achiral
10 (4, 0) 16 320 Q2,0, Q2,0 Non-rotated; achiral
11 (4, 1) 21 420 Le1,1, Ca2,1 Rotated; chiral**
12 (4, 2) 28 560 Q2,0, Ca2,1 Rotated by / 2s; chiral
13 (4, 3) 37 740 - Rotated; chiral
14 (4, 4) 48 960 Le1,1, Q2,0, Q2,0 Rotated by / s; achiral
15 (5, 0) 25 500 - Non-rotated; achiral
16 (5, 1) 31 620 - Rotated; chiral
17 (5, 2) 39 780 - Rotated; chiral
18 (5, 3) 49 980 Ca2,1, Ca2,1 Chiral/ achiral**
19 (5, 4) 61 1220 - Rotated; chiral
20 (5, 5) 75 1500 - Rotated; achiral
* c=cut; ** achiral, when the sequence CaR(CaS(M)) is used.
In case of a trivalent regular map, relations (17) and (18) can be rewritten as:
3 v 0 = 2 e0 = s 0 f 0 (49)
Keeping in mind the multiplication factor m (see (33)), the number of vertices and edges,
respectively, in the transformed map is:
v = m v0 (50)
3 v = 3 m v0 = 2 e
3 3 2
e= m v 0 = m e0 = m e0 (51)
2 2 3
The above operations introduce new hexagons, keeping the original faces. Thus, the
number of faces of any size s in M is:
fs = f6 + f0 (52)
Relation (49) becomes:
2 e = s f s = 6 f 6 + s0 f 0 (53)
Substitution of e from (51) in (54) leads to:
m 1
f6 = s0 f 0 (54)
6
m 1
fs = s0 f 0 + f 0 (55)
6
In the case of n-iterative operations, equations (44) hold for all the presented operations
running on a trivalent regular M0. The above relations are particularly true for the 3-valent
Platonic solids: tetrahedron T, cube C and dodecahedron D. Figure 48 illustrates realizations
of a chiral generalized operation.
(a) Ca3,2(D); m =19; v =380 v =380 ; optimized
(b) Ca3,2C(D); m =13; v =260 v =260 ; optimized
Figure 48. The generalized Ca3,2 and Ca3,2C operations performed on the Dodecahedron.
The operations above described have been proposed in view of rationalizing (see de La
Vaissire et al. 2001, Pisanski and Randi, 2000) the transformations observed in
nanostructures, in relation structure-property or in connection with their growth mechanisms.
Sequences of map operations can be used to design a desired tessellation, particularly those
showing disjoint hexagons (which according to the Clar theory could be more stable or more
aromatic) or even circulene disjoint domains, which could predict valuable properties, e.g.,
super-magnetic ones. It is not the place to continue this subject; in this respect, the reader can
consult our recent book (Diudea and Nagy 2007).
All the operations on maps were performed by the CageVersatile software package,
which works on any face, any vertex-degree maps and any type of surface.
5. All Ring Net Operations

A polygonal motif, covering a surface, can be embedded in a given surface, which is
locally planar, by operations on maps, (Section 4). Accordingly, a tessellation of a (locally
2D) map M we call a covering (Pisanski and Randi, 2000, Diudea, 2004). Other patterns are
essentially 3D objects which fill the space within a network. The operations providing such
units are the same as the above ones but working on all rings of a 3D net. We name these
operations on nets while a tiling (Blatov et al. 2004, Delgado-Friedrichs and OMcKeeeffe
2005), is a filling of space by tiles sharing faces. The tiles are elementary polyhedra of a 3D
net. A net N is a combinatorial representation of a space domain. The difference between the
two types of operations originates in the difference between face and (strong) ring: in a
(2D) map, any edge shares at most two rings (i.e., faces) while a (3D) net consists of edges
that can share more that two (eventually strong) rings. A strong ring is not the sum of other
smaller rings.
As above mentioned, the operations on maps (i.e., on faces) are now extended on all
strong rings. Our attention was focused on the following operations: dualization Du, medial
Me, truncation Tr, leapfrog Le, chamfering Q and capra Ca. To specify a 3D operation, the
suffix _all (meaning all edges or rings are operated) is added to the name of a map operation.
In the top of figures, sequence of net operations leading to the given structure and lattice data
are given; in some cases, the ring counting polynomial R(x) is given. Our original software
programs CageVersatile-CVNET, JSChem, Omega counter, and Nano-Studio enable such
operations and counting. The points/atoms of a net can be covered by an envelope (of a given
tessellation) and this envelope is ultimately a surface that obeys the Euler topological rule.
After an introduction to the all-ring operation realization, an extension of the Euler theorem
will be given and exemplified as well.
5.1. Operations on Multi-Shell Cages
Onion-like fullerenes have been observed experimentally and such structures is believed
to consist of polyhedra-into-polyhedra - shells of the same (or not) number of atoms,
connected (or not) to each others. It is known the interest of scientists in modifying a
chemical structure in order to modify its properties, in particular, the tessellation of fullerene
cages. It is also known the cube-into-cube 2C geometrical representation; the superscript

number in front of the cage name accounts here for the number of shells.
(a) 2C; v=16; e=32; d=4 R(x)= 24x 4 (b) Med(2C); v=24; e=60; d=5 R(x)= 16 x 3 + 36 x 4
Figure 49. Double-shell Cube and its medial Med transform.
In multi-shell cages, our program CVNET enables both shell-by-shell operations (when
only selected shells have to be transformed) and all-rings operations. In the following, the
manner of operating will be always specified.
Among the operations useful in this respect, we focused first on the medial Med
operation. This is because bisection (the other name used for Med) is the most frequent
operation in the nature and because interpenetrating networks exist in the realm of crystals
(Carlucci et al. 2003, Blatov et al. 2004).
Lets start with cage-into-cage structures: the shells are now identical (Figure 49 -a).
As an example, the Med operation (Figure 49 -b) is performed strictly at the level of shells,
with no involvement of edges and rings that join the shells to each others. These operations
can be used to modify either closed or open structures.
Lets perform the Med operation on all-rings, the rings joining the shells included: the
shells are again identical (Figure 50). The structures are quite complex and need some
detailed explanation.
(a) Med(2D)_all (b) Med(2I)_all

v=80; e=240; R(x)= 160 x 3 + 30 x 4 + 24 x 5 v=72; e=240; R(x)= 160 x 3 + 30 x 4 + 24 x 5
Figure 50. All-Med(M) transforms of multi-shell dodecahedron in (a) and icosahedron in (b).
Lets now perform the operations on the triple cube C3 and let the parent cage appear in
figure for a better understanding (Figures 51 to 55): in the left hand side, the transform is
given with the joint part (i.e., the substructure resulted by operating the joint rings - in red)
while in the right hand side only shell transforms (in yellow), which are disjoint.
(a) 3C & Med(3C)_all; v=24&52 (b) 3C & Med(3C); v=24&36
Figure 51. All-Med transform of the multi-shell 3C.
If the shell transforms are cut-off, the joint part remains as a connected (or not)
substructure; in case this remainder is connected, it can be viewed as a co-net CoN (see
below). In case of Du (Figure 52), the remainder (Figure 53) is connected: it is just the medial
of 2C (we named it CoN{Med(2C)}, with the detailed CoN in {}) and comes from the rings
joining the shells.
3
C & Du(3C)_all; v=24&42 3
C & Du(3C); v=24&18
Figure 52. All- Du(3C) transform of the multi-shell 3C.
3
C & Du(3C);CoN{Med(2C)} 3
C & Du(3C) & CoN{Med(2C)}
v=24&24 v=24&18&24
Figure 53. Intercalated nets of Du_all transform of 3C; CoN is just Med(2C).
Note that our Du_all operation is different from that used in dualizing the crystal
networks (Delgado-Friedrichs and OMcKeeeffe 2005): there, the operation is defined on tiles
not on rings, so that many symmetrical nets (e.g., the cubic pcu net), appear to be self-dual, a
result in disagreement with the well-known dualization of convex polyhedra.
3
C& Le(3C)_all; v=24&168 3
C& Le(3C); v=24&72
Figure 54. The leapfrog Le(3C)_all.
The operation Le_all (Figure 54) is related to the Du_all operation, in the sense the
remainder part (Figure 55) is related to the Med transform of the parent. However, this
relatedness is not completely apparent (some edges are needed to join the vertices of lower
connectivity located near the middle of the parent edges, as in case of Med) so that we left {}
empty.
3
C& Le(3C)_all CoN{} C3& Le(3C) & CoN{}
v=24&96 v=24&72&24
Figure 55. Intercalated nets of Le transform of C3; CoN is derived from Med(C2).
5.2. Operations on Centered Cages
A particular result is obtained when the all-ring operations are performed on point-into-
polyhedra (denoted by the suffix P added to the cage name). In case of Med(MP)_all, it leads
to structures in which the parent cage and its medial coexist (Figure 56).
TP CP OP DP IP
Figure 56. Med(MP)_all transforms: TP (v=10; e=30); CP (v=20; e=60); OP(v=18; e=60); DP (v=50;
e=150); IP (v=42; e=150).
TP CP OP DP IP
Figure 57. Du(MP)_all transforms: TP, CP, OP, DP and IP TP (v=10; e=30); Du(TP)=Med(TP); CP
(v=18; e=60); Du(CP)=Med(OP) OP(v=20; e=60); Du(OP)=Med(CP); DP (v=42; e=150);
Du(DP)=Med(IP) IP (v=50; e=150); Du(IP)=Med(DP).
In case of dual Du(MP)_all, the dual and its medial coexist (Figure 57). In case of
Le(MP), the transforms consists of Tr(M)&Tr(Du(M))&Tr(T) (Figure 58 -a), excepting
Le(TP) when there are only two interlaced Tr(T), connected by additional vertices (Figure
59). The Tr(MP) transforms consists of Tr(M)&M and some additional vertices (of the same
degree as the corresponding vertex in M) at each junction point (in all, v(M) points) of the
two cages (Figure 58 -b).
(a) Le(IP)_all; v=150{Tr(M)=60; (b) Tr(IP)_all

Tr(Du(M))=60; Tr(T)=30}; e=300 ; R=184 v=84; e=192; R=142
Figure 58. All-ring transforms of the IP cage by Le (a) and Tr (b); observe the C60 structure inside (a -
red) and outside (b - yellow) of these cages.
(a) Le(TP)_all v=30; e=60; r=40 (b) Le(TP)_all; simplified view
Figure 59. All-ring transforms of TP cage by Le (a) and Tr (b); observe the C60 structure inside (a - red)
and outside (b - yellow) of these cages.
(a) Med(2TOR(4,4)[5,25])_all (b) Med(2TOR(4,4)[5,25])_all (slide)

v=625; e=2000; R(G, x) = 1000 x 3 + 750 x 4 v=40; e=100; f3=40; f4=20; g = 1
Figure 60. Medial of a double shell toroidal structure.
TP CP OP DP IP
Figure 61. Med(Med(MP))_all transforms: MP=TP, CP, OP, DP and IP; core=Med(M) TP (v=30;
e=90); R(G, x) = 50 x3 + 44 x 4 ; Tile_ext=O; CP (v=60; e=276); R(G, x) = 84 x3 + 68 x 4 ; Tile_ext=O;
OP(v=60; e=156); R(G, x) = 52 x3 + 60 x 4 ; Tile_ext=CO; DP (v=150; e=450);
R (G, x) = 210 x + 210 x + 24 x Tile_ext=O;IP (v=150; e=390); R (G, x) = 130 x + 120 x + 24 x 5 ;
3 4 5 3 4
Tile_ext=CO.
The all-ring procedure was also applied on toroidal 2TOR structures (Figure 60). Observe
the cross-sections of the all-medialized torus are also (medial) toroids which join to each
other to form the corresponding supra-torus.
By iterating twice Med_all operation, complex structures are obtained (Figure 61). All
these structures show a core which is the medial Med(M) of the parent Platonic solid M.
Three of them, those derived from TP, CP and DP look like interlaced structures, consisting
of Octahedron units as external tiles. The others, those derived from OP and IP consist of
Cubeoctahedron units as external tiles assembled such as clearly delimited hollows appear,
like in zeolites. These two last structures we used in construction of crystal-like lattices.
Observe the number of vertices of the objects in Figure 61 are represent the number of
edges in Med(MP)_all objects (Figure 56), of which Med transforms are.
5.3. Euler Extended Formula for Multi-Shell Polyhedra
As mentioned above, the Euler (1758) formula relates the basic map parameters to the -
characteristic of the surface S and the genus g of a graph embedded in S.
In multi-shell polyhedra, the map M (a 2D lattice) is changed by the net N (a 3D lattice)
and faces are changed by (strong) rings. In a 3D lattice, an edge can share more than two
rings, this fact generating serious problems in counting SSSR (smallest set of smallest rings).
Within this paper, the rings are given in terms of the ring counting polynomial. The paradigm
of the present approach is: a multi-shell polyhedral structure can be expressed as the union of
the composing tiles.
Tiles are elementary polyhedra of a space domain which form a tiling by sharing faces
(face-to-face). A net N is carried by a tiling, which uniquely determines the net; the reciprocal
is not true since the decomposition of a net in tiles is not unique. Moreover, there are nets
formed by catenated rings, for which no tiling can be found. A tiling, consisting of the
smallest possible tiles, that preserves the symmetry of the net and their rings are all strong
rings, is called a natural tiling (Delgado-Friedrichs and OMcKeeeffe, 2005). For a tiling with
t tiles, f faces, e edges and v vertices per repeat unit, Coxeter (1973) gave de formula:
v e+ f t = 0 (56)
Table 10. Euler-Extended Formula in Multi-shell Polyhedra
Object: Ring Polynomial d (v) Formula Meaning

Platonics v + r e t ( s 1) = 2(1 g ) t
1 2
C: 24x 4 4 16+24-32-6=2 f (C)
3 5 (8) f (C)
2 C: 42x 4 24+42-52-62=2
4 (16)
3 2
D: 30 x 4 + 24 x 5 4 40+54-80-12=2 f ( D)
3 5 (20) f ( D)
4 D: 60 x 4 + 36 x5 60+96-130-122=2
4 (40)
5 2
I: 40 x 3 + 30 x 4 6 24+70-72-20=2 f ( I)
3 7 (12)
6 I: 60 x 3 + 60 x 4 36+120-114-202=2 f ( I)
6 (24)
7 2
O: 16 x 3 + 12 x 4 5 12+28-30-8=2 f (O)
3 6 (6) f (O)
8 O: 24 x 3 + 24 x 4 18+48-48-82=2
5 (12)
9 2
T: 8 x 3 + 6 x 4 4 8+14-16-4=2 f (T )
3 5 (4) f (T )
10 T: 12 x 3 + 12 x 4 12+24-26-42=2
4 (8)
In the light of the above paradigm, and being the case of a natural tiling, faces f can be
replaced by rings r. The Euler formula extended for multi-shell polyhedra reads as proposed
by Diudea and Nagy (2008):
v e + r t ( s 1) = 2(1 g ) (57)
where s is the number of shells; in case of s=1, the classical Euler formula is recovered (after
identifying r with f). We limit here to the calculation of the genus g, by means of the newly
introduced r and t parameters, the results being presented in Tables 10 to 14.
The difficulty of the relation (57) is to find the parameter t, corresponding to the natural
tiling. In case of identically transformed shells, t equals the number of faces of the parent map
(Tables 10 and 11). When shells are differently tessellated, t accounts for the common
features (Table 12). When all rings are operated, the vertex number of the parent map is
added (Table 13). In case of Med(3C)_all (Table 13), the tiles per one shell are illustrated in
Figure 62.
Table 11. Euler-Extended Formula in Multi-shell Closed/Open Polyhedra
Object: Ring Polynomial d Formula Meaning

Archimedeans v + r e t ( s 1) = 2(1 g ) t
1 2
Med( C): 16 x + 36 x 3 4 5 24+52-60-14=2 f (Med (C))
2 3
Med( C): 24 x + 66 x 3 4 5 36+90-96-142=2 f (Med (C))
3 2
Ca( C): 96 x + 48 x 4 6 4 112+144-224-30=2 f (Ca (C))
4 2
Q( C): 60 x + 24 x4 6 4 64+84-128-18=2 f (Q(C))
Archimedeans-Open
5 Op(Ca(2C)): 108 x 4 + 48 x 7 4(112) 160+156-296-24=2(1-3) f (Op(Ca (C)))
3(48)
6 Op(Q(2C)): 72 x 4 + 24 x 8 4(64) 112+96-200-12=2(1-3) f (Op (Q(C)))
3(48)
Table 12. Euler-Extended Formula in Multi-Shell Polyhedra Derived from

Centered Cages

Med(MP)-Platonics v + r e t = 2(1 g ) t
1 CP: 44 x 3 + 12 x 4 6 20+56-60-14=2 f (Med (C))
2 3
DP: 110 x + 24 x 5 6 50+134-150-32=2 f (Med (D))
3 IP: 110 x 3 + 20 x 4 + 12 x 5 10(12) 42+142-150-32=2 f (Med (I))
6(30)
4 OP: 52 x 3 + 6 x 4 8(6) 18+58-60-14=2 f (Med (O))
6(12)
5 TP: 30x 3 6 10+30-30-8=2 f (Med (T))
(a) (b) (c)
Figure 62. Med(3C)_all; (a) square face tile {Med(C)}; (b) trigon face tile {two tetrahedra incident in a
vertex}; (c) the fitting of the two tiles (per one shell).
Table 13. Euler-Extended Formula in Multi-Shell Archimedean Polyhedra:

All-rings Operated

Archimedeans-all v + r e t ( s 1) = 2(1 g ) t
1 Med( C)_all: 64 x + 24 x
2 3 4 6 32+88-96-22=2 f ( Med (C)) + v(C)
2 Med( C)_all: 120 x + 42 x
3 3 4 8 (12) 52+162-168-222=2 f ( Med (C)) + v(C)
6 (40)
3 Med(2D)_all: 6 80+214-240-52=2 f ( Med (D)) + v(D)
3 4 5
160 x + 30 x + 24 x
4 Med(3D)_all: 8 (30) 130+396-420-522=2 f ( Med (D)) + v(D)
3 4
300 x + 60 x + 36 x 5 6 (100)
5 Med(2I)_all: 10 (12) 72+214-240-44=2 f ( Med (I)) + v(I)
3 4
160 x + 30 x + 24 x 5 6 (60)
6 Med(2O)_all: 64 x 3 + 24 x 4 8 (6) 30+88-96-20=2 f ( Med (O)) + v (O)
6 (24)
7 Med(3O)_all: 120 x 3 + 42 x 4 8 (24) 48+162-168-202=2 f ( Med (O)) + v (O)
6 (24)
8 Med(2T)_all: 40 x 3 + 6 x 4 6 16+46-48-12=2 f ( Med (T )) + v(T )
9 Med(3T)_all: 60 x 3 + 24 x 4 8 (6) 26+84-84-122=2 f ( Med (T )) + v(T )
6 (20)
Table 14. Euler-Extended Formula in Multi-Shell Toroidal Polyhedra

TORI v + r e t = 2(1 g ) t
1 2
TOR(4,4)[7,7]: 49x 4 5 98+196-245-49=2(1-1) f (TOR (4,4)[7,7])
2 Med(2TOR(4,4)[7,7])_all: 8 (49) 245+686-784-147=2(1-1) f (Med (TOR (4,4)[7,7])) +
392 x 3 + 294 x 4 6 (196) v(TOR (4,4)[7,7]) =98+49
3 Med(2TOR (4,4)[5,25])_all: 8 (125) 625+1750-2000-375=2(1-1) f (Med (TOR (4,4)[5,25])) +
3
1000 x + 750 x 4 6 (500) v(TOR (4,4)[5,25]) =250+125
4 Spongy-Dodecahedron 6 (90) 150+274-390-44=2(1-6) f ( Med (I)) + v(I)
Med(Med(IP)) 4 (60)
130 x 3 + 120 x 4 + 24 x 5
5 Spongy-Cube 6 (36) 60+112-156-20=2(1-3) f ( Med (O)) + v (O)
Med(Med(OP)): 4 (24)
52 x 3 + 60 x 4
The structures of which calculation is given in Table 14 represent double-shell nets, both
as single and multi-tori (i.e., spongy-structures).
The spongy structures are of particular interest because of their hollows/channels. In case
they are synthesized from appropriate MOFs, a possible catalytic activity can be predicted
(Blatov et al., 2004).
5.4. Operations in Crystal-Like Lattices
A tiling is a filling of space by tiles sharing faces, see Baburin et al. 2005, Blatov et al.
2004, Delgado-Friedrichs and OKeeffe 2005. The characterization of a (3D) net, carried by a
tiling, is not a trivial task, first because of the increased dimensionality of the objects. Next,
none of the indices developed so far (e.g., the Schlfli, Wells numbers or the point group
symmetry) is unique and needs supplementary characterization. Moreover, the adjacency
matrix is hardly manipulated in case of (infinite) networks and the isomorphism checking is
an mp-complete problem, anyhow. Even the sequence of net operations is not unique in
drawing the relatedness of such structures.
When a polyhedral motif is repeated by translation along the coordinate axes the resulted
covering is called periodic. Most often, the pattern is embedded in a given surface, which is
locally planar. Such patterns are at most 2-periodic (i.e., double periodic), even the covered
objects/cages form 3D nets. They can be performed by operations on maps (Section 4).
Other patterns are essentially 3D objects and they can form either 2- or 3-periodic (i.e.,
tripli periodic) nets. The operations providing such units are the operations on nets.
5.4.1. 3-Periodic Tiling
This class can be constructed by: (a) operations on nets and (b) identifying faces of finite
cages generated by map operations.
(a) Du_all (b) Tr_all
(c) Med_all (d) Le_all
Figure 63. The cubic network and some of its all-ring operation transforms.
An all-ring operation (Diudea and Nagy 2007)is the operation performed on al strong
rings in a network. Among operations developed by us, dual Du, medial Med, truncation Tr
and leapfrog Le are the most important and are illustrated in case of the cubic net (as the start
net) in Figure 63.
(a) Med(C);[111]; t=1; v=12 r (G, x) = 8 x + 6 x ; e=48

3 4
(b) Med(C);[444]; t=64; v=300
(c) Med(C)_all; [222]; t=8; v=54 r (G, x) = 64 x + 45 x ; (d) Med(C)_all;[222] & CoN{Du(C)_all}
3 4
e=144 & CoN{Du(C)_all}; Ortho view
Figure 64. The cubic network and its Med_all (3-periodic) transform with the co-net {Du(C)_all}, in
orthoscopic view (c) and in 3D (d).
(a) Le(C); [111]; t=1; v=24 r (G, x) = 6 x 4 + 8 x 6 ; e=36 (b) Le(C); {4}; [444]; t=64; v =960
(c)Le(C)_all; {4}; [222]; t=8; v =144 r (G, x) = 42 x + 64 x ;

4 6
(d) Le(C)_all; self-CoN
e=240 &CoN{ Le(C)_all}; Ortho view
Figure 65. The cubic network and its Le_all (3-periodic) transform with the co-net {Le(C)_all}, in
orthoscopic view (c) and in 3D (d).
As in the case of fullerene tessellation, where a covering pattern, particularly a circulene

flower has its own co-flower (there are at least two patterns in any covering), a net N has its
own co-net CoN (written in {} -Figures 64 and 65).
5.4.2. 2-Periodic Tiling
This class includes structures built up by identifying faces of finite cages generated by
map operations. For example, Q is not suitable for all-ring operations because it preserves
the old (parent) points. In exchange, the cage unit Q(C) derived from the Cube can be
variously assembled by identifying either r4 or r6 or also r4 & r6 . Figure 66 illustrates the
Q(C);{4,6} (2-periodic) network, which is translationally periodic in two directions of the
space.
For a better characterization, particularly of the nanostructures, we proposed the Omega
polynomial, (Diudea 2006, Diudea 2009, Diudea et al. 2006a, 2009; Vizitiu et al. 2007),
which counts opposite edge strips ops in their associate graphs.
(a) Q(C);{4,6};[111]; t=1; v=32 (b) Q(C);{4,6};[444]; t=64; v=1280

r (G, x) = 6 x 4 + 12 x 6 e = 4 6 + 3 8 = 48
(c) Q(C);{4,6};[222]; v=192; t=8; (aOb)-view (d) Q(C);{4,6};[222]; v=192; t=8;

r (G, x) = 52 x + 92 x ; r=144
4 6
(aOc & bOc)-view
(G, x) = 8 x10 + 4 x14 + 4 x 20 + 2 x 24 + 2 x 28 ; e=320
Figure 66. The net Q(C);{4,6}; 2-periodic, by Q(M) operation.

Conclusion
Covering a surface or filling a space domain with various polygonal/polyhedral (repeat)
units was the aim of this paper, which tried to fulfil the requirements of two well-established
sciences: nano-science and crystallography, respectively.
Even the energetic characterization of the discussed structures was here eluded (the
reader can consult the quoted references), simple ways to design such structures, real or
hypothetical ones, were proposed. Majority of the discussed ways originate in the works of
TOPO GROUP Cluj, Romania, or are the most studied by our group, studies assisted by
original software, as mentioned in the first section. These programs enabled one to discretize
the well-known smooth surfaces or space domains in view of generating or transforming a
given structure, with well-defined covering/tiling.
In addition to some classical map operations, performed on the polygonal faces of a
covering, the generalized operations on maps and net operations represent valuable ways in
design of nanostructures. They provide input for more elaborate energy calculations devoted
to structure stability and reactivity or to dynamics of their interaction/distribution with various
media, from the inorganic realm up to the most complex biological systems.
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Chapter 18
Q UANTIFYING S TRUCTURAL C OMPLEXITY

OF G RAPHS : I NFORMATION M EASURES
IN M ATHEMATICAL C HEMISTRY
Matthias Dehmer1,, Frank Emmert-Streib2 ,

Yury Robertovich Tsoy3 and Kurt Varmuza4
1
Institute for Bioinformatics and Translational Research,
UMIT, Eduard Wallnoefer Zentrum 1, A-6060 Hall in Tyrol, Austria,
2
Computational Biology and Machine Learning,
Center for Cancer Research and Cell Biology, School of Medicine,
Dentistry and Biomedical Sciences, Queens University Belfast,
97 Lisburn Road, Belfast, BT9 7BL, UK,
3
Tomsk Polytechnic University,
Lenin Avenue 30, 634050 Tomsk, Russia,
4
Laboratory for Chemometrics, Vienna University of Technology,
Institute of Chemical Engineering,
Getreidemarkt 9/166, A-1060 Vienna, Austria
Abstract
In this chapter, we give a conceptional view about information measures for graphs
which can be used to quantify their structural complexity. We focus on treating such
measures in the context of mathematical chemistry but we want to mention that those
are also applicable for arbitrary complex networks. Besides reviewing the most known
information indices often used in chemical graph theory, we propose an information
functional that is based on degree-degree associations in a graph. This leads us to a
parametric graph entropy measure to quantify the structural information content of a
graph. A brief numerical example shows how the measure can be calculated explicitly.
1. Introduction
Statistical and information-theoretic methods to characterize networks are currently of
considerable interest, see [44, 47]. For example, this relates to development of statistical

E-mail address: Matthias.Dehmer@umit.at
480 M. Dehmer, F. Emmert-Streib, Y.R. Tsoy and K. Varmuza
correlation measures, information measures like entropy, conditional entropy, and mutual
information for structurally analyzing networks [3-7]. It is important to note that the ex-
isting classical approaches for quantifying structural complexity of chemical graphs are
mostly based on the application of S HANNONs entropy formula [45] to derive a finite
probability distribution induced by a certain equivalence criterion [8-15].
As the main contribution of this chapter, we define a novel information-theoretic func-
tional to quantify structural information of undirected and connected networks. By using a
recently proposed method [13] to determine the topological entropy of graphs, we finally
obtain a parametric family of graph entropy measures. Further, we give a review of ex-
isting information measures for characterizing chemical structures represented by graphs.
We want to emphasize that our resulting graph entropy measures can be applied to chem-
ical graphs [3, 49] as well as to general complex networks because its time complexity is
polynomial. This can be proven similarly as in [13].
This chapter is organized as follows: Section (2.) gives a short overview on the usage
of general topological descriptors in mathematical chemistry. Also, Section (2.) presents
some approaches from chemometrics to evaluate the topological descriptors statistically. In
Section (3.) we start the conceptual part of the chapter by stating some mathematical pre-
liminaries. The review of existing information indices often used in mathematical chemistry
is given in Section (4.). By using the outlined method of Section (3.1.), we define a novel
information functional based on degree-degree associations in Section (5.). As a result, we
obtain a parametric entropy measure for quantifying the structural complexity of graphs. A
numerical example is given in Section (5.1.). In Section (6.), the paper finishes with a short
summary and conclusion.
2. Topological Descriptors and Chemometrics

The development and efficient use of formal representations of chemical structures is
a prominent task in chemistry. A typical molecule in organic chemistry (chemistry with
carbon-containing molecules) consists of atoms connected by chemical bonds. Most com-
mon elements are carbon (C), hydrogen (H), nitrogen (N) and oxygen (O), but many others
may be present in an organic molecule. The most common bond types are single bond,
double bond, triple bond, and aromatic bond. A molecule is of course a 3-dimensional
structure, but a representation of only the connectivities (atoms, bonds) is often an efficient
approach for describing a molecule [29]. Graph theory is a powerful mathematical tool for
a simple representation of molecular structures. In general, weighted graphs are used with
(weighted) vertices for the atoms and edges for the bonds. Double and triple bonds between
atoms are described by the same number of edges between the vertices; aromatic bonds can
be replaced by alternating single and double bonds in an aromatic ring. Hydrogen atoms
are often not considered (H-depleted structures) in this representation. In numerous appli-
cations of graph theory for chemical structures only skeletons are considered, that means
all vertices (atoms) are considered to be equal and all edges (bonds) are considered to be
equal (see Figure (1)).
A topological descriptor is usually a graph invariant characterizing a certain feature of
the graph and thus of the chemical structure [48]. During the last decades chemists have
defined some hundreds of topological descriptors, some of them are rather abstract (and
Quantifying Structural Complexity of Graphs 481
Figure 1. Various representations of the molecule acetic acid: two forms of brutto formu-
lae, connectivities including H-atoms, H-depleted structure, and skeleton (a 3-dimensional
molecule is not shown).
less accepted by some parts of the chemistry community), others are based on chemical
considerations. A topological index is independent from vertex numbering and of course
independent from any 2D-representation of the graph. A topological descriptor is often a
single number (called a molecular topological index) or is a sequence of numbers. Usually,
topological indices are calculated from H-depleted molecular graphs; some consider the
different atoms and bonds, other do not and only consider the skeleton.
Topological indices characterize structural features, such as branching, symmetry, shape
or size. A number of topological indices are based on topological distances between atoms
(corresponding to the number of bonds). Further concepts are based on counting the num-
ber of vertices and edges or on determining subgraph isomorphisms. Global topological
indices describe the entire chemical structure, local topological indices refer to the atoms.
A special type of topological descriptors are topological information indices [3, 12]. Start-
ing from a molecular graph, a probability distribution can be derived by applying certain
equivalence criteria to group graph elements (e.g., vertices) into equivalence classes. This
procedure results in concrete information measures that represent the entropy of the un-
derlying graph topology (also see Section (4.)). Such measures are also interpreted as the
structural information content of a graph.
In general, molecular descriptors have been defined as the final result of a logical and
mathematical procedure which transforms chemical information encoded within a symbolic
representation of a molecule into a useful number or the result of some standardized exper-
iments [48]. Besides topological descriptors a great number of other descriptors have been
suggested to characterize various features of molecular structures. Not all descriptors are
useful because many descriptors are highly correlating or even identical. A commercial
software [19] calculates more than 2000 descriptors from molecular structures if 3D-atom
coordinates and all hydrogen atoms given. Depending on the structural data used, we dis-
tinguish 0D-descriptors (e.g. number of atoms), 1D-descriptors (e.g. quantities of electrical
charges in a molecule), 2D-descriptors (e.g. topological indices including information in-
dices), 3D-descriptors (e.g. sum of geometrical distances between selected atoms). Further,
to characterize chemical structures by a set of numbers (molecular descriptors) is a vehicle
for the treatment of essential problems in chemistry, such as the construction of chemical
structure databases, searches for identical or similar chemical structures, and especially for
generating mathematical models describing relationships between chemical structures and
physical/chemical/biological properties of chemical compounds.

Besides characterizing chemical graphs by using topological indices, the comparison of
chemical structures - based on molecular descriptors - is an important task in chemoinfor-
matics. The similarity of chemical structures is often expressed by the similarity of vectors
consisting of binary components [54]. Each vector component denotes the presence (value
1) or absence (value 0) of a given substructure, and is called a binary substructure descrip-
tor; a substructure may be e. g. a benzene ring, a methylester group -CH2-COOCH3, or
simply a given number of nitrogen atoms. Appropriate sets of substructures - covering a
wide area of chemical structures - have been defined and software is available for a fast
computation of say 1000 such descriptors for some 10,000 chemical structures [53]. An ap-
propriate and widely used measure for the similarity of such binary vectors is the Tanimoto
index, also called Jaccard similarity coefficient [51, 54]. Let xA and xB be binary vectors
with m components for two chemical structures A and B, respectively; the Tanimoto index
t is given by
P
AN D(xAj , xBj )
t= P , j = 1, 2 . . . , m, (1)
OR(xAj , xBj )
P
where
P AN D() stands for the number of binary descriptors with a 1 in both vectors, and
OR() denotes the number of binary descriptors with a 1 in at least one of the vectors.
The Tanimoto index reaches the maximum value 1 if all descriptors are pairwise equal; in
this case structures A and B are considered to be very similar or are even identical. The
distribution of t for randomly selected pairs of structures has been suggested as a measure
of the diversity of a chemical structure database [16].
Quantitative relationships between chemical structure data and properties or activities
of chemical compounds (QSPR or QSAR) are of great interest in chemoinformatics [25]
and drug design [33, 55]. In this context chemometrics plays an important role because
multivariate data analysis methods are applied for the development of QSPR/QSAR mod-
els [17]. Main parts of chemometrics are devoted to analytical chemistry [51] but the aim of
this discipline has been more generally defined as providing maximum chemical informa-
tion from chemistry-relevant data [30]. The prominent mathematical and statistical tools
applied in chemometrics belong to multivariate data analysis.
A successful strategy for the development of QSPR/QSAR models is to characterize
chemical structures by a set of molecular descriptors (x1 , ..., xm ) collected in a vector x,
and to create an empirical regression model y = b0 + xT b with y for a predicted property
y, b the vector with regression coefficients, and b0 the intercept. Such models are data-
driven (empirical) because a set of n (typical 30 to 300) chemical structures with known
properties y is used to develop and to test the model. Multiple regression methods, widely
used in chemometrics, are applied, e. g. PLS regression (partial least-squares regression)
because this method allows an optimization of the complexity of the model (avoids overfit-
ting), accepts data with more variables (m) than objects (n), and is insensitive to highly cor-
relating variables [17]. The descriptors best suitable for a particular QSPR or QSAR model
are usually not known in advance; thus one may start with some hundred potentially rele-
vant descriptors and then apply variable selection methods - often a genetic algorithm [36].
Essential is a careful estimation of the prediction performance for new cases; appropriate
strategies are repeated double cross validation [24] or bootstrap methods [20].
The relationships between chemical structure data and properties of chemical com-
pounds are very complex and no general theory exists that could be applied for new cases.
Therefore, the development of new molecular descriptors is of continuing interest, although
a large number of descriptors have already been defined. Chemical structures (even if rather
simply represented by graphs) exhibit a great diversity requiring a great variety of molecu-
lar descriptors. Information indices characterize the inner symmetry of graphs (molecular
skeletons) which is an important feature for some properties and activities of compounds.
Topological descriptors have often not been evaluated by using large chemical databases
consisting of real chemical structures. They have often been evaluated only on using syn-
thetic graphs, e.g. generated isomers. Recently, we showed for an information-based topo-
logical descriptor that the result is considerably different for real chemical structures (from
a spectroscopic database) and for generated isomers [12].
3. Mathematical Preliminaries
Before starting with the main definition, we briefly express some mathematical and
known definitions, see [8,16]. We call G = (V, E), |V | < a finite undirected graph if
E V2 . G is called connected if for arbitrary vertices vi and vj there exists an undirected

path from vi to vj . Otherwise, we call G unconnected. GU C denotes the set of finite,

undirected and connected graphs. The degree of a vertex v V is denoted by (v) and
equals the number of edges e E which are incident with v. We call the set GR k the class of
k-regular graphs. It holds G GR k iff (v) = k v V . Starting from G = (V, E) G

UC,
(v) = maxuV d(u, v) is called the eccentricity of v V , where d(u, v) denotes the
shortest distance between u and v. d(u, v) is an integer metric. (G) = maxvV (v) is
called the diameter of G. Further, we define for G = (V, E) GU C the following vertex
sets.
Sj (vi , G) := {v V | d(vi , v) = j, j 1}, (2)
is called the j-sphere of vi regarding G. For introducing S HANNONs entropy, [11, 45], let
X be a discrete random variable with alphabet A and p(xi ) = P (X = xi ) be the probability
mass function of X. Then, the entropy of X is defined by
X
H(X) := p(xi ) log(p(xi )). (3)
xi A
3.1. Graph Entropies Based on Information Functionals

In order to introduce our novel information functional as well as the corresponding
family of graph entropy measures, we briefly repeat the basic approach for determining the
entropy of graphs, see [13]. Let G GU C and let S be a certain set, e.g., a set of vertices or
paths etc. We call the mapping f : S R+ an information functional of G. We always
assume that f is monotonous. Now, we start with G GU C and define for vi V the
quantities
f (vi )
Pf (vi ) := P|V | , (4)
j=1 f (vj )
where f represents an arbitrary information functional. Obviously, the quantities Pf (vi )

can be interpreted as vertex probabilities because
Pf (v1 ) + Pf (v2 ) + + Pf (v|V | ) = 1, (5)
holds. The corresponding probability distribution is denoted by
PGf (V ) := (PfG (v1 ), PfG (v2 ), . . . , PfG (v|V | )). (6)
Starting from Equation (4), the entropy of the underlying graph topology of G has been
defined as [13]:
|V |
X
If (G) := Pf (vi ) log (Pf (vi )) , (7)
i=1
|V |
X f (vi ) f (vi )
= P|V | log P|V | . (8)
i=1 j=1 f (vj ) j=1 f (vj )
4. Review of Existing Information Indices

In this section, we give a review of the most known information indices which have been
used for quantifying structural information of chemical structures [9,12]. In QSAR [18]
and QSPR [18], partition-based information measures have been used for characterizing
molecular graphs structurally by using a graph invariant X and an equivalence criterion .
The main step to construct these measures is as follows: The application of the equivalence
criterion produces a partitioning of the vertex set V into k subsets whose cardinalities are
denoted by |Vi |. Starting from such a partitioning, the structural information content of a
chemical graph G can be defined by [3]
k
X
I(G, ) = |X| log(|X|) |Xi | log(|Xi |), (9)
i=1
k k

X X |Xi | |Xi |
I(G, ) = Pi log(Pi ) = log . (10)
|X| |X|
i=1 i=1
Equation (9) and Equation (10) are graph entropy measures for quantifying structural infor-
mation of G. Equation (9) and Equation (10) represent the total and the mean information
content of G, respectively [3]. As a technical note, we will always take the logarithms to
the base 2 because we express the structural information contents in bits. In the following,
we give a brief review on further classical information indices and on such information
measures, which are based on graph distances [46].
4.1. Classical Information Indices

For deriving information indices for graphs, one of the first studied graph invariant was
the number of graph vertices regarding vertex degree and extended vertex degree. This
study led to the methods of R ASHEVSKY [43] and T RUCCO [50]. As a result, the so-called
orbital information indices [48]
k
X
IORB (G) = |V | log(|V |) Ni log (Ni ) , (11)
i=1
and
k
|Ni | |Ni |
IORB (G) =
X
log , (12)
|V | |V |
i=1
have been developed [43]. |Ni | stands for the number of topologically equivalent vertices
in the i-th vertex orbit of G and k is the number of different orbits, respectively. In general,
vertices are considered as topologically equivalent if they belong to the same orbits of a
graph G. Similarly, T RUCCO [50] applied the same approach to the edge automorphism
group and obtained
k
X
E
NiE log NiE ,

IORB (G) = |E| log(|E|) (13)
i=1
and
k
|N E | |NiE |

E
X
i
IORB (G) = log , (14)
|E| |E|
i=1
where |NiE | stands for the number of edges belonging to the i-th edge orbit [3, 48] of G.
After this, M OWSHOWITZ [12-15] was the first who expressed a mathematically rigorous
approach for determining the structural information content of a graph by developing fur-
ther the method of R ASHEVSKY [43]. For example, he expressed the relative complexity of
graphs based on the concept of determining their structural information contents. Further,
he explored graph operations like complement, sum, join etc. and investigated the change
of the corresponding information index. This examination was of considerable interest for
the information-based modeling of chemical reactions [3]. Moreover, M OWSHOWITZ [39]
defined the chromatic information content (based on graph colorings) and examined this
measure for different graph classes. As an extension of R ASHEVSKYs measure (Equa-
tion (11)), B ERTZ [2] used as a graph invariant the number of two-edge subgraphs to define
a measure of molecular complexity [2]. Starting from Equation (11) and then by adding the
term |V | log(|V |), he obtained the complexity index
k
X
C(G) = 2|V | log(|V |) Ni log (Ni ) . (15)
i=1
The reason for adding this additional term was that Equation (11) does not properly reflect
the number of the invariants used [2] because it holds IORB = 0 when all invariants are
equal, independent from the fact how large the order of the graph is [2].
Another information index which takes advantage of the well known H OSOYA-Index
Z [28] was developed in [9]. To construct this index, we start with the characteristic poly-
nomial of a graph G that can be calculated from its adjacency matrix. In case of acyclic
molecules, the H OSOYA-Index was defined as the sum of the moduli of the corresponding
polynomial coefficients p(G, k). Then, by defining the probability value p(G,k)
Z , B ONCHEV
et al. [9] expressed the information content for polynomial coefficients of a given graph G
as
[N/2]
X
Ipc (G) = Z log(Z) p(G, k) log(p(G, k)), (16)
k=0
and
[N/2]
X p(G, k) p(G, k)
Ipc (G) = log . (17)
Z Z
k=0
[N/2] denotes the greatest integer that does not exceed N/2. Numerical studies to compare
Z and Ipc (G), Ipc (G) were also performed in [9]. The last information index [7]
|E|
X
k k
I(G, OX) = OX log(OX) X log X , (18)
k=0
we want to introduce for this section relies on the overall value OX,
|E|
X
k
OX(G) = X; {OX(G)} = {0 X, 1 X, . . . , |E| X}, (19)
k=0
of a certain graph invariant X by summing up its values in all subgraphs [7]. These will
be partitioned into terms of increasing orders (increasing number of subgraph edges k) [7].
In the simplest case, it holds that OX is equal to the subgraph count (OX = SC) [4, 7].
Based on the just mentioned method [7], several overall information indices have been
obtained, such as overall connectivity (the sum of total adjacency of all subgraphs) [5],
overall W IENER index W (the sum of total distances of all subgraphs) [6], overall Zagreb-
Indices [10], and the overall H OSOYA index [7]. More classical information indices can be
also found in [3, 48].
4.2. Information Indices Based on Distances

The first information indices for graphs which are not based on algebraical principles
to introduce vertex partitions were developed by B ONCHEV et al. [9]. Starting from an
inferred distance matrix D of a graph under consideration, B ONCHEV et al. [9] introduced
the information indices
(G)
X
2 2
ID (G) = |V | log(|V | ) |V | log(|V |) 2ki log(2ki ), (20)
i=1
and
(G)
1 1 X 2ki 2ki
ID (G) = log log , (21)
|V | |V | |V |2 |V |2
i=1
by assuming that the distance of a value in the distance matrix D appears 2ki times. Simi-
larly, B ONCHEV et al. [9] also introduced information indices
(G)
X
W
ID = W log(W ) iki log(i), (22)
i=1
and
(G)
X iki i
ID
W
(G) = log , (23)
W W
i=1
which are based on the W IENER-Index [8], i.e.,
(G)
X
W = iki . (24)
i=1
As an important result, it turned out that these indices possess a high discrimination power
[9, 32] to measure the structural information content of chemical graphs. Additionally, by
using these information measures, B ONCHEV et al. [9] proved some information inequal-
ities for special graphs, i.e., chain graphs, simple trees, and star graphs. Generally, infor-
mation inequalities can be very interesting for describing relations between the information
indices under consideration, e.g., to study the influence of a special information functional
on the resulting graph entropies. By considering certain information functionals for graphs
and the resulting parameterized information measures, such a study has been recently per-
formed in [13].
In [31], KONSTANTINOVA et al. introduced further information indices which are based
on graph distances. By defining the quantity
|V |
X
d(vi ) = d(vi , vj ), (25)
j=1
the entropy measure

|V |
X d(vi , vj ) d(vi , vj )
ID (vi ) = log , (26)
d(vi ) d(vi )
j=1
was obtained. In contrast to the previous shown distance-based information indices for
characterizing a graph G, this measure represents the information distance of the vertex
vi V . Then, the information distance of a graph G was defined as [31]
|V |
|V |
X
ID (G) = ID (vi ). (27)
i=1
Also, by using the matrix S = (|Sj (vi , G)|)ij , i = 1, . . . , |V |, j = 1, . . . , (G) of j-

sphere [14, 26] cardinalities of a graph G, the same kind of information indices as just
mentioned were derived [31]:
(vi )
X |Sj (vi , G)| |Sj (vi , G)|
IS (vi ) = log , (28)
|V | |V |
j=0
and
|V |
X
ID (G) = IS (vi ). (29)
i=1
Finally, the following similarly inferred measures [31]
|V | |V |
X X d(vi , vj ) d(vi , vj )
ID (G) = log , (30)
2W 2W
i=0 j=0
and
|V |
i
X d(vi ) d(vi )
ID (G) = log , (31)
2W 2W
i=0
also represent information indices to calculate the structural information content of G. In
order to finalize our review on distance-based information indices, we express an entropy-
based molecular descriptor developed by BALABAN et al. [1]. Here, the main purpose
was to define novel information indices whose degree of degeneracy is comparably low.
Generally, a topological descriptor is called degenerated if for more than one structure the
index possesses the same value. By starting from the entities
|V | (vi )
X X
d(vi ) = d(vi , vj ) = jgj , (32)
j=1 j=1
BALABAN et al. first obtained the mean information on the magnitude of distances for each
vertex vi
(vi )
X jgj j
u(vi ) = log . (33)
d(vi ) d(vi )
j=1
The quantity gj indicates how many vertices there exist having distance j starting from vi .
Obviously, this notation simply expresses the cardinality of the j-sphere of a vertex vi , see
Equation (2). Based on Equation (33), the local information on the magnitude of distances
was defined by
w(vi ) = d(vi ) log(d(vi )) u(vi ). (34)
Now, by applying the well known formula developed by R ANDI C [42], a main result of [1]
were the information indices
|E| X 1
U (G) = [u(vi )u(vj )] 2 , (35)
+1
(vi ,vj )E
and
|E| X 1
W (G) = [w(vi )w(vj )] 2 , (36)
+1
(vi ,vj )E
where denotes the cyclomatic number of G, see [1]. As similarly shown in Equation (26)
and Equation (28), these measures result from applying an information-theoretic approach
locally (i.e., with respect to the vertices) [1]. Further, it turned out that the indices are
less degenerated than the most known topological indices known in chemical graph theory.
Further information indices which are based on graph distances can be found, e.g., in [3,
32, 48].
5. A Novel Information Functional:

Degree-Degree Associations
In this section, we define a novel entropy measure for finite, undirected and connected
graphs which is based on a special information functional. Generally, the idea to measure
the entropy of graphs by using vertex probabilities depending on an information functional
has been introduced in [13]. This procedure avoids the problem to determine vertex parti-
tions for obtaining a finite probability distribution. For constructing the mentioned informa-
tion functional, we use degree-degree associations of underlying shortest paths of the graph
in question. We start with the following definitions.
Definition 5.1. Let G GU C . We set Sj (vi , G) := {vaj , vbj , . . . , vzj }, 1 j (G),

1 i |V |. For vi V , we define the sets of shortest paths
P1j (vi ) := (vi , vaj 1 , vaj 2 , . . . , vaj j ), (37)

P2j (vi ) := (vi , vbj1 , vbj2 , . . . , vbjj ), (38)
.. ..
. .
Pkjj (vi ) := (vi , vzj1 , vzj2 , . . . , vzjj ). (39)
Definition 5.2. Let G GU C . We define the following degree sequences:
sj1 (vi ) := ((vi ), (vaj 1 ), (vaj 2 ), . . . , (vaj j )), (40)

sj2 (vi ) := ((vi ), (vbj1 ), (vbj2 ), . . . , (vbjj )), (41)
.. ..
. .
sjkj (vi ) := ((vi ), (vzj1 ), (vzj2 ), . . . , (vzjj )). (42)
We call these strings the property strings starting from the vertex vi to all other vertices
in G.
We want to emphasize that these property strings capture structural information of G. Now,
starting from Definition (5.3) that uses the degree-degree associations of the set of shortest
paths for a certain vertex vi , we define the following quantities.
Figure 2. An undirected and connected graph.
Definition 5.3. Let G GU C . For vi V , we define
G (vi , 1) = |(vi ) (va11 )| + + |(vi ) (vz11 )|, (43)

G (vi , 2) = |(vi ) (va21 )| + + |(vi ) (vz21 )| (44)
+ + |(vz21 ) (vz22 )|, (45)
.. ..
. .
G (vi , (G)) =|(vi ) (va(G)
1
)| + + |(va(G)
(G)1
) (va(G)
(G)
)| (46)
+|(vi ) (vz(G)
1
)| + + |(vz(G)
(G)1
) (vz(G)
(G)
)|. (47)
In Definition (5.3) the differences |(x) (y)| are called degree-degree associations.
By taking Definition (5.3) into account, we are now able to define a parameterized informa-
tion functional for measuring the entropy of G as follows.
Definition 5.4. Let G GU C . We define the information functional f (vi ) as

G (v G (v G (v
f (vi ) :=c1 i ,1)+c2 i ,2)++c(G) i ,(G))
,
ck > 0, 1 k (G), > 0. (48)
We want to remark that in practical applications the variable can be set to = e.
Definition 5.5. Let G GU C and let

PGf (V ) := (PfG (v1 ), PfG (v2 ), . . . , PfG (v|V | )), (49)
be the derived probability distribution by incorporating f . We define the entropy of G as

|V |
f (vi ) f (vi )
X
If (G) := P|V | log P|V | . (50)
(v ) (v )
i=1 j=1 f j j=1 f j
As a result, we obtained a novel family of graph entropy measures. We notice that

by varying the parameters ci and , one can weight structural properties, e.g., hubs for
determining the entropy of G. In order to get a better understanding about the meaning of
the final graph entropy measure, we state the following assertions.
k . The probability distribution
Theorem 5.1. Let G GR

maximizes the entropy If (G).
Proof. We start with a given k-regular graph. According to the definition (see Section (3.)),
k iff (v) = k v V . From this, we obtain
it holds G GR
s11 (vi ) = (k, k), (52)
s12 (vi ) = (k, k), (53)
..
.
s1k1 (vi ) = (k, k), (54)
..
.
sj1 (vi ) = (k, k, . . . , k), (55)
sj2 (vi ) = (k, k, . . . , k), (56)
..
.
sjkj (vi ) = (k, k, . . . , k), (57)
where 1 j (G). We note that sj (vi ) = (k, k, . . . , k) has j + 1 entries. But this results
in G (vi , 1) = 0, . . . , G (vi , j) = 0. Further, this implies f (vi ) = 0 = 1 and, finally,

1 1 1
=( , ,..., ). (59)
|V | |V | |V |
This completes the proof.
Corollary 5.2. Let K|V |,|V | be the complete graph with |V | vertices. The probability dis-
tribution
f K K K
PK |V |,|V |
(V ) := (Pf |V |,|V | (v1 ), Pf |V |,|V | (v2 ), . . . , Pf |V |,|V | (v|V | )), (60)
maximizes the entropy If (K|V |,|V | ).

The interpretation of Theorem (5.1) leads to the following observation: The given prob-
ability distribution maximizes the entropy of a graph G if all vertices are topologically
equivalent. From this, we conclude that the entropy of G decreases with an increasing di-
versity regarding the neighborhood of the vertices. We want to emphasize that this result
clearly depends on the considered entropy measure. For example, the application of the
classical graph entropy measure IORB [43] results in IORB (K|V |,|V | ) = 0.
5.1. Numerical Example
In order to illustrate the above given definitions, we first consider Figure (2). In the
following, we only exemplarily calculate the just defined quantities for the vertex v1 because
the calculation for the remaining vertices can be done analogously. We yield:
P11 (v1 ) = (v1 , v2 ), (61)

P21 (v1 ) = (v1 , v6 ), (62)
P12 (v1 ) = (v1 , v2 , v3 ), (63)
P22 (v1 ) = (v1 , v2 , v5 ), (64)
P32 (v1 ) = (v1 , v6 , v5 ), (65)
P42 (v1 ) = (v1 , v6 , v7 ), (66)
P13 (v1 ) = (v1 , v2 , v3 , v4 ), (67)
P23 (v1 ) = (v1 , v2 , v5 , v4 ), (68)
P33 (v1 ) = (v1 , v6 , v5 , v4 ), (69)
s11 (v1 ) = (2, 3), (70)

s12 (v1 ) = (2, 3), (71)
s21 (v1 ) = (2, 3, 2), (72)
s22 (v1 ) = (2, 3, 3), (73)
s23 (v1 ) = (2, 3, 3), (74)
s24 (v1 ) = (2, 3, 1), (75)
s31 (v1 ) = (2, 3, 2, 2), (76)
s32 (v1 ) = (2, 3, 3, 2), (77)
s33 (v1 ) = (2, 3, 3, 2), (78)
and
G (v1 , 1) = 1 + 1 = 2, (79)
G
(v1 , 2) = 1 + 1 + 1 + 0 + 1 + 0 + 1 + 2 = 7, (80)
G
(v1 , 3) = 1 + 1 + 0 + 1 + 0 + 1 + 1 + 0 + 1 = 6, (81)
G
(v1 , 4) = 0. (82)
Hence, we get
f (v1 ) := 2c1 +7c2 +6c3 . (83)
If we perform these steps for every vertex in G, we obtain the special entropy measure
2c1 +7c2 +6c3

2c1 +7c2 +6c3
2c1 +4c2 +6c3
2c1 +4c2 +6c3

If (G) = log log
DG DG DG DG
c1 +4c2 +5c3 +11c4
c1 +4c2 +5c3 +11c4
c1 +3c2 +9c3
c1 +3c2 +9c3

log log
DG DG DG DG
c1 +6c2
c1 +6c2
3c1 +3c2 +5c3
3c1 +3c2 +5c3

log log
DG DG DG DG
2c1 +5c2 +6c3 +10c4
2c1 +5c2 +6c3 +10c4

log , (84)
DG DG
where
DG := 2c1 +7c2 +6c3 + 2c1 +4c2 +6c3 + c1 +4c2 +5c3 +11c4 + c1 +3c2 +9c3
+ c1 +6c2 + 3c1 +3c2 +5c3 + 2c1 +5c2 +6c3 +10c4 . (85)
6. Summary and Conclusion

In this chapter, we first reviewed the most known information indices to characterize
chemical structures by calculating their structural information content. Then, we gave a
short overview on the usage of molecular descriptors which are often used in mathematical
chemistry and also on approaches in chemometrics. Here, we used information indices
(measures) to quantify structural complexity of graphs. However, the main contribution
of the chapter was to define a novel information functional that is based on degree-degree
associations. This led us to a special information measure for graphs (graph entropy) and
we proved that maximum entropy is obtained for a fully connected and regular network.
To evaluate the measure by using real chemical structures and to explore its mathemat-
ical properties in depth will be a part of our future research. As a final remark, we note
that the mergence of statistics, information theory and graph theory bears a considerable
potential [22, 41] that is largely unexplored so far.
Acknowledgements
We thank Danail Bonchev and Abbe Mowshowitz for fruitful discussions. This work
was supported by the COMET Center ONCOTYROL and funded by the Federal Ministry
for Transport Innovation and Technology (BMVIT) and the Federal Ministry of Economics
and Labour/the Federal Ministry of Economy, Family and Youth (BMWA/BMWFJ), the
Tiroler Zukunftsstiftung (TZS) and the State of Styria represented by the Styrian Business
Promotion Agency (SFG) [and supported by the University for Health Sciences, Medical
Informatics and Technology and BIOCRATES Life Sciences AG].
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Chapter 19
TOPOLOGICAL INDICES OF NANOSTRUCTURES
Ali Reza Ashrafi*

Department of Mathematics, Faculty of Science, University of Kashan,
Kashan 87317-51167, I. R. Iran
Abstract
Let be the class of finite graphs. A topological index is a function Top from into real
numbers with this property that Top(G) = Top(H), if G and H are isomorphic. Obviously, the
number of vertices and the number of edges are topological index. The distance d(u,v) :=
dG(u,v) between two vertices u and v is the length of a shortest (u,v)-path. The Wiener index is
the first reported distance-based topological index and is defined as half sum of the distances
between all the pairs of vertices in a molecular graph. In the last decade or so, various
topological indices have been introduced. Recently many authors have devoted their studies to
this subject and many results have been published. In this lecture we restrict ourselves to the
modeling of nanostructures by chemical indices.
Keywords: Molecular Graph, Nanostructure, Topological index.
1. Introduction
A nanostructure is an object of intermediate size between molecular and microscopic
structures. It is a product derived through engineering at the molecular scale. The most
important of these new materials is carbon nanotubes [1-3]. They have remarkable electronic
properties and many other unique characteristics. For these reasons it is of interest to study
the mathematical properties of these materials.
Mathematical chemistry is a branch of theoretical chemistry for discussion and
prediction of the molecular structure using mathematical methods without necessarily
referring to quantum mechanics [4-6]. Chemical graph theory is a branch of mathematical
chemistry which applies graph theory to mathematical modeling of chemical phenomena [7].
This theory had an important effect on the development of the chemical sciences. The
*
E-mail address: ashrafi@kashanu.ac.ir
500 Ali Reza Ashrafi
pioneers of the chemical graph theory are Alexandru Balaban, Ivan Gutman, Haruo Hosoya,
Milan Randic and Nenad Trinajsti. Nowadays, hundreds of researchers work in this area
producing thousands of articles annually.
A molecular graph is a simple graph such that its vertices correspond to the atoms and
the edges to the bonds. Note that hydrogen atoms are often omitted. By IUPAC terminology,
a topological index is a numerical value associated with chemical constitution purporting for
correlation of chemical structure with various physical properties, chemical reactivity or
biological activity [8-14].
Diudea was the first scientist to study the mathematical properties of nanostructures [15-
21]. In some research papers he computed some topological indices of nanotubes and
nanotori. After leading works of Diudea, one of us (ARA) and their co-authors continued this
problem to compute some topological indices of nano-materials [22-44]. In recent years,
several papers on computing Wiener, PI, Szeged, Schultz and Balaban indices of
nanostructures have been published, and we encourage interested readers to consult also these
papers for background materials as well as basic computational techniques [45-59].
2. Definitions
In this section we describe some definitions which will be kept throughout. A graph is a
collection of points and lines connecting a subset of them. The points and lines of a graph
also called vertices and edges of the graph, respectively. If e is an edge of G, connecting the
vertices u and v, then we write e = uv and say "u and v are adjacent". A path P in a graph G is
a sequence v1, v2, , vr of vertices such that vi and vi+1 are adjacent, 1 i r-1. A path graph
is a graph consisting of a single path. A connected graph is a graph such that there exists a
path between all pairs of vertices. The distance d(u,v) = dG(u,v) between two vertices u and v
is the length of a shortest (u,v)-path in G.
Let G be a graph. The vertex and edge sets of G are denoted by V(G) and E(G),
respectively. A graph H is called a subgraph of G if V(H) V(G) and E(H) E(G). A cycle
graph Cn of order n is a graph with V(G) = {v1, v2, , vn} and E(G) = {v1v2, v2v3, , vn-1vn,
vnv1}. An acyclic graph or tree is a graph without a subgraph isomorphic to cycle graphs.
Two graphs which contain the same number of graph vertices connected in the same way
are said to be isomorphic. Formally, two graphs G and H are said to be isomorphic if there is
a one-to-one and onto function f: V(G) V(H) such that uv E(G) if and only if f(u)f(v)
E(H).
Let be the class of finite graphs. A topological index is a function Top from into real
numbers with this property that Top(G) = Top(H), if G and H are isomorphic. Obviously, the
number of vertices and the number of edges are topological index. The Wiener index is the
first reported distance based topological index and is defined as half sum of the distances
between all the pairs of vertices in a molecular graph. In the last decade or so, various
topological indices are introduced.
Let G be a connected graph and e = uv be an edge of G. The number of vertices of G
whose distance to the vertex u is smaller than the distance to the vertex v is denoted by nu(e).
Analogously, nv(e) is the number of vertices of G whose distance to the vertex v is smaller
than u. Suppose x is a vertex of the graph G. The distance between e and x is equal to d(x,e) =
min{d(u,x) , d(v,x)}. Then mu(e) is the number of edges of G whose distance to the vertex u is
Topological Indices of Nanostructures 501
smaller than the distance to the vertex v. Analogously, mv(e) is the number of edges of G
whose distance to the vertex v is smaller than the distance to the vertex u. Note that edges
equidistant to u and v are not counted.
The vertex Szeged index is another topological index which is introduced by Ivan
Gutman [12]. It is defined as the sum of [nu(e) nv(e)], over all edges of a graph G. The edge
Szeged index of G is a recently proposed topological index defined as the sum of [mu(e)
mv(e)], over all edges G. The vertex and edge Szeged indices of the graph G are denoted by
Szv(G) and Sze(G), respectively. Therefore,
Sz v (G) nu (e) nv (e) and Sz e (G) mu (e) mv (e)

e e
Motivated by the success of the vertex Szeged index, Padmakar Khadikar [10,11]
proposed a seemingly similar molecular structure descriptor, that in what follows we call the
edge-PI index. In analogy with definition of the vertex Szeged index the edge-PI index is
defined as PI e (G) [m
e
u (e) mv (e)]. Quite recently the vertex-version of the PI index
was also considered [14]. It is defined as PI v (G ) [n

e
u (e) nv (e)] and named the
vertex-PI index of G. There is an evident symmetry between the vertex and edge version of
PI index, as well as the vertex and edge version of Szeged index. For this symmetry, it is
reasonable to examine some important classes of nanostructures under these topological
indices.
3. Edge and Vertex PI Indices of Some Nanostructures

In this section the edge-PI index of the molecular graph of some nanostructures are
computed. Suppose G is a graph with edge set E = E(G) and f = uv. Define N(f) = |E| (mu(f)
+ mv(f)). Then
PI(G) = |E|2 fE N(f) (1)
We say that e = xy is parallel to f = uv if d(x,f) = d(y,f). In this case, we write e || f.

Therefore, for computing the PI index of G it is enough to calculate N(f), the number of
parallel edges to f, for every f E.
If T is an acyclic graph containing n vertices then PI(T) = (n-1)(n-2). In particular, PI = 0,
for acyclic graphs when n = 1 and 2. Moreover, if Kn denotes a complete graph with n
vertices then PI(Kn) = n(n-1)(n-2). We now investigate an important property of the edge PI
index.
Result 1
Let G be a connected graph with exactly m edges. Then PI(G) m(m1) with equality if
and only if G is a cycle of odd length or an acyclic graph.
Proof
Suppose e = uv is an edge of G. It is clear that nu(e) + nv(e) + N(e) = m and so PI(G) = m2

eE N(e). But N(e) 1 and hence eE N(e) eE 1 = m. Therefore, PI(G) = m2
eEN(e) m2 m = m(m1). We now assume that PI(G) = m(m1). By Result 1, it is
enough to consider non-acyclic graphs. Thus G has a cycle C of minimum length k, k 3. If
there exists an edge e for which N(e) > 1 then eE N(e) > m and so PI(G) < m(m1), which
is a contradiction. Hence for every edge e, N(e) = 1. Suppose C = x1x2, x2x3, , xk-1xk, xkx1.
We now consider two cases that k is odd or even.
Case 1.
k is even. Suppose f = x1x2 is an edge of C. Consider the edge g = xk/2+1xk/2+2. Since C has
minimum length, d(g,x1) = d(g,x2) = k/21. Thus, g is equidistant from both end of the edge f
and hence N(f) 2, a contradiction.
Case 2.
k is odd. Suppose f = x1x2 and v = x2+(k-1)/2. If deg(v) > 2 then we can choose an edge g =
uv, in which u is distinct from xis. Hence d(g,x1) = d(g,x2) = (k1)/2, which is impossible.
Hence deg(x1) = 2. Using a similar argument, we can see that for any i, 2 i k, deg(xi) = 2.
But G is connected, so G = C, as desired.
Conversely, if G is a tree then by Result 1, PI(G) = m(m1), in which m = |E(G)|. Also,
in every cycle G with odd length k, we have PI(G) = m(m1), which completes the proof.
We now consider the molecular graph T(h) constructed from a phenylene with h six-
membered rings in which each four-membered ring in the phenylene is replaced by a linear
array consisting of k, k = 4, 7, 10, ..., four-membered rings, Figure 1.
Figure 1. The graph of linear phenylenes.
Suppose e is an arbitrary edge of the graph of Figure 1. Then PI(T) = |E|2 eE N(e).
But |E(T)| = 6h + (h1)(3k1) and so PI(T) = 36h2 + (h1)2(3k1)2 + 12h(h1)(3k1) eE
N(e). Therefore, for computing the PI index of T, it is enough to calculate N(e), for every e
E. To calculate N(e), we consider three cases that e is vertical, horizontal or oblique. If e is
horizontal or oblique then N(e) = 2 and for vertical edges we have N(e) = hk + h k + 1.
Thus,
PI(T) = 36h2 + (h1)2(3k1)2 + 12h(h1)(3k1)

2[6h-2+2(h1)(k1)] (hk+hk+1)2.
If we put k=0 in the last formula, then we obtain the PI index of polyacenes which is
computed before by Khadikar, Karmarkar and Varma [60]. Therefore, we prove that:
Result 2
Let T be the chemical graph of the linear phenylene with h six-membered rings in which
each four-membered ring in the phenylene is replaced by a linear array consisting of k, k = 4,
7, 10, ..., four-membered rings. Then
PI(T) = 36h2 + (h1)2(3k1)2 + 12h(h1)(3k1)

2[6h2+2(h1)(k1)] (hk+h-k+1)2
In particular, the PI index of polyacenes with h hexagons is 24h2. Vukievi and

Trinajsti [61] obtained formulae for Wiener indices of a class of pericondensed benzenoid
graphs consisting of one, two and three rows of hexagons of various lengths. They introduced
the graph G(m,n) to be the pericondensed benzenoid graph given by Figure 2, in which m and
n are positive integers. Here we continue this study to calculate the PI index of these chemical
graphs. Without loss of generality, we can assume that n m.
Figure 2. A pericondensed benzenoid graphs consisting of two rows of n and m hexagons, m n.
It is easy to see that G(m,n) has exactly 5n + 3m + 2 edges. Suppose A and B are the set
of all vertical and oblique edges. To compute the size of A, we notice that there are two rows
of vertical edges. In the first row, N(e) = n+1 and in second N(e) = m+1. Thus eA N(e) =
(m+1)2 + (n+1)2. To compute eB N(e), we define:
{ Ek , E2n k 1 , E4n k 3 } k is even and 4 k 2m 2

{ E , E k is odd and 1 k 2m 1
k 2n k 1 , E4n k 1 }
Bk = .
{ Ek , E2n k 1 } k 2 or (k is even and 2m 4 k 2n)

{ Ek , E2n k 1 } k is odd and 2m 1 k 2n - 1
It is easy to see that the collection P = {B1, B2, , B2n} is a partition for B and if we
define X = 1 i 2n & |Bi| = 3 Bi and Y = 1 i 2n & |Bi| = 2 Bi then eB N(e) = eX N(e) + e Y
N(e) = e X 3 + e Y 2 = 3|X| + 2|Y|. Since |X| = 6m and |Y| = 4(n m), eB N(e) = 3|X| +
2|Y| = 10m + 8n. Therefore, PI(G(m,n)) = 8m2 + 24n2 + 30mn + 10n + 2. So we prove the
following result:
Result 3
If n m then PI(G(m,n)) = 8m2 + 24n2 + 30mn + 10n + 2.

We now present a computational method for computing PI index of fullerenes. Fullerene
was discovered for the first time in 1985 [62,63]. Fullerenes are carbon-cage molecules in
which a large number of carbon atoms are bonded in a nearly spherically symmetric
configuration. Let p, h, n and m be the number of pentagons, hexagons, carbon atoms and
bonds between them, in a given fullerene F. Since each atom lies in exactly 3 faces and each
edge lies in 2 faces, the number of atoms is n = (5p+6h)/3, the number of edges is m =
(5p+6h)/2 = 3/2n and the number of faces is f = p + h. By the Eulers formula n m + f = 2,
one can deduce that (5p+6h)/3 (5p+6h)/2 + p + h = 2, and therefore p = 12, v = 2h + 20 and
e = 3h + 30. This implies that such molecules made up entirely of n carbon atoms and having
12 pentagonal and (n/2 10) hexagonal faces, where n 22 is a natural number equal or
greater than 20.
Using Table 1, the PI indices of the fullerene graphs of C24, C36, C48, C60, C72, C84, C96,
C108, C120 and C132 are computed as PI(C24) = 996, PI(C36) = 2280, PI(C48) = 4188, PI(C60) =
6672, PI(C72) = 9816, PI(C84) = 13512, PI(C96) = 17856, PI(C108) = 22848, PI(C120) = 28488
and PI(C132) = 34776.
Result 4
For n 12, PI(C12n) = 324n2 516n + 1248.
Proof
From Figure 3, one can see that there are six types of edges of the fullerene graph C12n.
These are the first and second types of vertical edges (I, II), the first and second types of
oblique edges (III, IV) and the edges of central and outer hexagons (V,VI). In the following
table the values of N(e) for these type of edges are computed.
By Table 2 and equation given the first paragraph of this section, the proof is complete.
Our calculations for working with topological indices of graphs are done by GAP
SYSTEM. The method described in last result is quite general, and can be extended to solve
several problems in computational chemistry.
Table 1. The Values of mu(e) and mv(e) for some Exceptional Cases of C12n
Edges C24 C36 C48 C60 C72 # edges
Type V and VI
15,15,6 20,20,14 25,25,22 27,27,36 29,29,50 12
Edges
Type I Edges - 20,23,11 35,25,12 48,29,13 31,63,14 12
Type IV Edges 12,15,9 21,19,14 20,33,19 20,48,22 20,66,22 12(n-3)
35,42,13 39,55,14
Type II Edges - - 30,30,12 42,35,13 47,47,14 6(n-2)
55,39,14
24,78,6
60,24,26
24, 42,6 42,60,6
Type III Edges 24,24,6 42,42,6 12
42,24,6 60,42,6
60,24,26
78,24,6
Edges C84 C96 C108 C120 C132 # edges
Type V and VI
29,29,68 29,29,86 29,29,104 29,29,122 29,29,140 12
Edges
Type I Edges 79,31,16 31,97,16 115,31,16 133,31,16 151,31,16 12
102,20,2
Type IV Edges 84,20,22 120,20,22 138,20,22 156,20,22 12(n-3)
2
41,122,17 41,140,15
41,104,17 53,109,18 127,53,16
86,41,17
70,41,15 91,53,18 95,66,19 113,66,17
53,75,16
51,60,15 66,79,17 81,81,18 81,97,18
Type II Edges 64,64,16 6(n-2)
60,51,15 79,66,17 66,95,19 97,81,18
75,53,16
41,70,15 53,91,18 109,53,18 66,113,17
41,86,17
41,104,17 122,41,17 53,127,16
140,41,15
24,168,4
24,150,6
24,132,6 42,150,4
24,114,6 42,132,6
24,96,6 42,114,6 60,132,4
42,96,6 60,114,6
42,78,6 60,96,6 78,114,4
60,78,6 78,96,6
Type III Edges 60,60,6 78,78,6 96,96,4 12
78,60,6 96,78,6
78,42,6 96,60,6 114,78,4
96,42,6 114,60,6
96,24,6 114,42,6 132,60,4
114,24,6 132,42,6
132,24,6 150,42,4
150,24,6
168,24,4
Table 2. The Values of N(e) for Six Types of Distinguishable Edges
Edges #N(e) No Edges #N(e) No

Type I Edges 22 6 17
Type II Edges 6 6(n2) 18
Type III Edges 16 24 19
20
Type IV
22 (n1) times 12
Edges
20
Type V and VI 18n58 12
19
18
17
This software was constructed by GAPs team in Aachen [64]. Here, GAP stands for
Groups, Algorithms and Programming. The name was chosen to reflect the aim of the
system, which is a group theoretical software for solving computational problems in group
theory. Recently, after including GRAPE into GAP it is possible to apply this computer
algebra system to solve problems in graph theory.
A typical edge of
central hexagon
A second type
oblique edge
A second type
vertical edge
A first type
oblique edge A first type
vertical edge
A typical edge of
outer hexagon
Figure 3. The Fullerene Graph C12n.
The last years have seen a rapid spread of interest in the understanding, design and even
implementation of graph theoretical algorithms. These are gradually becoming accepted both
as standard tools for a working group theoretician, like certain methods of proof, and as
worthwhile objects of study, like connections between notions expressed in theorems. GAP is
a free and extensible software package for computation in discrete abstract algebra. The term
extensible means that you can write your own programs in the GAP language, and use them
in just the same way as the programs which form part of the system (the library). More
information on the motivation and development of GAP to date, can be found on GAP web
page that you find on http://www.gap-system.org.
We apply this software to compute, edge-PI, vertex-PI, edge-Szeged and vertex-Szeged
indices of molecular graphs. To do this, we first draw the molecule by HyperChem [65]. Then
compute the distance matrix of its molecular graph by TopoCluj [66], a software constructed
by Diudea and his team in Cluj. Finally, we prepare a GAP program for computing the vertex
PI and Szeged index of the molecular graph under consideration. Our programs are accessible
from the authors upon request.
e10
e5
e1
e4
e6
e4
e2
e3
e8 e7
Figure 4. The Fullerene Molecule F24n + 12 Containing 24n + 12 Carbon Atoms.
We now compute the vertex PI index of a new type of fullerenes with 24n + 12 carbon
atoms. At first, we present a simple formula for computing vertex PI index of molecular
graphs. Suppose G is a molecular graph, E = E(G) and V = V(G). Define N(e) = |V| (nu(e)
+ nv(e)). Then
PIv(G) = e uv [|V | N ( e )] | V || E | e uv N ( e ) .
By this equation, one can compute the vertex PI index of every fullerene graphs by
computing the number of vertices co-distant from the ends of a given edge e of F. It is
possible to prepare a GAP program for computing the vertex PI index of graphs. To do this,
we assume that G is an n atom molecular graph with adjacency matrix A and distance matrix
D. The distance matrix D = [dij] of G is another n n matrix defined by dij is the length of a
minimum path connecting vertices i and j, i j, and zero otherwise.
To compute the vertex PI index of G, we first draw it by HeperChem and then apply
TopoCluj to compute the adjacency and distance matrices of G. We now upload A and D in
our GAP program to compute the vertex PI index of G.
From Figure 4, one can see that there are ten types of edges of fullerene graph F = F24n +
12. In the following table, the value of N(e) is computed for each case.
Table 3. The Number of Co-Distance Vertices of F for Edges e1, , e10.
The Number of Similar

Edge Types N(e)
Edges
E1 0 6(5n-22)
E2 2 12
E3 4 12
E4 6 24
E5 12 24
E6 14 24
E7 16 6(n-3)
E8 24 12
E9 56 12
E10 76 24
By this table and Figure 4, one can prove the following result:
Result 5
If F denotes the fullerene molecule of Figure 4, then the vertex PI index of F is computed
as follows:
PIv(F) = 864n2 + 2832n 3144.
4. Edge and Vertex Szeged Indices of Some Nanostructures

In this section we consider the problem of computing edge and vertex Szeged indices of
molecular graphs into consideration. We begin with nanotubes and nanotori covered by C4.
We first introduce some concepts. Suppose G and H are graphs. The Cartesian product G H
of graphs G and H has the vertex set V(GH) = V(G)V(H) and (a,x)(b,y) is an edge of GH
if a = b and xy E(H), or ab E(G) and x = y. It is well known that the Cartesian product is
commutative and associative, |V(GH)| = |V(G)||V(H)| and |E(GH)| = |E(G)||V(H)| +
|V(G)||E(H)|. On the other hand, if (a,x) and (b,y) are vertices of G H then
dGH((a,x),(b,y)) = dG(a,b) + dH(x,y), see [67] for details. Consider the path and cycle graphs
with n vertices. Then R = PnCm and S = CnCm are nanotubes and nanotori with mn vertices
covered by C4. On the other hand, |E(R)| = 2mn m, |E(S)| = 2mn, Sz(Pn) = n(n2 1)/6 and
m3
m is even
Sz( Cn ) 4 .
m( m 1 )
2
m is odd
4
In [68], the authors proved that the Wiener and Szeged indices of the Cartesian product of
two graphs are given as Sz(GH) = |V(G)|3Sz(H) + |V(H)|3Sz(G). Then by these formulae and
above calculations, one can see that
Result 6
The vertex Szeged index of nanotubes and nanotori covered by C4 are computed as
follows:
nm 3 (5n 2 2)
m is even
Sz ( R) 12 ,
nm(5n m 6n m 3n 2m ) m is
2 2 2 2 2
odd
12
n3m3
n & m are even
23 3
2n m 2m n 2m n m n mn
3 2 2 3 3 3
n & m are odd
Sz ( S ) 3 3 4 .
2 n m 2 n 3 2
m n 3
m
n is even & m is odd
4
2n 3 m 3 2n 2 m 3 nm 3
m is even & n is odd
4
.
We now present a powerful method for computing vertex and edge Szeged indices of
molecular graphs. To explain our method, we consider the molecular graph a water-soluble
polyaryl ether dendrimer G[n], Figure 5.
Let G be graph. A subgraph S of G is called convex if for each vertex x,y V(H) there
exists no shortest path in G from x to y which involves a vertex w V(G) V(H). Define
H[n] to be the graph constructed from G[n] by deleting almost on half of its vertices and
edges, Figure 5. In [69], the authors proved that if {Fi}1 i k is a partition of E(G) such that for
each i, 1 i k, G Fi is a two component graph with convex components then W(G) = 1 i
k |V(GFi(1))|.|V(GFi(2))|, where GFi(1) and GFi(2) are two components of G Fi.
Figure 5. The Molecular Graph of G[4].
If we omit an edge outside hexagons of G[n] then the components of new graph are
easily convex. On the other hand, the graphs obtained from G[n] by deleting two non-
adjacent parallel edges of a hexagon are also convex. These subsets constitute a partition
{Fi}1ik of E(G) and H[n] = G[n] Fi has the required properties of the mentioned result.
Define gn = |V(G[n])| and hn = |V(H[n])|. Then
& gn = 2hn + 16 = 5 2n+3 4.
Suppose a* = a(gn a). Then we have:
Result 7
The Wiener and vertex-Szeged indices of G[n] are computed as follows:
W(G[n]) = 502 3440.4n + 8000.n.4n + 28000.n.2n + 8548.2n

Sz(G[n]) = 726 + 11200n4n + 3920.n.2n 3600.4n + 11592.2n
Proof
Consider a hexagon C6 in H[n] G[n]. From Figures 68, one can see that G[n] {e1,e4}
has exactly two components, both of them are convex and one of the components has h 3
vertices, 0 n. We notice that the number of such hexagons is 2n-. Similarly, G[n]
{e2,e5} and G[n] {e3,e6} have also two components, both of them are convex and one of
their components has h-1 + 5 vertices, 0 n. Suppose e is an edge outside cycles of
G[n]. Then G[n] e has exactly two convex component. One of these components has h, h
+ 1 or h + 2 vertices and the number of such edges is 2n-, 1 n. For = 0, one can see
that there is 2n hexagons and G[n] {e1,e4}, G[n] {e2,e5} and G[n] {e3,e6} have exactly
two components, where both of them are convex and one of them has 7 vertices. There is a
similar argument for other edges of G[n] and so there is a partition {Fi}1ir in which G Fi
has two convex components. Therefore,
n 1
eH[n] m(e) i 0 2i [(h n i 3) * 2(h n i1 5)*] 2n.3.(g n 7 ) *
i 1 2i [(h n i 2) * (h n i 1) * (h n i )*]
n
2n [2(g n 1) * (g n 2) * (g n 4)*]
Figure 6. The Molecular Graph of H[4].
Figure 7. The Position of Edges in a Hexagon.

Figure 8. The Core of G[n].
On the other hand, if S is the core of G[n], then we have:
*
g
eS
m(e) 2[h*n (h n 1) * (h n 2) * 3(h n 5)*] n .
n
Therefore, W(G[n]) = 2eH[n]m(e) + eSm(e) = 502 3440.4n + 8000.n.4n +

28000.n.2n + 8548.2n. This completes the first part of the result. To prove the second part, we
choose the set F = {uv}, where uv is an edge outside hexagons of G[n]. By definition of the
Szeged index and partition of edges described above, nu(e)nv(e) = |V(GF(1))|.|V(GF(2))|.
Similarly, if F = {uv,ab} then nu(e)nv(e) = na(e)nb(e) = |V(GF(1))|.|V(GF(2))|. So, by a
similar argument as above,
n 1
euvE(H[n]) n u (e)n v (e) 2i 0 2i[(h n i 3) * 2(h n i 1 5)*] 2n 1.3.(g n 7 ) *
i 1 2i [(h n i 2) * (h n i 1) * (h n i )*]
n
2n [2(g n 1) * (g n 2) * (g n 4)*],
*
g
e uvE(S) n u (e) n v (e) 2[h*n (h n 1) * (h n 2) * 3.2(h n 5)*] n .
n
Therefore, Sz(G[n]) = 2e=uvE(H[n])nu(e)nv(e) + e=uvE(S)nu(e)nv(e) = 726 + 11200n4n +

3920.n.2n 3600.4n + 11592.2n, which completes our argument.
We now compute the Szeged index of the zig-zag polyhex nanotube T = TUHC6[p,q],
Figure 9(a). It is clear that T has exactly 2pq vertices and p(3q 1) edges. Suppose A and B
are the set of all vertical and oblique edges of T, respectively. Then Sz(T) = e=ijAni(e)nj(e) +
e=ijB ni(e)nj(e). We assume that Sz1(T) = e=ijA ni(e)nj(e) and Sz2(T) = e=ijB ni(e)nj(e). To
compute Sz(T), we first compute Sz1(T).
Suppose e = uv is an arbitrary vertical edge in the ith row, Figure 9(b). One can see that T
has exactly p vertical edges in each row and so there are 2pi vertices above the ith row, which
are all closer to v than u. Therefore,
Sz1(T) = e=ijA ni(e)nj(e) = = 2/3p3q(q2 1)

(a) (b)
Figure 9. (a) A zig-zag polyhex nanotube, (b) 2-Dimensional Lattice of T.
Figure 10. Oblique and Vertical Lines of T with p < q.
To calculate Sz2(T), we consider five separate cases that q p, p+1 < q < 2p, q = p+1, q
= 2p, q > 2p. We explain our method for computing summations which are needed for
calculating Szeged index of T. Without loss of generality, suppose e = x33x34. To calculate
the number of closer vertices to x34, we first draw two copies of 2dimensional lattice of T
and then cut e by an oblique line and pass a vertical line through x3(p+4). Then vertices closer
to x34 lie in the triangular region between those two lines. In general, to calculate ni(xi(i+1)), we
compute the number of vertices in the triangular or trapezoidal region, Figure 10, surrounded
by the vertical line passes through xi,p+i+2 and oblique line passes through eii = xiixi(i+1).
Suppose q p and eis = xis xi(s+1), eir = xir xi(r+1) are two arbitrary oblique edges of T,
Figure 10. Since T is bipartite, ni(xir) + ni(xi(r+1)) = ni(xis) + ni(xi(s+1)) = 2pq. So, it is sufficient
to consider one oblique edge in each zig-zag. So, ni(xii) = 1 + 2 + + q + q(p q + i 1) =
Tq + q(p q + i 1), where Tq = 1 + 2 + + q is the qth triangular number. And ni(xi(i+1)) =
2pq (Tq + q(p q + i 1)) = Tq + q(p i). Therefore,
Sz2(T) = e=ijB ni(e)nj(e) = 2p

=2p3q3 + 1/6pq3 1/6pq5
Using a similar argument as above we can compute the Szeged index of T in other cases
and we have:
Result 8
With above notations, we have:
8 3 3 2 3 1 3 1 5
3 p q 3 p q 6 pq 6 pq q p

5 p 6 43 p5 35 p 4 5 p3 1 p 2 q p 1
2 6 6 6 3

p3q3 p3q pq p 2 1 pq5 4 p 2 q 4
2 2 2 2
3 3 15 15 5 3
Sz (T ) .
5 8 1 4
pq3 p 2 q 2 p 4 p5q p 6 1
p 1 q 2 p
3 3 3 3 5
89 5 1
p6 p4 p2 q 2p
5 3 15
3 3 4 3 2 2 4 5 13 6
2 p q p q p p q p p q 2p
4
3 15 3 15
Figure 11. The One-Heptagonal Carbon Nanocone CNC7[4].
We end this section by computing edge Szeged index of one-pentagonal carbon

nanocones. One pentagonal carbon nanocones originally discovered by Ge and Sattler in
1994, [70]. These are constructed from a graphene sheet by removing a 60 wedge and
joining the edges produces a cone with a single pentagonal defect at the apex. The inclusion
of the heptagons in the hexagonal lattice leads to the appearance of negative curvature, Figure
11. The single sevenfold in the plain graphene lattice was theoretically studied in [71], but
this situation, unfortunately, has not been observed in the experiment yet. The heptagons were
observed in the nanotubes [72] and in the work [73] the magnetic properties of negatively
curved structures were calculated.
To simplify our argument, we assume that S = CNC7[n]. Two edges e = xy and f = uv of
a graph G are said to be co-distant if and only if d(x,u) = d(y,v), d(x,v) = d(y,u) and |d(x,u)
d(x,v)| = 1. The number of edges parallel to a given edge e = uv is denoted by N(e). Suppose
n denotes the number of edges in the boundary of S CNC 7 [n ] . Then n n 1 14
and 1 21 . So n 7 14n . On the other hand, there are 7n edges such that connect the
boundary of CNC 7 [n ] to the boundary of CNC 7 [n 1] . Thus
E(CNC7 [n]) n 7n E(CNC7 [n 1]) 7 21n E(CNC7[n 1])
Define x n E (CNC 7 [n ]) to find the recurrence relation x n 7 21n x n 1 . This

is a linear recurrence equation with x1 35, as initial condition. By solving this equation, we
have x n E (S ) (7 / 2)(3n 2 5n 2) . There are two types of edges in molecular graph
of S: one type of edges is those that are parallel to every edge of central heptagonal.
Suppose i , 1 i 7 , are edges of central heptagonal and i are their equidistant edges in
the boundary of S, respectively. For every i , there are n+1 co-distant edges toi. Another
type of edges in S are 2n edges which are located between every i and i+1. We denote these
2n edges in a fixed region with e1 x1 x2 , e2 x2 x3 , , e2 n x2 n x2 n1 . These are having
this property that N (e1 ) N (e2 n ), N (e2 ) N (e2 n1 ), N (en ) N (en1 ) , and so it is
enough to compute N (e 2 j 1 ) , for 1 j n .
From the molecular graph of S CNC 7 [n ] , one can see that there are n+1 edges which
are co-distant to i. Besides that there are (3/ 2)(n n) edges in the triangle region of S
2
which are parallel to i. So N ( i ) (1/ 2)(3n 5n 2) , therefore,

2
mai (i ) mbi (i ) (1/ 2)( E(S ) N (i )) (3/ 2)(3n2 5n 2) . By orthogonal cut

method of John, Khadikar and Singh, one can see that all of edges parallel to e 2 j 1 are co-
distant edges of e 2 j 1 for 1 j n . It now follows from the molecular graph of CNC 7 [n ] ,
there are n+j+1 edges parallel to e 2 j 1 and so N (e 2 j 1 ) n j 1 , 1 j n . Now we
are ready to state the main results of this paper.
Result 9
The edge Szeged index of one-heptagonal carbon nanocones is as follows:

2835 63091 71827 76111 12173 22603

Sz e n6 n5 n4 n3 n2 n 63 .
16 80 48 48 12 60
Proof
By above calculations, the values of mai ( i ) and mbi ( i ) , 1 i 7 , were computed.

Now we compute m x 2 j 1 (e 2 j 1 ) and m x 2 j (e 2 j 1 ) , 1 j n . By Figure 11 and
calculations given above, mx2 j1 (e2 j 1 ) mx2 j1 (e2 j 1 ) (n j 1) (2n 2 j 2) .

By solving this recurrence relation, we have mx2 j1 (e2 j 1 ) (3/ 2) j 2
(3n 3 / 2) j (n 1) . By substituting this value in
mx2 j1 (e2 j 1 ) mx2 j (e2 j 1 ) n j 1 E (S ) , we conclude that
m x 2 j (e 2 j 1 ) (7 / 2)(3n 2 5n 2) (3/ 2) j 2 (3n 5 / 2) j . Therefore,
7 n
Sze ( S ) mai ( i ).mbi ( i ).(n 1) mx2 j1 (e2 j 1 ).mx2 j (e2 j 1 ).(n j 1)
i 1 j 1
3
7.( (3n 2 5n 2)) 2 .(n 1)
2
n
3 3 3 5
7. j 2 (3n ) j n 1 . E ( S ) j 2 (3n ) j .(n j 1)
j 1 2 2 2 2
2835 63091 71827 76111 12173 22603
n6 n5 n4 n3 n2 n 63,
16 80 48 48 12 60
which completes the proof.

Between three methods given here, we believe that the computational method, which is a
combination of three softwares HyperChem, TopoCluj and GAP, is very efficient and can be
used for most parts of molecular graphs raised by nanostructures.
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Chapter 20
ON UNIFORM REPRESENTATION OF PROTEINS

BY DISTANCE MATRIX
M. Randia,*, M. Vrako a, M. Novi a and D. Plavi b

a
Laboratory for Chemometrics, National Institute of Chemistry, Hajdrihova 19, 61115
Ljubljana, Slovenia
b
Center for NMR, Institute Rudjer Bokovi, Zagreb, Croatia
Abstract
We outline an approach that associates with each protein a 2020 distance matrix, regardless
of protein size. In this way, for the first time, all proteins are represented uniformly. The
distance matrix is constructed from a lattice representation of proteins in which to each amino
acid is assigned a pair of integer Cartesian coordinates by averaging the coordinates for all
amino acids of the same kind. The new uniform representation of proteins is illustrated on
ND6 proteins of chimpanzee. The possibility of using this novel distance matrix for a uniform
nomenclature of proteins is also discussed.
Introduction
During the past 30 years Chemical Graph Theory has made impressive advancements in
mathematical representations and characterizations of molecules, which have led to a better
understanding of Molecular Structure-Molecular Property relationships and opened novel
approaches to the Quantitative Structure-Activity Relationships (QSAR) [1]. These
developments resulted in novel structure-property and structure-activity insights, such as
regularities in physico-chemical properties of isomers with the count of paths of length two
and length three [2-7]; characterization of molecular shape by quotients of the count of paths
and walks [8]; stability of the regression equations with orthogonalized molecular descriptors
[9-12]; characterization of pharmacophores [13-15]; characterization of aromaticity and local
aromaticity [16-23], to mention only a few achievements. During the last ten years some of
the tools of Discrete Mathematics that had been hitherto confined to molecules have been
*
E-mail address: mrandic@msn.com
522 M. Randi, M. Vrako, M. Novi et al.
generalized and applied to DNA [24-31], the secondary structure of RNA [32, 33], proteins
[34-40] and proteomics maps [41-53] and proteome [54, 55]. In this contribution we will
briefly review major directions in the Graph Theoretical Approach to Bioinformatics and will
outline a novel uniform representation of proteins.
Graphical Representation of DNA

One of the central topics of molecular biology is the comparative study of biopolymers,
in particular DNA, RNA and proteins. A straightforward, though computationally very
intensive, approach is to consider raw bio-sequences and develop suitable computer software
that allows pair-wise and multiple alignments of such sequences [56-58]. In 1983 Hamori and
Ruskin came to an ingenious idea and reported an alternative approach [59-61], which gave
birth initially to the graphical approach to DNA, and has led later to graphical representations
of RNA and proteins. In their graphical approach to DNA, they represented the four
nucleotide bases graphically in 3D by assigning to these four bases four directions in the (x,
y) plane and displaying each such step in the z-direction for each successive base. Between
mid-1990 and mid-2005 several alternative graphical representations of DNA were proposed
of which we will illustrate a few:
2D Lattice Representation of DNA
In Figure 1 we have illustrated a lattice representation of the first exon of the -globin
gene of human, lemur and opossum, by following the approach of Nandy [62], who assigned
x directions to G, A and y directions to C,T. Observe that (x, y) coordinates for all
nucleotides are integers, thus we refer to such systems as lattice representation.
Figure 1. Graphical representation of the coding sequences of the first exon of -globin gene of human,
lemur and opossum (from top to bottom).
While there is some loss of information accompanying such 2D representations of DNA,

a great advantage is the visual insight that they offer. Just by glancing at Figure 1 one can
On Uniform Representation of Proteins by Distance Matrix 523
immediately see that the first exon of the -globin gene of human and lemur are fairly similar,
while the first exon of the -globin gene of opossum is visibly different.
Highly Condensed Representation of DNA
In Figure 2 we illustrate a 2D representation of the first exon of the -globin gene of

human based on the magic square of Jeffrey [63, 64].
Figure 2. The first exon of human -globin gene as represented by the modified Chaos Game approach
of Jeffrey.
Jeffrey has adopted the Chaos Game representation of random sequences introduced
shortly earlier in mathematics by Barnsley [65] to be used for a graphical representation of
DNA. Jeffrey specified the polygon of the Chaos Game to be a square, to the four corners of
which he assigned the four nucleotide bases. He then started at the center of the square and
for the first base placed a spot half-way between the center and the corner having the label of
the first base. Then he continued by moving half-way towards the corner having the label of
the second base, and so on. The first exon of the -globin gene of human is thus represented
as a set of 92 spots within the interior of a square [66]. The magic square method as we
colloquially refer to the approach of Jeffrey, was intended and designed for very lengthy
DNA sequences, having between 10,000 100,000 bases, which is analogous to very lengthy
random sequences of Barnsley, which in this way produced fractal-like patterns [65].
We should add that in several publications we have explored with our collaborators use
of the magic square method on short and very short DNA sequences, including codons, and
have in this way arrived at the Table of Codons [35, 36], which offered a way to graphical
representation of proteins.
Spectral Representation of DNA
Finally we would like to briefly outline one of spectral representations of DNA. A simple
spectral representations of DNA are obtained by assigning to the four bases A, C, G, T
numerical values, such as 1, 2, 3, and 4, respectively [67-70]. In Figure 3 we have illustrated
the four-line spectral representation of the first exon of -globin gene of human.
Figure 3. Spectrum-like graphical representation of the coding sequence of the first exon of human -
globin gene.
Figure 4. Graphical illustration of the degree of alignment of the ND6 proteins of human and gorilla.
Such graphical representations still offer limited visual insights but their great advantage
is that they allow simple numerical manipulation with sequences, such as plotting the
difference of two sequences, which indicates visually the degree of alignment as illustrated in
Figure 4, and if necessary by considering differences of shifted sequences [71, 72].
In summary let us emphasize that the difference of computer-based studies of DNA and
graphical studies of DNA is that the former ones apply only to comparative studies of two or
more sequences; however, graphical approaches use graphical and sequence invariants for
characterization of DNA, which is analogous to the use of mathematical invariants, such as
the so-called topological indices [73-89] as molecular descriptors, allow one to characterize a
single DNA sequence, and thus make possible to compile a catalog DNA something that is
outside the scope of computer-based approaches.
Graphical Representation of the Secondary Structure of RNA
It is of interest in comparative studies of single-strand RNA to incorporate in the analysis

the RNA secondary structure. Until very recently it was customary to differentiate the free
four bases A, C, G and U from the same four bases when hydrogen-bonded in pairing A-U
and C-G, by using eight symbols: A, C, G, U and A', C', G' U'. However, recently Liao et al.,
[90] have shown that there is some loss of information inherent to such approaches, because
two different secondary structures can have the same eight-symbol representation. It has been
shown that when one differentiates pairings A-U and C-G from pairings U-A and G-C, which
lead to twelve symbol representation: A, C, G, U, A', C', G', U', A", C", G", U", one obtains
unique representations of secondary RNA structures [33].
Graphical Representation of Proteins
Graphical representations of proteins are of more recent time. The delay of about 25
years between the appearance of the first graphical representation of DNA and the first
graphical representation of proteins is undoubtedly due to the combinatorial complexity
associated with twenty factorials involving the ordering of twenty natural amino acids in
contrast to four factorials accompanying the ordering of four nucleotide bases. Readers
should consult the recent review on graphical representation of proteins for description of
various graphical models of proteins [91]. It suffices here to mention only that there are 2D
spectral representations of proteins [92, 93], highly compact 2D representations of protein
[36, 93], and star-like graph based-graphical representations [94]. Conspicuously missing
until very recently has been a lattice representation of proteins, the representation with the
most valuable visual insight! Because the uniform graphical representation of proteins
which is the topic of the present contribution is based on a lattice representation of proteins
[95], we will illustrate here the construction of a lattice representation of a protein. For this
purpose we have selected ND6 protein of Human, having 174 amino acids:
MMYALFLLSVGLVMGFVGFSSKPSPIYGGLVLIVSGVVGCVIILNFGGGYMGLMVFLI
YLGGMMVVFGYTTAMAIEEYPEAWGSGVEVLVSVLVGLAMEVGFVLWVKEYDGV
VVVVNFNSVGSWMIYEGEGSGFIREDPIGAGALYDYGRWLVVVTGWPLFVGVYIVIE
IARGN
In Figure 5 we show a 1010 part of the Cartesian grid on the periphery of which are the
locations of twenty amino acids arranged anticlockwise in decreasing order of their
abundance in proteins starting from leucine in the right lower corner. Thus (x, y) coordinates
of leucine are (5, 5), of serine are (5, 3), and so on.
Figure 5. The locations of 20 amino acids in the Cartesian coordinate system arranged anticlockwise
starting from leucine in decreasing order of their abundance in proteins.
In Table 1 using these coordinates we illustrate for the first dozen amino acids the
construction of lattice representation of ND6 protein of human, which is fully illustrated in
Figure 6, together with the lattice representation of ND6 protein of chimpanzee and opossum.
The starting amino acid is methionine (3, 5). Because the next amino acid is again
methionine , one proceeds to add the coordinates of the second amino acid (3, 5) to existing
arriving at (6, 10). The third amino acid tyrosine (Y) with coordinates (5, 5) leads to (
11, 15), etc. A glance at the three proteins in Figure 6 immediately shows considerable
similarity between the ND6 proteins of human and chimpanzee while the ND6 protein of
opossum shows quite different patterns. Thus just as has been the case with the 2D graphical
representation of DNA by Nandy of the first exon of -globin gene, here we arrived at lattice
representation of proteins with similar visual qualities.
Figure 6. Lattice representations of Human ND6, Chimpanzee ND6 and opossum.

Table 1. The (x, y) coordinates and cumulative coordinates for the first dozen amino
acids of lattice representation of human ND6 protein
cumulative cumulative
x y x y
origin 0 0
M 3 5 3 5
M 3 5 6 10
Y 5 5 11 15
A 5 1 6 16
L 5 5 1 21
F 5 1 6 22
L 5 5 1 27
L 5 5 4 32
S 5 3 9 35
V 5 3 14 32
G 5 1 19 31
L 5 5 24 36
Protein Distance Matrix

The problem that we want to consider is a mathematical characterization of the lattice
representation of proteins illustrated in Figure 6. One possibility, which has been already
outlined in the literature, is to use reduced matrices, which are based on graphical
representations of reduced lattice graphs. Here we will introduce distance matrices for lattice
representations of proteins in the following way: We will group each of twenty amino acids
present in a protein separately and find the corresponding average (x, y) coordinates. For
example, methionine appears ten times in human ND6 protein, at positions 1, 2, 14, 51, 63,
64, 73, 98, and 125, the (x, y) coordinates of which are:
(3, 5), (6, 10), (26, 38), (91, 29), (98, 38), (109, 49), (106, 54), (119, 49),
(208, 42), and (267, 23) respectively. The above sequence yields for the average
methionine coordinates (101.5, 33.7).
In Table 2 we have listed the average coordinates for the 18 amino acids present in
human ND6 protein and their average (x, y) coordinates, which are depicted at the upper part
of Figure 7, where we have added as 19th point the center of all amino acids, which is at
(185.7348, 16.9803).
Observe that representation of ND6 protein illustrated in Figure 7 is geometrical rather
than graphical, because all points have fixed (x, y) coordinates. Because of this we can
immediately construct 1818 distance matrix for the protein considered. In the general case
one will arrive in this way to a 2020 distance matrix, but ND6 is missing glutamine and
histidine. If one connects all points representing the 18 amino acids with the central point at
(185.7348, 16.9803) as illustrated in the lower part of Figure 7 one obtains a star graph, but
one of fixed geometry and fixed orientation (within the Cartesian coordinate system).
Table 2. The average Cartesian coordinates for amino acids of human ND6 protein
x y
A 197.71 8.57
R 309.00 16.00
N 232.25 1.25
D 268.33 4.33
C 86.00 30.00
E 269.83 11.17
G 166.00 19.79
I 192.67 10.50
L 131.94 26.76
K 153.50 32.50
M 101.50 33.70
F 141.70 25.50
P 158.20 16.20
S 132.50 29.70
T 181.67 25.67
W 278.50 11.00
Y 157.10 24.90
V 184.82 10.11
Figure 7. Amino acid map of human ND6 protein and corresponding embedded star graph of fixed
geometry. Observe use of different scale for the x and y coordinates.
Table 3. New (2020 symmetrical) distance matrix of human ND6 protein. Amino acids are ordered alphabetically based on their three
letter codes
A R N D C Q E G H I L K M F P S T W Y V
Ala 0 113 35 70 113 72 33 5 68 50 23 44 50 68 23 80 43 12
Arg 0 78 45 227 47 147 119 182 162 213 172 154 182 133 40 157 126
Asn 0 36 149 38 68 40 103 84 134 93 75 103 56 47 78 48
Asp 0 184 6 103 75 138 118 169 128 110 138 89 12 113 83
Cys 0 184 80 108 46 67 15 55 73 46 95 193 71 100
Gln 0
Glu 0 104 77 138 169 169 128 111 138 89 8 113 85
Gly 0 28 34 17 65 24 8 34 16 112 10 21
His 0
Ile 0 62 44 94 53 34 63 18 85 38 7
Leu 0 22 31 9 28 2 49 147 25 55
Lys 0 52 13 16 21 28 126 8 38
Met 0 41 59 31 80 178 56 86
Phe 0 18 10 39 137 15 45
Pro 0 29 25 120 8 27
Ser 0 49 147 25 55
Thr 0 97 24 15
Trp 0 122 93
Tyr 0 31
Val 0
In Table 3 we have listed the 2020 distance matrix for human ND6 protein, in which the
rows and columns belonging to glutamine and histidine are shown as empty.
The significance of the novel protein distance matrix is that regardless of the size of
protein, this approach results in uniform-size matrices for all proteins. This is the first time
that such uniform matrices have been constructed for proteins a novelty which is bound to
have useful consequences not only in comparative studies of proteins but also may be of
interest for auxiliary protein nomenclature as illustrated in the following section.
Uniform Auxiliary Nomenclature for Proteins

The condensed graphical representation of ND6 protein in Figure 7 offers a novel
approach to protein nomenclature.
In Table 4 we have listed the average coordinates for amino acids of human ND6 protein
relative to the coordinates of the center of the lattice representation (x0 = 185.7348, y0 =
16.9803) and the corresponding polar coordinates with respect to the overall center for
average for all amino acids. These coordinates determine the quadrant in which are individual
amino acids relative to the center (x0, y0), which allows one to determine the polar angle.
Table 4. The average coordinates for amino acids of human ND6 protein relative to the
coordinates of the center of the lattice representation (x0 = 185.7348, y0 = 16.9803) and
the corresponding polar coordinates with respect to the overall center for average for all
amino acids
xx0 yy0 R
A 11.9795 8.40887 14.6362 0.612026
R 123.2652 32.9803 127.6010 0.261432
N 46.5152 15.7303 49.1030 0.326102
D 82.5985 12.647 83.5611 0.151934
C 99.7348 13.0197 100.5810 0.129809
E 84.0985 5.8136 84.2992 0.069019
G 19.7348 2.8054 19.9332 0.141209
I 6.9319 6.4803 9.48923 0.751740
L 53.7936 9.7844 54.6762 0.179921
K 32.2348 15.5197 35.7763 0.448704
M 84.2348 16.7197 85.8781 0.195942
F 44.0348 8.5197 44.8514 0.191115
P 27.5348 0.7803 27.5459 0.028330
S 53.2348 12.7197 54.7333 0.234539
T 4.0681 8.6864 9.59182 1.132804
W 92.7652 5.9803 92.9578 0.064378
Y 28.6348 7.9197 29.7098 0.269831
V 0.9134 6.8732 6.93363 1.438680
Thus A, R, N, D, E, I, W are in the first quadrant; P, V are in the second quadrant and C,
G, L, K, M, F, S, T, Y are in the third quadrant, which allows amino acids in each quadrant to
be ordered in increasing magnitude of the polar angle . As a result the 18 amino acids of
human ND6 protein are ordered as:
WEDRNAIPVCGLFMSYKT
By adding at the end the nonexistent amino acids (alphabetically):
WEDRNAIPVCGLFMSYKTHQ
we obtained a particular ordering for this protein. Different proteins will show different
orderings of amino acids, but even though one does not expect often to find proteins having
the same ordering, in view that there are 20! possible arrangements of 20 letters in a
sequence, and in view of large number of different proteins, one should expect different
proteins having the same ordering. To distinguish such we can associate with each protein
also a 20 component vector that lists the radial distances of average amino acid centers from
the center of the lattice representation of the protein. For the above case, if we truncate the
radial magnitudes to integer parts only, one obtains:
(92, 84, 83, 127, 49, 14, 9, 27, 6, 100, 19, 54, 44, 85, 54, 29, 35, 9, 0, 0).
It is very unlikely that there will be two proteins that will have identical both the
alphabetic and the numerical sequence, and if there is overlap in numerical sequences, one
can always include the decimal part of radial distances to discriminate such cases. We
propose therefore as auxiliary notation of proteins the use of the alphabetic and the numerical
sequences as described above for human ND6. The proposal has an important advantage: any
person in any laboratory can easily construct the binary notation for proteins, and if such
binary labels are used by the rest of the protein community, one will facilitate search of
protein data.
Acknowledgments
This research was supported in part by the ARRS grant L1-7230 and grant P1-017
from the Ministry of High Education, Science and Technology of the Republic of
Slovenia. We thank Professor A. T. Balaban (Texas A&M University at Galveston, TX)
for numerous helpful comments that led to improvement of the manuscript. MR thanks
the Laboratory for Chemometrics, the National Institute of Chemistry, Ljubljana for
warm hospitality.
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Chapter 21
TIMISOARA SPECTRAL STRUCTURE ACTIVITY

RELATIONSHIP (SPECTRAL-SAR) ALGORITHM:
FROM STATISTICAL AND ALGEBRAIC
FUNDAMENTALS TO QUANTUM CONSEQUENCES
Mihai V. Putz1,* and Ana-Maria Putz2

1
2
Laboratory of Inorganic Chemistry, Timioara Institute of Chemistry of Romanian
Academy, Av. Mihai Viteazul, No.24, Timioara RO-300223, Romania
Abstract
With the present-day interest in correlating chemical structure with biological activity, the
quantitative structure-activity relationships (QSARs) are reviewed both on their fundamental
statistical and advanced algebraic frameworks allowing for the so- called Spectral-SAR
reformulation of the classical Multilinear regression in terms of data vectors and orthogonal
conditions, while being suited for inter-endpoint (computed activity) paths and maps of inter-
conversion. This way there is presented a novel, fresh and fruitful picture of regression
analysis aiming to closely approach the quantum interpretation of data and of ligand-receptor
interaction by means of systematic orthogonal and scalar (dot) product of either molecular
(chemicals or toxicants) descriptors between them and with the observed (recorded, measured)
activities. The resulted Spectral- or Quantum- SAR widely employs the present data as whole
vectors, to be associated in principle with the eigen-states in quantum Hilbert space, opens the
way for assigning a sort of wave function or wave packet for the congeneric active molecular
series rather than for a single molecule as used to be; this way the specific interaction may be
eventually modeled by structure (intrinsic)-metabolic (extrinsic) quantum rather than
quantitative correlation picture.
*
E-mail addresss: mvputz@cbg.uvt.ro, mv_putz@yahoo.com; Web: www.mvputz.iqstorm.ro. Tel: +40-256-
592633; Fax. +40-256-592620. (Author of correspondence)
540 Mihai V. Putz and Ana-Maria Putz
1. Introduction
In the last years, the worlds scientific research was focused on the so-called green
chemistry, which consists in the efforts to reduce or eliminate the use or production of
dangerous substances (with toxic potential) in synthesis, main stream and application of the
chemical compounds through pre-industrial or computational design [1].
As such, on all meridians, new specific organizations and laws of validation of the
entered compounds in environment or everyday and medical life have been raised: the first
taxonomical groups emerged in the United States by the Environmental Protection Agency [2]
followed by the European agency Umweltbundesamt (1997) and by Environment Canada
(1999). However, at the level of European Union, since the Strategy on Management of
Substances (SOMS, 2001) [3] program, the first step was made towards establishing by the
European Commission, on 23 October 2003, with the Registration, Evaluation, Authorization
and Restriction of Chemicals (REACH) norms establishing, through its directive EC no.
1907/2006, that starting from 2009 any substance with carcinomic or mutagenic potential
entering in the life-cycle through market will be made only with authorization of the
European Chemical Agency (ECMA) at Helsinki [4,5].
Also Romania, although from the legislative point of view has already the governmental
directive OG no. 200/2000, approved by the law no. 451/2001, since 2003 was member of the
Rotterdam Convention (10 September 2003) being part of the so-called Prior Informed
Content (PIC) procedure relating the priory consent about the risk or toxicity degree of a
specific chemical that will be circulating or imported across the country.
Moreover, since the official membership of Romania in the European Union (1 January
2007), all chemicals on Romanian territory have to agree with the REACH normative. In this
context, the fundamental research is at its turn driven by the EU laws through the directives of
the Organization of Economical and Cooperation Development (OECD) that already credits
the quantitative structure-activity relationship (QSAR) methodology as the only and certain
source of computational design for the tested compounds with bio-, eco-, and pharmaco-
logical impact [6,7].
Being used in Chemistry during the second half of 20th century as an extended statistical
analysis [8-15], the quantitative structure-activity relationship (QSAR) method had attained in
recent years a special status, officially certified by the European Union as the main
computational tool (within the so-called in silico approach) for the regulatory assessments
of chemicals by means of non-testing methods [2-7,16-18].
However, while QSAR primarily uses the multiple regression analysis [8-15], alternative
approaches such as neuronal-network (NN) or genetic algorithms (GA) have been advanced
to somehow generalize the QSAR performance in delivering a classification of variables
used, in the sense of principal component analysis (PCA) and partial least squares (PLS)
methodologies.
Still, the claimed advantage of the NN over QSAR techniques is limited by the fact the
grounding physical-mathematical philosophies are different since highly non-linear with basic
multi-linear pictures are compared, respectively [19-26].
Actually, the chemical-physical advantage of QSAR stands in its multi-linearity
correlation that resembles with superposition principle of quantum mechanics, which allow
meaningful interpretation of the structural (inherently quantum) causes associated with the
Timisoara Spectral Structure Activity Relationship (Spectral-SAR) Algorithm 541
latent or unobserved variables (sometimes called common factors) into the observed effects
(activity) usually measured in terms of 50%-effect concentration (EC50), associated with
various types of bioaccumulation and toxicity [27].
Nevertheless, many efforts have been focused on applying QSAR methods to non-
linearity features from where the expert systems emerged as formalized computer-based
environments, involving knowledge-based, rule-based or hybrid automata able to provide
rational predictions about properties of biological activity of chemicals or of their fragments;
it results in various QSAR based databases: the model database (QMDB) - inventorying the
robust summaries of QSARs that can be appealed by envisaged endpoint or chemical, the
prediction database (QPDB) - when data from QMDB are used for further prediction to be
stored, or together towering the chemical category database (CCD) documentation [28-34].
Therefore, a certain conceptual-computational analysis of a compound of a series of
compounds in the view of assigning its toxicity degree naturally two levels: one addresses the
atomic-molecular structure together with related quantum properties while the other envisages
the correlations of these properties, e.g. hydrophobicity, polarizability, steric effects, etc.,
with the bio, eco- or pharmacological observed activities.
Finally, it gets out the molecular mechanistic <picture> of the reactions involved in the
studied chemical-biological interaction or, with other words, of the quantum chemical
strength established between the ligand (the effector or the chemical) and receptor (in the
target site or organism).
Still, either the structure or the quantum chemical binding aspects require the advanced
studies upon them, firstly in a separate manner, and then combined both at the intrinsic
structural level and for correlating the interaction, based on the versatility of the atomic and
molecular world to generate surprisingly structures and interactions just because the quantum
character involved (i.e. undulatory, thus allowing the tunneling even for the energetic
inaccessible potential barriers) when forming new apparently not explicated or controllable
compounds by means of macroscopic procedures.
Still, whatever the computational procedure approached, either of that of Hansch type
[35-43], 3D [44-54], decisional [26,55-66], or orthogonal ones [67-80], the problem of
delivering the molecular interaction mechanism as a QSAR analysis result was only recently
furnished by the so called Spectral-SAR that proposes a purely algebraic rethinking of the
traditional statistic QSAR, which allows, through the new concepts introduced (e.g. the
orthogonal space of variables, the vectorial length of the biological activity, or the algebraic
correlation factor as an intensity measure of the chemical-biological interaction) the building
of an optimized chart of the molecular action pathways grounded on the minimum spectral
path principle, [ A, B] = 0 with A and B the endpoints, within a generalized space of the
action norms and correlation factors [81-90].
The present review will present the Spectral-SAR method, developed at Timisoara
(Romania), as a natural continuation and generalization of the classical standard (statistical)
quantitative structure-activity relationship (QSAR) towards the quantum assessment of the
ligand-receptor cellular specific interactions, paths and maps.
2. Statistic QSAR
2.1. Scalar (Dot) Product Basics
Often very useful for mathematical elegance but also with a deep insight for the present
Spectral-SAR methodology, the vectorial modeling of data may be associated with
generalized classical-to-quantum description of variables on Hilbert space, beneficial for
emphasizing many properties especially those related with orthogonality, i.e. independency of
descriptors; this way the quantum most efficient description of a dynamical systems projected
on the associated minimum set of commutative (independent) operators assure the maximum
predictability in computation and viability in conceptual modeling. Skipping the formal
mathematical details, while capping the essence of the computations, being the main
operation on Hilbert space (a vectorial space) the scalar or dot product its main features are
shortly reviewed in what follows.
Given two vectors
u = u1 , u 2 ,..., u n , v = v1 , v 2 ,..., v n (1)
their scalar (or dot) product writes as:
def n
u v = u i vi = u1v1 + u 2 v 2 + ........ + u n v n (2)
i =1
Since the self scalar product looks like:
n
u u = u i2 (3)
i =1
one may introduce the so called norm (or length) of the vector by:
n
u = uu = u
i =1
2
i (4)
The length property of the vectorial norm may be easily visualized through computing
the modulus of an arbitrary 3D vector r = u1 , u 2 , u 3 :
r
r = u12 + u 22 + u 32 = u1 , u 2 , u 3 u1 , u 2 , u 3 = r r = r (5)
Consequently, the distance between two vectors is written in terms of their difference
norm
n
d( u , v ) = u v = u v = uv uv = (u i vi ) 2 (6)
i =1
From last relation (but also from the fact that scalar product is positively defined, see
above) the distributivity and commutativity properties of scalar product may be employed for
any t towards equivalent expressions
u tv u tv 0, t
( u v t )( u t v ) 0
` v v t 2 u v t + u u 0
2
(7)
The last inequality says that the right side second order equation has no solution or has
single equal solutions, a condition fulfilled when its discriminator is less or equal with zero,
respectively, leading with the famous Cauchy-Schwartz inequality:
2
u v uu vv (8)
rewritten as:
n n n
u i vi
i =1
ui2
i =1
v
i =1
2
i (9)
or as
u v u v (10)
Cauchy-Schwartz inequality is usually successfully employed in probability theory,

variance theory and correlation factors, as will be illustrated soon in what following.
2.2. Basic Statistical Indices
Having a set of causes-effects covered Universe with either individual and coupled
probabilities, as given in Table 1, the ergodic statistical (or normalization) condition for their
discrete realizations is expressed respectively as:
p
i =1
i = 1, (11a)
p
j =1
j = 1, (11b)
M N
p
i =1 j =1
ij =1 (11c)
Table 1. Schematic representation of the Universe by the probability table (and

values) with which a certain cause xk produces certain effect yk
X x1 ... xk ... xM
Y p1 ... pk ... pM
y1 p1 p11 ... p1k ... p1M
y2 p2 p21 ... p2k ... p2M

yk pk pk1 ... pkk ... pkM
...
...
...
...
...
yN pN pN1 ... pNk ... pNM
Yet, in integral representation of the probability field extended to the Universe or

actions, the condition (11c) rewrites in terms of probability density function f ( x, y ) as
P( x, y ) UNIVERSE = f ( x, y )dxdy = 1 (12)

x y
while introducing the average of a given observable on a given domain of reality D in the
same manner with the quantum mechanical measurement postulate [91]:
A = A d = A d = A d = A f(x,y)dxdy
2
(13)
D x y
2
where one easily recognizes the quantity as the probability density.
In these conditions the average for x-values writes as
x = xf ( x, y )dxdy (14)
D
producing the chain of individual values departure from average
x1 x , x 2 x , (15)
and, even more, their squared (positive) counterparts

(x1 x ) , (x
2
2 x ) ,K
2
(16)
for defining the x-dispersion (or x-variance) statements

(x x )2 = (x x )2 f ( x, y )dxdy

2
(17)
Dx = ( x x ) = pi xi xi pi
2
i i
2
1 xi 1 xi
n i n i
either expressed under integral, probability, or uniform probability
1
pij = pi = p j =
n (18)
N = M = n
For alternative, more practical definition of variance, one may use the quantum average
properties to successively get the forms
Dx = (x x )
2
= (x x )(x x ) 2
= x2 2 x x + x
2 2 2
= x2 2 x x + x = x2 2 x + x
2
= x2 x (19)
thus providing the celebrated dispersion form (used in Heisenberg indeterminacy principle)
from where also its meaning as measuring the error in attributing the average (14) for the x-
set of values in Table 1 [92]. Yet, the eq. (19) may be further adapted to the integral,
probability and uniform variants, as before:

x 2 x 2 = x 2 f ( x, y )dxdy
( xf ( x, y)dxdy ) 2
2
2
D x = x x = xi p i xi pi
2 2 (20)
i i
2
= 1 xi2 1 xi
n i n2 i
Closely related with the dispersion index stays the so called covariance index, which
generalizes the variance for two different quantities, here viewed as x-causes and y-effects; it
takes one of the forms
C xy = (x x )( y y )
= xy x y x y + x y = xy x y x y + x y
= xy 2 x y + x y
= xy x y (21)
being immediately transcribed into hierarchical way from integral, discrete probabilities, and
uniform probabilities, as above

(
xy x y = xyf ( x, y )dxdy xf ( x, y )dxdy
)( yf ( x, y)dxdy )

C xy = xy x y = xi y j p ij xi pi y j p j (22)
i, j i j
1
= xi y i 1 xi y i
n i n2 i i
Note that the covariance meaning is best understood through imagine the case of its
cancellation,
C xy = 0 xy = x y f ( x, y ) = f ( x) f ( y ) , (23)
the case in which the bi-dimensional probability density factorizes into two one-dimensional
ones, from where the covariance should account for the non-separability of x-causes and y-
effects realization probabilities, being this another point where one statistical quantity is
reflected by a quantum reality. Worth here remarking that someone would say that this is
natural since the quantum theory is often interpreted in terms of probability and in statistical
way in general; this is only partially true, while remarking the subtle difference that still exists
between quantum mechanics and quantum statistics, to some degree equivalent, but
manifestly distinct in regarding time and temperature dependence, respectively [93].
Next, by working with squares of the dispersions, i.e. by defining the standard deviations
()
x = Dx , y = D y (24)
One can combine the covariance and dispersion into the ratio called as the (Pearson)
correlation coefficient, written in simple way as:
C xy (x x )( y y ) (x i x )( y i y )
rxy = = = i
(25a)
x y (x x ) (y y ) 2 2
( x i x )2 ( y i y )2
i i
or in equivalent scalar product fashion:
xx y y
rxy = (25b)
xx xx yy yy
The last form gives the elegant opportunity to show its probabilistic character by
applying the Cauchy-Schwartz inequality (8) for the vectors (states) x x > , y y > , that
is
xx y y xx xx y y y y (26)
thus proofing the realm of eq. (25b) as being sub-unitary
rxy 1 (27)
If necessary, further discrete probability version of Pearson correlation coefficient (25)

x y i j pij xi pi y j p j
i j
rxy =
ij (28a)
2 2

x p i xi pi y p j y j p j
2 2
i j
i i j j
or under uniform probability (18) variant

n xi yi xi yi
rxy = i i i (28b)
2 2

n xi xi n y i y i
2 2
i i i i
may be considered with the same interpretation as showing how much from the combined
causes-effects probability may be represented as combining separated causes and effects
probabilities; if this relation is identity it means that the causes and effects are distinct
realities and may be treated as such, otherwise, for correlation bellow unity there appears that
causes are mixed with effects already in their stage of causes, being the effects less
observable as distinct (measurable) reality. This heuristic (yet meaningfully) interpretation

may be also geometrically treated through remembering the classical scalar product
between two vectors
r r r r r r
x y = x y cos( x , y ) (29)
furnishes the value of the angle between them as the cosines

r r
r r xy
cos( x , y ) = r r (30a)
x y
easily to be generalized for the present vectorial representation of causes and effects data
recordings of Table 1:
x y x y x yi i
cos( x , y ) = = = i
(30b)
x y x x y y xi2
i
yi2
i
Since the sub-unitary value of the cosines, the expression (30b) may be treated as another
definition of the Pearson correlation (25b) involving just the original data (vectorial) sets, or,
equivalently, when their averages are vanishing, x = 0, y = 0 . From this point of view there
is clear that the Pearson definition (25b) is more general since involving the average at
whatever values, while the eq. (30b) fixes the angle between the causes and effects states: as
the angle expresses orthogonality as the cosines goes unity and the two states are better
correlated but in the sense of inferring one from other and not interfering one with other. This
is a subtle message which we like to stress in synthesizing two conclusions:
The orthogonality between two correlating sets of data is essential in establishing the
qualitative degree of correlation and do not depend on the average of data sets but
only by their vectorial length and scalar product through the angle cosines given by
eq. (30b);
Instead, the quantitative degree of correlation is established by invoking the average
of concerned data sets through modifying/generalizing the eq. (30) towards the
Pearson coefficient (25b).
These are fundamental ideas underlying the motivation and the philosophy of
quantitative activity (for effects)-structure (for causes) relationships, to be in next step by step
unfolded.
2.3. Linear Correlation
Going on with the correlation analysis lets explore the linear correlation between one-
cause the effect relationship and to see the role the correlation factor play on it. For that we
consider the one-to-one data sets for x-cause and y-effect, within uniform probability
realization of eq. (18), here summarized as the data rows:
X x1 x2 ... xn
Y y1 y2 ... yn
Basically, the regression problem consists in finding the best modeling of observed
effects by the computed one
y iobs = axi + b + ei = y comp + ei (31)

123
y comp
through minimizing the errors of such approximation, that is:
ei2 = [ y i (axi + b)]2

e 2 min (32)

i
i
Analytically, if the minimization function is introduced as the sum of squared errors
f (a, b) = ei2 = ( y i axi b ) min

2
(33)
i i
then the optimization procedure is to be done in respecting the linear parameters as the free
terms and the slope of regression, i.e. providing the system
f (a, b)
a = 0
(34a)
f (a, b) = 0
b
equivalently unfolded as
2 ( yi axi b )( xi ) = 0
i
(34b)
2 ( yi axi b )(1) = 0
i
or even as:
yi xi = a xi2 + b xi n
i i i
(34c)
yi = a xi + bn ( xi )
i i i
solved for the solutions:

n xi y i y i xi
a=
i i i , (35)
2

n xi2 xi
i i
y x x x y
i
2
i i i i
b= i i i i
2
(36)

n xi2 xi
i i
Now, worth observing that by multiplying the second equation of the system (34c) with
the factor 1 / n one gets the meaningful expression
1 1

n i
y i = a xi + b
n i
(37)
telling that the linear correlation is in fact precisely fulfilled by the data set averages of cause
and effect, respectively, i.e.
y = ax + b (38)
However, looking to the slope expression (35) and comparing it with the Pearson
coefficient (28b) one easily recognize that they are in different statistic quantities although
linked by the x- and y- standard deviations (24) with dispersions of (20) type, namely as
y C xy y C xy
a = rxy = = (39)
x x y x D x
where the dependence of slope (35) by the x-y covariance of (22) and x-dispersion (20) was
also emphasized.
With these, it is clear that the monovariate linear correlation has the correlation factor as
the direct information included in its slope; indeed, if the x- and y-standard deviations are
considered approximately the same
x =y (40)
that happens in the ideal case when both the x- and y- data sets are described by the same
normal distribution, it results in the identity:
a = rxy (41)
However, since, in general, we have the case
y
1 (42)
x
it is clear that this ratio modulates the correlation slope a of eq. (35) to provide the
correct, sub-unitary, correlation factor; this explaining why, even in the practical cases of
slope higher than unity ( a > 1 ), the correlation factor still records sub-unitary values.
Returning to the general linear regression now we can consider the slope-Pearson
correlation coefficient of eq. (39) as driven the instantaneous equation
y
y = rxy x+b (43a)
x
along its averaged form, in accordance with eq. (38),
y
y = rxy x +b (43b)
x
as well as their difference
y
y y = rxy (x x ) (44a)
x
from where the computed (predicted) instantaneous effects directly writes from averaged
observed ones corrected in a perturbation sense by corresponding instantaneous cause
departure fro its average modulated by the Pearson coefficient, which is sub-unitary as earlier
proofed by eq. (27), and the ratio of effect-to-cause standard deviations
y
y comp = y + rxy (x x ) (44b)
x
Finally, worth giving a practical rule aiming to assure as much possible the premises of a
good or relevant correlation in sense of increasing the Pearson correlation factor; it may look
like
rxy n 1 3 (45a)
which offers a quite reasonable framework depending of the dimension of the data sets
accounted as causes and recorded as effects. As such, there is clear that even for data sets
containing ten points the condition (42) is still not satisfied,
n=10 => n 1 = 3 , rxy 3 < 3 (46a)
while at least from seventeen dimension of vectorial state with instantaneous cause-effect
points the regression analysis may become reasonable:
n=17 => n 1 = 4 , rxy n 1 3 (46b)
Nevertheless, from (45a) an even more relaxed condition may be inferred by squaring it
to the condition:
rxy2 (n 1) 9 (45b)
which may be satisfied even for data sets with cardinal laying in the range 10 . Worth
observing that as the data sets for causes is more restrained the correlation factor has to be
closer to unity for goodness of the fit. Again, the present discussion has two subtle
consequences, namely:
The cause-effect (linear) regression is meaningful when the number of points included in
analysis is significant, and in any case larger than ten;
The correlation analysis is still relevant, even for lower square of Pearson coefficient as
far the number of included cause-effects points is higher enough such that condition (45b) to
be fulfilled; this consequence prevent the ab initio exclusion of the correlation models with
correlation coefficient not laying in the unity vicinity, but when considerable large data set
was assumed.
Further insight on correlation coefficient and of its alternative practical definition is to be
in next exposed.
2.4. Correlation by Normal Distribution Function
After introducing the main statistical indices and concepts, worth generalizing them with
the aid of the distribution function defining the so called (statistical) moment of K-th order for
the x-variable (cause):
K = (x x ) = (x x )
K K
f ( x )dx (47)
Consequently, the first three moments are easily recognized as:

the normalization condition through the zero-th order moment
0 = ( x x ) 0 = 1 = 1 = f ( x)dx (48)
cancellation of the first moment:
1 = ( x x )1 = xf ( x)dx x f ( x)dx = x x = 0 (49)
the standard deviation through the second moment:
2 = (x x ) = x2 = ( x x ) f ( x)dx
2 2
(50)
The remaining problem is the identification of the distribution function; it can be

nevertheless chosen as the normal distribution, with the form
1 (x x )2
f ( x) = exp , x (51)
2 x 2 x2
for which the first three moments are verified from eqs. (49)-(51) with the help of Appendix,
respectively as:
1
+
( x x )2 1
0 = exp
2 x

2 x
2 d ( x x ) =
2 x 1
=1, (52a)
2 x2
1
+
( x x )2
1 = ( x x ) exp 2 x2 d ( x x ) = 0 ,
2 x
(52b)
1
+
(x x ) 2
1 1
2 = (x x ) exp 2 2 x2 = x2 (52c)
2
d ( x x ) =
2 x 2 x 2 x 2 1
2 x2
Next, having checked the reliability of the normal function for one variable, the
generalized bi-dimensional form may be proposed through considering both the
multiplication rule for independent probabilities (say for x-causes and y-effects) tuned by the
degree of reciprocal correlation by the Pearson coefficient presence, with the working form:
1 1 ( x x ) 2 ( y y) 2 ( x x )( y y ) (53)
f ( x, y ) = exp + 2rxy
2 x y 1 rxy
2 (
2 1 rxy
2
) x
2
y2
x y
Note that when the x- and y- distributions are really independent, i.e. with rxy = 0 , it
reduced to the factorization of the distribution functions of the associate probability fields
1 ( x x ) 2 1 ( y y)2
f rxy =0 ( x, y ) = exp
2 exp = f ( x) f ( y ) (54)
2 x 2 2
x y
2 2
y
in the same manner as the covariance behavior, previously quoted by the note (23), with the
same meaning: when the causes and effects are at all correlated they may be true
simultaneously, thus abolishing any ordering hierarchy between them.
Nevertheless, for better emphasizing on the cause role of the x-variable, the conditioned
distribution function may be considered as the ratio of the bi-variate normal probability (51)
reduced (normalized) by that corresponding to the cause probability, while better modeling
the degree with which the effect probability arises when the cause manifestation is certain
(and before it); thus the effect conditioned probability function by the cause appearance is
successively written as:
g (y x) =
f ( x, y )
f ( x)
1 1 (x x )2 ( y y)2 ( x x )( y y ) ( x x ) 2
= exp + 2rxy +
2 y 1 rxy2 2(1 rxy ) x
2 2
y 2
x y 2 x2
1 1 (x x)2 ( y y)2 ( x x )( y y ) (1 rxy )( x x )

2 2
= exp + 2rxy
2 y 1 rxy2 2(1 rxy ) x
2 2
y 2
x y x2

1 1 2 (x x )2 ( y y)2 ( x x )( y y )
= exp r + 2 r
x2 y2 x y
xy xy
2(1 rxy )
2
2 y 1 rxy2
1 1 2 (x x) 2 ( y y)2 ( x x )( y y )
= exp r + 2 r
x2 y2 x y
xy xy
2(1 rxy )
2
2 y 1 rxy2
y y x x
2
1 1
= exp 2
rxy
2 y 1 rxy2 2 (1 r )
x
xy y

1 1 y
2

= exp y y rxy (x x ) (55)
2 y 1 rxy2 2(1 rxy ) y
2 2
x
It may, for instance, be used to check out the instantaneous computed/predicted effect,
providing successively the expressions
y comp = y g ( y x ) = yg ( y x )dy
+
y
= y y rxy (x x ) g ( y x )d y y rxy y (x x )

x 4244 44444 x
1444444 444 4443
=0
y +

+ y + rxy (x x ) g ( y x )d y y rxy y (x x )
x 1 x

44444 42444 444 3
=1
y
= y + rxy (x x ) (56)
x
until recovering the perturbative form (41) earlier proofed within the linear regression
context.
However, being with eq. (56) convinced by the usefulness of the conditioned probability
function (55) one may use it for computing the important statistical quantity as the minimum
of the squared errors sum, or the sum of residues SR in observing the effects from a set of
causes, being practically equivalent with the variational calculation of the eq. (34). Indeed,
through the following successive identities
(
SR y = min yiobs yicomp )2
i
2
y
= (y obs
i y i )
comp 2
g(y x)
= y y rxy
x
(x x )
g(y x)
2
y
= y y rxy (x x ) g (y x )d y y rxy y (x x )
x x
(
= 1 rxy y
2 2
) (57)
one gets the equation
SR
= 1 rxy2 (58)
y2
leaving with the so called standard or statistical correlation factor

(y )
2
obs
i y icomp
SR
R = 1 = 1 i
(59)
(y )
2 2
y
obs
i y
i
The result of eq. (59), although formally equivalent wit the Pearson correlation factor
(28b) adds a very important feature: it describe the correlation cause-effect only through the
observed and computed effects so that hiding the causes in the instantaneous
computed/predicted effects based upon the regression equation effects-causes.
Such formulation is of the first importance and use in evaluating the correlation factors
when the multi-regression analysis is employed, since the presence of the many-causes
probabilities and correlations a problem that is avoided when the correlation factor is based
only on computed and observed effects, as formula (59) display.
Nevertheless, variants of it for may be formulated, for instance the corrected correlation
factor that accounts for the dimension of causes and effect vector (state), i.e. the cardinals M
and N of Table 1, but this is relevant only for refining applicative discussions, while here we
will restraint to only presenting and commenting the fundamental statistical regressions.
In this line, in next, the multi-linear correlation is analytically exposed to complete the
statistical presentation of the cause-effect correlation paradigm for the structure-activity
modeling, respectively.
2.5. Multilinear Correlation
The many-variable correlation problem may be resumed by finding the bs parameters of

the instantaneous equation
Y = b0 + b1 X 1 + b2 X 2 + .... + bM X M (60)
when knowing the set of independent (xs) and observed dependent (y) variables of Table 2.
Table 2. The realization of the Table I within the uniform probability for evaluated
(selected) causes of Xk and observed effects of Y columns, respectively
X X0 X1 Xk XM
Y
y1 1 x11 x1k x1M
y2 1 x21 x2k x2M

yk 1 xk1 xkk xkM

yN 1 xN1 xNk xNM

While recognizing the eq. (60) as being associated with the computed instantaneous
effect (activity), when the observed counterparts is considered the corresponding errors
appear provided the system (61) is fulfilled.
y1obs = b0 + b1 x11 + b2 x12 + ... + bM x1M + e1

obs
y 2 = b0 + b1 x 21 + b2 x 22 + ... + bM x2 M + e2
(61)
....
y obs = b + b x + b x + ... + b x + e
N 0 1 N1 2 N2 M NM N
The minimization of the squared sum of errors from (61) respecting each of the searched
parameters looks like
N 2
ei = 0
b0 i =1
N 2
ei = 0
b1 i =1 (62a)
...

N 2
ei = 0
bM i =1
as a generalization of the linear variational procedure of system (34a); it unfolds analytically

firstly as
2 [ y i (b0 + b1 xi1 + b2 xi 2 + ... + bM xiM )] 1 = 0

i =1
N
[ y i (b0 + b1 xi1 + b2 xi 2 + ... + bM xiM )] xi1 = 0

2
i =1 (62b)
...

N
2 [ yi (b0 + b1 xi1 + b2 xi 2 + ... + bM xiM )] xiM = 0

i =1
which can be then rearranged with the form

N N N N
i y = b0 N + b 1 i1 x + b 2 i2 x + ... + b M xiM
i =1 i =1 i =1 i =1
N N N N
yi xi1 = b0 xi1 + b1 xi 2 + ... + bM xiM xi1

2
i =1 i =1 i =1 i =1 (62c)
...

N N N N
i iM = 0 iM + 1 i1 iM + + M xiM
2
y x b x b x x ... b
i =1 i =1 i =1 i =1
Yet, since the last system has to be solved for bs coefficients a general (formal) solution
may be furnished by recognizing it as the formal matrix equation
[X ]T [Y ] = [X ]T [X ][B] (63)
with the notations:
y1 1 x11 x12 ... x1M b1 e1

y2 1 x x ... x b2 e2
[Y ] = , [X ] = 21 22 2 M
, [B ] = ....

, [E ] = .... (64)
.... .....

y 1 x x ... x b e
N N1 N 2 NM M N
Equation (63) can be nevertheless directly obtained by reconsidering the system (61)
rewritten with notations (64) under the matrix form
[Y ] = [X ][B ] + [E ] (65)
upon which the optimization condition (62a) is now becoming formally:

[B ]
(
[E ]T [E ] = 0 ) (66)
T
and where [ X ] stands for the transposition of the [ X ] matrix.
In any case, the solution of the eq. (63) is immediately abstracted as
[B ] = ([X ]T [X ]) [X ]T [Y ]
1
(67)
often called as the Moore-Penrose matrix. Yet, although elegantly obtained it involves the
inverse matrix operation which may be quite cumbersome in cases of higher dimensions of
the observed effects through the selected causes; it may suffers as well by the indeterminacy
in cases in which the matrix inverse is not possible or with singularities. However, it allows
for computer routines and is implemented in the majority of the statistical packages.
Since having somehow hidden structure the solution (67) should be checked for the
linear-regression case for the knowing analytical solution as given by eqs. (35) and (36). For
this special case the system (61) restrains to the simple one
y1obs = b + ax1 + e1
obs
y 2 = b + ax2 + e2
(68)
....
y obs = b + ax + e
N N N
whereas the involved matrices in general solution (67) are now shaped as
y1 1 x1

y2 b = b0 1 x 2
[Y ] = , [B ] = , [X ] = (69)
... a = b1 M M

y 1 x
N N
Therefore, we firstly construct the matrix to be inversed, namely
1 x1 N

N x
[A] = [ X ]T [ X ] =
1 1 L 1 1 x 2 i

= i
(70)
x1 x2 L x N M M N N

1 x i xi2
xi
N i
whose determinant is immediately yielded
2
N
N
det[ A] = N x xi
2
i (71)
i i
while providing also the minor determinants
N N
~
A11 = ( 1)1+1 xi2 = xi2 , (72a)
i i
N N
~
A12 = (1)1+ 2 xi = xi , (72b)
i i
N N
~
A21 = (1) 2+1 xi = xi , (72c)
i i
~
A22 = (1) 2+2 N = N (72d)
entering the matrix
N 2 N

A12
~ ~ xi xi

[A]* = A~11 ~ = i i (73)
A22 x
N
A21 i N
i
All in all the inverse matrix of (70) is obtained as
N N

i
xi2 xi
i

N N
2 N
N

2
N xi xi
2
N xi2 xi
[A]1 =
[ A]
*

= i i i i (74)
det[A]
N
xi
i N
N N
2 N
N

2
N xi xi
2
N xi2 xi
i i i i
which together with the other matrices product
y1 N
yi
[X ]T [Y ] =
1 1 L 1 y 2 i
= (75)
x1 x2 L x N M N
xi y i
y i
N
construct the Moore-Penrose matrix for the mono-linear regression
N 2 N N N

x i y i x i xi y i
i i i i
N
N

2
N xi xi
2

[B ] = [A]1 ( )

[X ] [Y ] = N i N i N
T b0 b
= b = a (76)
xi y i + N xi y i 1
i i i
N
N

2

N xi xi
2

i i
recovering by its components the solutions (35) and (36). There is however clear by this
presentation that as the linear regression is extended to many more (Xi) causes as the
complexity and difficulty in analytically expression of the solution factors are increasing;
moreover, through such algorithm there appears that no reference and control of the
orthogonality or independency among the (Xi) causes are involved, or are so hidden to
produce meaningful quantum interpretation for the ligand-receptor specific interaction.
With these the statistical fundaments for treating and understanding the quantitative
(regression) structure (cause) activity (effects) relationships are exposed, while containing
the germens for alternative and in some respects the generalized algebraic treatment of
correlation in assessing for the ligand-receptor specific interaction an analytical pattern
towards quantization, as will be presented din the sequel.
3. Algebraic QSAR
3.1. Multivariate Spectral Regression on Hilbert Space
The key concept in SAR discussion regards the independence of the considered structural
parameters in Table 3. As a consequence we may further employ this feature to quantify the
basic SAR through an orthogonal space. The idea is to transform the columns of structural
data of Table 3 into an abstract orthogonal space, where necessarily all predictor variables are
independent, solve the SAR problem there and then referring the result to the initial data by
means of a coordinate transformation.
Table 3. The vectorial descriptors in a Spectral-SAR analysis
Activity Structural predictor variables

YOBS ( ERVED ) X0 X 1
X k
XM
y1-OBS 1 x11 x1k x1M
y2-OBS 1 x21 x2k x2M
M M M M M M M
yN-OBS 1 xN1 xNk xNM
Since QSAR models aims correlations between concerned molecular structures and
measured (or otherwise evaluated) activity, appears naturally that the structure part of the
problem to be accommodated within the quantum theory and of its formalisms. In fact, there
are few quantum characters that we are using within the present approach [94]:
Any molecular structural state (dynamical, since undergoes interaction with

organism) may be represented by a ket state vector, in an abstract space of
allowed states within Hilbert space, following the bra ket Dirac formalism [95];
such states are to be here represented by any reliable molecular index, or, in
particular in our study by hidophobicity LogP , polarizability POL , total
optimized energy E tot , just to name only the so called Hansch parameters, usually
employed for accounting the diffusion, electrostatic and steric effects for molecules
acting within organisms cells, respectively.
The (quantum) superposition principle that assures that sum combinations of
molecular states map on other resulting molecular state, here interpreted as bio-, eco-
or toxicological activity, e.g. Y = Y0 + C LogP LogP + C POL POL + ... with
Y0 meaning the free or unperturbed activity (when all other influences are absent).
The orthogonalization feature of quantum states, a crucial condition for that the
superimposed molecular states generates other molecular state (here quantified as
molecular-linking organism activity); analytically, the orthogonalization condition is
represented by the bra ket scalar product of two envisaged states (molecular
indices) whom value if it is evaluated to be zero, bra ket = 0 , then the states are
said orthogonal and molecular descriptors independent, therefore suitable to be added
as states in resulted activity state and as molecular indices in activity correlation.
Further details on scalar product and related properties are given in Appendix A1,
while in what follows the Spectral-SAR correlation method is resumed.
Therefore the analytical procedure is unfolded under three fundamental steps.
Step 1
Given a set of N molecules being studies against biological activity they produce by
means of their M structural indicators, all input information (the states) may be vectorial
expressed by the columns of the Table 3 and correlated upon equation
YOBS ( ERVED ) = b0 X 0 + b1 X 1 + ... + bk X k + ... + bM X M + prediction error
= YPRED ( ICTED ) + prediction error (77)
whith the unity vector X 0 = 1 1 L 1N added to account for the free term.
In order equation (77) to represent a reliable model of the given activities, the molecular
states (indices) assumed should constitute an orthogonal set, having this constraint a quantum
mechanically fundament, as above described. However, unlike other important studies
addressing this problem [67-80], the present employed Spectral-SAR assumes the prediction
error vector in eq. (77) as being from beginning orthogonal on all others, since it cannot be
considered input data as the others,
YPRED prediction error = 0 (78)

being not known apriori any correlation is made. Moreover, from eqs. (77) and (78) there
follows that the prediction error vector has to be orthogonal on all other descriptor states of
predicted activity.
X i =0, M prediction error = 0 (79)
for consistency of the present vectorial (quantum formalized by means of ket states)
approach. In other terms, conditions (78) and (79) confirm the form (77) in the sense that
prediction vector and the prediction activity YPRED (with all its sub-intended states
X i =0,M ) belongs to disjoint (thus orthogonal) Hilbert spaces; or even more, one can say
that the Hilbert space of the observed activity YOBS may be decomposed into a predicted
and error independent Hilbert sub-spaces of states. Therefore within Timisoara Spectral-SAR
procedure the very beginning step in orthogonalization is prediction vector orthogonalization
to prediction activity and of its predictor states, while the remaining orthogonalization
algorithm do not search for optimizing the minimization of errors, but for producing the ideal
correlation between YPRED and the given descriptors X i =0, M .
Step 2
Next, the Gram-Schmidt orthogonalization algorithm is applied through constructing the

orthogonal set of descriptors by means of the consecrated iteration [96-98]:
0 = X 0 , (80a)
k 1 X k i
k = X k rik i , rik = , k = 1, M (80b)
i =0 i i
providing the orthogonal correlation:
YPRED = 0 0 + 1 1 + ... + k k + ... + M M , = k Y , k = 0, M (81)

k
k k
Step 3
Remarkably, while the studies dedicated to orthogonal problem usually stops at this stage
the Spectral-SAR uses it to provide the solution for the original searched correlation, eq. (77)
with the error vector orthogonal on the predicted activity and on all its predictor states of
Table 3. This can be adequately achieved through rearranging eqs. (80) and (81) so that the
system of all descriptors of Table 3 to be written in terms of orthogonal descriptors:
YPRED = 0 0 + 1 1 + ... + k k + ... + M M

X0 = 1 0 + 0 1 + ... + 0 k + ... + 0 M

X1 = r01 0 + 1 1 + ... + 0 k + ... + 0 M
(82)
........................................................................................

X k = r0 0 + r1 1 + ... + 1 k + ... + 0 M
k k
........................................................................................

X M = r0M 0 + r1M 1 + ... + rkM k + ... + 1 M

The system (82) has no trivial (orthogonal) solution if and only if the associated extended
determinant vanishes; this condition introduces the Spectral-SAR determinant and of its
equation [81-83]:
YPRED 0 1 L k L M
X0 1 0 L 0 L 0
1
X1 r 0 1 L 0 L 0
M M M M M =0 (83)
Xk r0k r1k L 1 L 0
M M M M M
M M M
XM r 0 r1 L r k L 1
If the determinant of eq. (83) is expanded on it first column, and the result rearranged so
that to have YPRED on left side and the rest of states/indicators on the right side the searched
QSAR solution of the initial problem of eq. (77) is obtained as Spectral-SAR vectorial
expansion (from where the spectral name is justified as well) with the error vector already
absorbed in the orthogonalization procedure.
In fact Spectral-SAR procedure uses the double conversion passages: one forward from
the given problem of eq. (77) to the orthogonal one of eq. (81) in which the error vector is
orthogonally dissolved; and the reverse one, back from the orthogonal to the real
descriptors throughout the system (82), leaving with the determinant (83) to be expanded as
the QSAR solution.
The result is that now QSAR/Spectral-SAR equation is delivered directly by the
determinant (83) and not through matrices products as in statistical Pearson approach, see
Section 2.5, while furnishing directly the Spectral-SAR correlation equation and not only the
parameters of multi-variate correlation [8-15]. Moreover, the Spectral-SAR algorithm is
invariant also to the order of descriptors chosen in orthogonalization procedure, providing
equivalent determinants just with rearranged lines, a matter that was not previously achieved
by other orthogonalization techniques [67-80].
Remarkably, apart from being conceptually new through considering the spectral
(orthogonal) expansion of the input data space (of both activity and descriptors) throughout
the system (82), the present method also has the computational advantage of being simpler
than the classical standard statistical way of treating SAR problem previously exposed.
That because, one has nothing to do with computations of matrix of the coefficients (64) or
(67), this being a quite involving and time consuming procedure for higher dimensional
systems. Instead, one can write directly the Spectral-SAR solution (equation) as the expansion
of a (M+2)-dimensional determinant of eq. (83) whose components are the activity and
structural vectors involving the Gram-Schmidt and the spectral decomposition coefficients,
ri k and k , respectively.
However, although different from the mathematical procedure, both standard- and
spectral-SAR give similar results due to the theorem that states that [96]: if the matrix X, as
that from (64), with dimension N(M+1), N>M+1, has linear independent columns, i.e. they
are orthogonal as in the spectral approach, then there exists an unique matrix [Q] of
dimension N(M+1) with orthogonal columns and a triangular matrix [R] of dimension
(M+1)(M+1) with the elements of the principal diagonal equal with 1, as identified in the
first small determinant in eq. (83), so that the matrix [X] can be factorized as
[ X ] = [Q][ R ] (84)
When combining equation (84) with the optimal equation (63) one can get, after straight
algebraic rules, that the [B] vector of estimates takes the form
( )1
[ B ] = [Q]T [Q] [Q]T [Y ] (85)
in close agreement with previous normal one, see equation (67). However, by comparison of
matrices [X]T[X] and [Q]T[Q] of equations (67) and (85), respectively, there is clear that the
last case certainly furnishes a diagonal form which for sure is easier to handle (i.e. to take its
inverse) when searching for the vector [B] of SAR coefficients.
However, worth being convinced by the equivalence of the present Spectral method with
the standard statistical one by specializing the general problem (77) to the linear case
YPRED = b0 X 0 + b1 X 1 (86)
and to check whether this is unfolded through the Spectral-equation (83) as providing the
parameters of linear regression given by eqs. (35) and (36). In this respect, actually, we deal
with the particular equation
YPRED 0 1
1 0 1 0 1
0= X0 1 0 = YPRED 1 X 0 10 + X1 (87)
r0 1 r0 1 1 0
X1 r01 1
which is immediately rearranged as

14243
(
YPRED = 0 r011 X 0 + )
{1 X 1 (88)
b a
so that to identify the actual with the previous linear coefficients of eqs. (35) and (36):
a = 1 , b = 0 r011 (89)
Going to evaluate the expressions of (89) within the Spectral-SAR algorithm, there is
instructive to identify form Table 3 only the relevant actual variables, with convenient
denotation of instantaneous structural ones as the columns:
YPRED X0 X1
y1 1 x1
y2 1 x2
M M M
yN 1 xN
Other working tools are the zero-th and the first orthogonal vectors, accordingly
considered and computed respectively as
0 = 1 1 L 1N , (90a)
1 = X 1 r01 0
N N N
1 1 1
= x1 x2 ... x N
N
xi 1 1 1 ... 1 = x1
i =1 N
xi ... x N
i =1 N
x
i =1
i (90b)
with the help of coefficient
X 1 0 1 N
r01 =
0 0
=
N
x
i =1
i
(91)
specialized from the general definition (80b).

In the same manner, the other specific Spectral coefficients from the general orthogonal
recipe (81) are now for linear regression computed as the zero-th order contribution
0 Y 1
0 =
0 0
=
N
yi
i
(92)
while the first orthogonal one recovers precisely the previous linear slope of eq. (35):
1 Y
1 =
1 1
x1 N 1 xi ... x N N 1 xi y1 ... y N
= 2

i xi N 1 i xi

i yi xi N 1 i xi i yi xi N 1 i yi i xi
= =

2
2 2
2

i i
x N 1
i i xi + N xi 2 N 1 xi xi
x
i
i i

N y i xi y i xi
= i i i =a (93)
2

N xi2 xi
i i
as prescribed by the the correspondence of (89). Additionally, also its companion free term
coefficient of relationship (88) may be now straightly evaluated as
b = 0 r011

N yi xi yi xi
1 1 i i
= y i xi i 2
N i N i
N xi xi
2
i i
2

yi xi xi yi xi
= i i i i
2
(94)

N xi2 xi
i i
as well successfully regaining the previously computed linear free terms counterpart as eq.
(36), yet by means of variational statistical (optimization of errors squares summation)
procedure.
With this there is clear that the Timisoara Spectral-SAR algebraic SAR methodology not
only recovers in great details the standard statistical QSAR routine but also generalizes to a
great analyticity extent towards better assessment of mechanistically ordering and influences
in practical eco- and biological applications.
3.2. Algebraic Correlation Factor
Lets explore in next whether the present spectral regression gives the opportunity in
defining another correlation index, beyond the standard statistical one given by eq. (59) [94].
One starts with the simple connection between the observed, predicted and error vectors
of eq. (77), however specialized on their instantaneous entries:
Yi OBS = Yi PRED + pei (95)
where pe stays here as abbreviation for prediction error.

Then, by means of squaring relation (95),
Yi 2OBS = Yi 2 PRED + pei2 + 2Yi PRED pei (96)
and summing for all working N-molecules (of Table 3),
N N N N
Y
i =1
2
i OBS = Yi 2 PRED + pei2 + 2 Yi PRED pei
i =1 i =1 i =1
(97)
the last relation simplifies to:
N N N
Y
i =1
2
i OBS = Y
i =1
2
i PRED + pei2
i =1
(98)
based on applying of scalar product definition (2) and of prediction error orthogonalization
condition (78) upon the last term of (97), i.e.
Y
i =1
i PRED pei = YPRED pe = 0 (99)
Now, substituting the prediction error values of (95) into remaining expression (98) one
firstly gets:
N N N
Y = Yi 2 PRED + (Yi OBS Yi PRED )

2 2
i OBS (100)
i =1 i =1 i =1
or the equivalent identity
N N
Yi 2 PRED = Yi OBS Yi PRED

i =1 i =1
(101)
which further rewrites, recalling the norm and scalar product definitions of eqs. (2)-(4),
respectively, as:
2
YPRED = YOBS YPRED (102)
Finally, the Cauchy-Schwarz form (10) is employed on the right side term of (102),
noting that the observed and predicted activities are of the same nature for a given molecule
i.e. either both positive or both negative thus providing their scalar product as positively
defined; with these, the relation (102) immediately reads as the inequality:
2
YPRED YOBS YPRED (103)
leaving with the predicted-observed norms hierarchy
YPRED YOBS (104)
that guarantees the consistent probability definition while introduceing algebraic correlation
factor with the form:
YPRED
RA rALGEBRAIC = 1 (105)
YOBS
Nevertheless, there remains to compare this new correlation factor, written in

algebraically manner as the ration of predicted to observed norms of investigated
molecular activity or of their effects, with the fashioned statistical counterpart given by eq.
(59); this issue will be addressed in what follows.
3.3. Algebraic vs. Statistic Correlations
Timisoara Theorem (on the algebraic Spectral-SAR correlation): for any QSAR
analysis, once considering the measured/observed and computed/predicted activity data as the
vectors YOBS and YPRED with the associate norms through the scalar products of eqs. (2)-
(4), the algebraic norm order (105) valid in defining the algebraic correlation factor (104),
sets also the hierarchy at the levels of correlations factors in a sense that the algebraic one of
always exceed the standard correlation factor (59):
rSALGEBRAIC
SAR
STATISTIC
rQSAR (106)
Proof: by straight algebraic translation the condition (106) firstly it rewrites as:
YPRED YPRED YOBS YPRED YOBS YPRED

1 (107)
YOBS YOBS YOBS YOBS YOBS YOBS
where we have introduced the averaged observed activity
N
1
YOBS =
N
y
i =1
i OBS (108)
and its associate N-dimensional vector (state in Hilbert space):
1 N

YOBS =
N
yi =1
i OBS 1 1 K 1N

(109)
Note that the inequality (107) becomes equality in the case of perfect identity between
observed and predicted activity values, i.e. perfect correlation, the case in which the second
term of the right hand side vanishes while that of the left hand side become unity. For all
other non-perfect correlations strict inequality holds and this will be considered in next, for
the equivalent expression
YPRED YPRED YOBS YOBS YOBS YOBS

[
> YOBS YOBS YOBS YOBS YOBS YOBS YOBS YPRED YOBS YPRED ] (110a)
which may be further rearranged as
[Y PRED YPRED YOBS YOBS ][ Y

OBS YOBS 2 YOBS YOBS + YOBS YOBS ]
+ YOBS YOBS [Y OBS YOBS 2 YOBS YPRED + YPRED YPRED ] > 0 (110b)
At this point, after obvious simplifications and factorization may easily recognize and
employ both the identities (102) and (104), specific to algebraic correlation
2 YPRED YPRED YOBS YOBS 2 YOBS YOBS YOBS YPRED

14243
YPRED YPRED
14444 4244444 3
[
+ [ YOBS YOBS YPRED YPRED ] 2 YOBS YOBS YOBS YOBS ]> 0 (110c)
0
the simplified expression is obtained
2 YOBS YOBS > YOBS YOBS (111a)

that finally is analytically explicated with the aid of introduced vector (109) of the average
activity to the unfolded scalar ordered products
N
1 N
N 1 N
1 N

2 y i OBS y i OBS > yi OBS y i OBS (111b)
i =1 N i =1 i =1 N i =1 N i =1
leaving with the equivalent strict inequality
2 2
2 N 1 N
yi OBS > yi OBS (111c)
N i =1 N i =1
fully satisfied by the natural ordering as 2 > 1 . Therefore, there was proofed both the
(qualitative) simplicity and the (quantitative) superiority of algebraic correlation factor. Many
applications proof these statements also on dedicated molecular-biological or molecular-
ecotoxicological cases. Yet, one modern bi-component molecular system concerned the ionic
liquids (IL) toxicological actions are in next explained in its paradigmatic form.
3.4. Spectral-SAR for Ionic Liquids
Since their emergence a decade ago, ionic liquids have had a constantly growing
influence on organic, bio- and green chemistry, due to the unique physico-chemical properties
manifested by their typical salt structure: a heterocyclic nitrogen-containing organic cation (in
general) and an inorganic or organic anion [99], with melting points below 100 C and no
vapor pressure [100]. The latter property leads to the practical replacement of conventional
volatile organic compounds (VOCs) from the point of view of atmospheric emissions, though
they do present the serious drawback that a small amount of IL could enter the environment
through groundwater [101]. This risk makes it necessary to perform further eco-toxicological
studies of IL on various species, in order to improve the "design rules" for synthesized IL
with minimal toxicity to environment integrated organisms.
Ionic liquids display variable stability in terms of moisture and solubility in water, polar
and nonpolar organic solvents [102]. Various values of ionic liquid hydrophobicity and
polarity may be tailored [101] with the help of nucleoside chemistry [103] according to the
main principles of green chemistry [104, 105]: the new chemicals must be designed to
preserve effectiveness of function while reducing toxicity, and not persisting in the
environment at the end of their usage, but breaking down into inoffensive degradation
products.
In this respect, the costs of all approaches for sustainable product design can be reduced
using SAR and QSAR methods [84, 85, 89]. It has already been proved that the anti-
microbial activity of quaternary ammonium chlorides is lipophilicity-dependent [106]. While
the 1-octanol-water partition coefficient could be seen only as the first approximation for
compound lipophylicity, bioaccumulation and toxicity in fish, as well as sorption to soil and
sediments assumes that lipophylicity is the main factor of anti-microbial activity [107].
Nevertheless, aiming at a deeper understanding of the specific mechanistic description of IL
eco-toxicity, it is worth considering that the ionic liquid properties are more comprehensively
quantified through lipophylicity, polarizability and total energy as a unitarily complex of
factors in developing appropriate structure-activity relationship (SAR) studies.
However, the main problem in assessing the viable QSAR studies to predict ionic liquid
toxicities concerns the anionic-cationic interaction superimposed on the anionic and cationic
subsystems containing ionic liquids. There are basically two complementary ways of attaining
this goal. One may address the search of special rules for assessing the anionic-cationic
structural separately from the individual anionic and cationic ones, and then generating the
QSAR models. Yet, because the cationic and anionic effects on liquid toxicity are merely
separately studied at the moment, the appropriate strategy would be to firstly derive the
anionic and cationic QSARs and only then to move on to a QSAR of the ionic liquid viewed
as an anionic-cationic interaction.
As recently communicated [89], when the ionic liquids activity is evaluated two different
additive models for modeling anionic-cationic interaction can be examined.
The first one is based on the vectorial summation of the produced anionic and cationic
biological effects Y , named the |1+> model, and which is constructed on the superposition
of the anionic (subscripted with A) and cationic (subscripted with C) activities [84]:
1+
Y AC = YC + Y A (112)
The second S-SAR model, named |0+>, is employed when the additive stage is
considered at the examined Hansch factors X = LogP, POL, ETOT , which are firstly
combined to produce the anionic-cationic (subscripted with AC) indices that are further used
to produce the spectral mechanistic map of the concerned interaction [85]:
= O S SAR 0 + = O S SAR f ({ X A }{ })

0+
YAC , XC (113)
with the particular specifications of the spectral vectors:
f (LogPA , LogPC ) LogPAC = log(e LogPA + e LogPC ) { X 1 AC } , (114a)
( )
f (POL A , POLC ) POL AC = POL1A/ 3 + POL1C/ 3 { X 2 AC
3
} [3], (114b)
f (E A , EC ) E AC = E A + E C 627.71 q A qC { X 3 AC } [kcal/mol] (114c)

1/ 3
POL AC
The open issue addresses whether the |0+> & |1+> states yields with the same results or
in which aspects they might differ in the IL ecotoxicity upon certain species. Nevertheless, a
practically criteria of deciding upon activity or structure additivity models, between eqs. (112)
and (114), respectively, may be set respecting the so called ionic liquid internal angle
between the anion-cationic activity vectors, with y iA , y iC , i = 1, N components, abstracted

from the general definition (30b), following the prescription [89]:
y iC yiA
0.707107 ... 0 + MODEL
cos AC = i =1
(115)
N N
2 < 0.707107 ... 1 + MODEL
yiC yiA
2
i =1 i =1
The illustration of the presented S-SAR-IL models was already performed by studying
the aquatic species Vibrio fischeri, Daphnia magna and Electric El recorded ecotoxicity
against a given tested ionic liquids, appropriately chosen so that containing a wide variety of
heads, side chains, and anions. This way, the present methodology may be extended over a
wide range of organisms towards designing specific eco-toxicological ionic liquid batteries
[87,108].
4. Spectral-SAR Paths and Quantum-SAR Maps

Having in deep presented the way in which structure activity correlations may be
realized from N recorded activity viewed as effects of M-structural causes, there remains to
explore the combinatory of the models (endpoints) obtained along considering different sets
of predictor variables in Table 3; this is nothing than the QSAR counterpart for what in
quantum theory is known as the complete set of commutative operators (CoSCOpe) since in
both cases the discussion is to find the minimum (however complete) operators in quantum
theory and structural variables in QSAR to behave as independent one each other so that to be
independent or orthogonal one each other. Therefore the discussion and analysis based on the
various possibilities a QSAR is realized from different structural indices implicitly or
explicitly targets the quantum description of the correlation space; here we try to show the
first step in exploitation this possibility [109].
Given a set of N-molecules, one can chose to correlate their observed activities Ai =1, N
with M-selected structural indicators in as many combinations as:
M!
C = k =1 C Mk , C Mk =
M
(116a)
k!( M k )!
linked by different endpoint paths, as many as:
K = k =1 C Mk
M
(116b)
indexing the numbers of paths built from connected distinct models with orders (dimension of
correlation) from k=1 to k=M.
Basically, for each of the C-combinations a correlation (endpoint) QSAR equation is

determined, say Yl =1,C = {y il }i =1, N , containing all computed activities for all considered N-
l =1,C
molecules within the l-selected correlation.

Note that the Spectral-SAR version of QSAR analysis computes these activities in a
complete non-statistical way, i.e. by assuming the vectors for both observed (activities) and
unobserved (latent variables) quantities while furnishing their correlation throughout the
specific Spectral-SAR determinant, see eq. (83), obtained from the transformation matrix
between the orthogonal (desirable) and oblique (input) correlations. Yet, besides producing
essentially the same results as the statistical least-square fit of residues the Spectral-SAR
method introduces new concepts reviewed here within three families as follows [109]:
Family 1
The Spectral-SAR concepts:
The endpoint (computed) spectral norm
N
Yl = Yl Yl = y
i =1
2
il , l = 1, C (117a)
allowing the possibility of the unique assignment of a number to a specific type of correlation,
i.e. performing a sort of resumed quantification of the models;
The algebraic correlation factor of eq. (105) here rewritten as

N
Yl y 2
il
R ALG , l = = i =1
N
, l = 1, C (117b)
A
A
i =1
i
2
viewed as the ratio of the spectral norm of the predicted activity to that of the measured one,
giving the measure of the overall (or summed up) potency of the computed activities
respecting the observed one rather than the local (individual) molecular distribution of
activities around the mean statistical yields; thus, it is a specific measure of the molecular
selection under study, always with a superior value to that yielded from statistical approach,
however preserving the same hierarchy in a shrink (less dispersive) manner being therefore
better suited for intra-training set molecular analysis.
Family 2
The QSAR map of end-points [109]:

The spectral path, with the distance defined in the Euclidian sense as:
[l , l '] = (Y l Yl ' )
2
+ (Rl Rl ' ) , ( l , l ' ) = 1, C
2
(118)
allows for defining complex information as path distances in norm-correlation space with
norms computed from eq. (117a) while correlation free to be considered either from statistical
(local) or algebraically (global) eqs. (59) and (117b), respectively; note that as far as
computed activity Yl corresponds to the measured activity Al defined as logarithm of inverse
of 50%-effect concentration (EC50), see bellow, both modulus of Yl vectors and R values
have no units so assuring the consistency of the eq. (118).
The least spectral path principle, formally shaped as:
[l1 ,...lk ..., lM ] = 0; l1 ,..., lk ,..., lM : ENDPOINTS (119)
that provides a practical tool in deciding the dominant { ,...} hierarchies along the paths
constructed by linking all possible k-models (i.e. models with k correlation factors) from
(116a) combinations selected one time each on a formed path generating the so called M-
endpoints containing ergodic path on K-paths assembly of (116b). However, the
implementation of the principle (119) is recursively performed through selecting the least
distance computed upon systematically application of eq. (118) on ergodic paths; if, by
instance, two paths are equal there is selected that one containing the first two models with
shorter norm difference in accordance with the natural least action; the procedure is repeated
until all C-models where connected on shortest paths; there was already conjectured that only
the first M-shortest paths (called as 1 ,..., M ) are enough to be considered for a
comprehensive (and self-consistent) mechanistic analysis [34-40].
Family 3
The Quantum-SAR indices and analysis [109]:
The inter-endpoint norm difference (IEND)
Yl l ' = Yl ' Yl , ( l , l ' ) { 1 ,..., M } (120)
that accounts for norm differences of the models lying on the M-shortest spectral paths
linking M- from the C-models of Equation (116a);
The inter-endpoint molecular activity difference (IEMAD)
l l' 1 1 (EC50 )i l
Ai j = Alj' Ail = ln ln = ln (121)

(EC50 ) j
l'
(EC50 )i
l
(EC50 )lj'
is considered from activity difference between the fittest molecules (i, j), in the sense of
minimum residues, for the models (l, l) belonging to the shortest paths 1 ,..., M for which
the inter-endpoint norm difference is given by eq. (120).
This way, we can interpret the two fittest molecules (i, j) as reciprocally activated by the
models (l, l) through the spectral path whom they belong; put in analytical terms, the
difference between quantities of eqs. (120) and (121) may assure the jump or transition
activity that turns the effect of i molecule on that of j molecule across the least spectral (here
revealed as metabolization) path connecting the models l and l:
1 l l'
ln l l'
Yl l ' Ai j
(122)
q i j
Note that if we rearrange eq. (122) in terms of 505 - effect concentrations of eq. (121)
one gets the wave-like form of molecular EC50 inter-molecular transformation:
(EC50 )li = (EC50 )lj' qil lj' exp(iYl l ' ) (123)
providing the analytic continuation in the complex plane for the IEND of eq. (120) was
l l'
assumed, i.e. Yl l ' iYl l ' outside the factor qi j . Remark that although the differences in
eqs. (120) and (121) were considered mathematically along the arrow i-to-j the quantum
transformation of eq. (123) suggests that the bio-chemical-physical equivalence
(metabolization) of the concentration effects evolves from j-to-i, revealing a typical quantum
l l'
behavior with the factor qi j
playing the propagator role as the quantum kernels in path
integral formulation of quantum mechanics [48]. This way, we may assert that eq. (123)
stands as the present quantum-SAR equation because:
it involves the wave-type expression of molecular effect of concentration, however,

for special selected molecules (the fittest out of the C-models) and for special
selected paths (the least for the M-ergodic assembly), being M and C related by eq.
(116a);
it provides the specific transition or specific transformation of the effect of a certain
molecule into the effect of another special molecule out from the N-trained
molecules, paralleling the phenomenology of consecrated quantum transitions;
it has the amplitude of transformation driven by the so called quantum-SAR factor of
an exponential form
l l'
(
qi j = exp Ai j Yl l '
l l'
) (124)
defining the specific quantum-SAR wave;
it allows the identity
(EC50 )li = (EC50 )li (125)

when the reverse effects is considered
(EC50 )lj' = (EC50 )li 1

l l'
qi j
exp iYl l '( ) (126)
and substituted in the direct one (123), as absorption and emissions stand as
reciprocal quantum effects;
it has a phase with unity norm, in the same manner as ordinary quantum wave
functions, allowing the inter-molecular real quantum-SAR transformation
(EC50 )li = qi j (EC50 ) j

l l' l'
(127)
exclusively regulated by the quantum-SAR factor of eq. (124), in the same fashion as
quantum tunneling is characterized by the transmission coefficient;
when multiple transformations take place across paths with multiple linked models,
say (l, l, l), the inter-molecular transformation ijt is characterized by the
overall quantum-SAR factor (124) written as product of intermediary ones
l l '' l l' l ' l ''

qi t = qi j q j t (128)
due to the two-equivalent ways the (EC50 )i effect may be described directly from t
l
or intermediated by j molecular effect transformations, respectively:
(EC 50 )li = q i t (EC 50 )t

l l '' l ''
( )
(129)
= q i j (EC 50 ) j = q i j q j t (EC 50 )t
l l' l' l l' l ' l '' l ''
in the same way as the quantum propagators behave along quantum paths [48];
certainly, such contraction scheme may be generalized for least paths connecting the
M-contained k-endpoints giving an overall quantum-SAR (metabolization power)
factor as:
M
qi11 i MM = qi ww11 i ww
l l l l
(130)
w= 2
Equation (123) supports the self-transformation as well, with the driven qua-SAR
factor given by:
l l'
(
qi j = i = exp Yl l ' ) (131)
during its evolution along the least paths when the same molecule (i=j) is
metabolized by activating certain structural features (ll) though specific indicators
(variables) in correlation (bindings with receptor site); this case resembles the
stationary quantum case according which even isolated (or with free motion), the
molecular structures suffer dynamical wave-corpuscular or fluctuant transformation
along their quantum paths.
With the present Quantum-SAR methodology one can appropriately identify the
molecular pairs that drive certain bio-/eco- activities against given receptor by means of
selected descriptors in a wave- or quantum mechanistic formal way. The ultimate goal
will be the computation of quantum-SAR factors along the least paths of actions that give the
quantum-map information of the conversion power of the fittest molecules in their specific
bindings [109]. This line is to be in the near future more applied and refined.
5. Conclusion
Paradoxically, the main problem for QSAR resides not in performing the correlation
itself but setting the variable selection for it; the mathematical counterpart for such problem is
known as the factor indeterminacy [110-114] and affirms that the same degree of
correlation may be reached in principle with an infinity of latent variable combinations.
Fortunately, in chemical-physics there are a limited (although many enough) indicators to be
considered with a clear-cut meaning in molecular structure that allows for rationale of
reactivity and bindings [115,116].
Therefore, although undoubtedly useful, the official trend in employing QSAR
methods is to classify, over-classify and validate through (external or molecular test set)
prediction. A gap between the molecular computed orderings and the associate mechanistic
role in bio-/eco- activity assessment remains as large as the QSAR strategy has not turned
into a versatile tool in identifying the inter-molecular role in receptor binding sites through
recorded activities by means of structurally selected common variables; that is to use QSAR
information for internal mechanistic predictions among training molecules to see their inter-
relation respecting the whole class of observed activities employed for a specific correlation.
Such an approach will also be helpful for checking the chemical domain spanned by training
molecules a feature of paramount importance also for further external tests.
The modern in silico (computational) chemical analysis respecting the bioactivity and
availability of analogues substances, potentially beneficial or detrimental for specific
interaction in organs and organisms, faces a paradoxical dichotomy: if searching for the best
correlation useful for prediction of specific molecular bio- or eco- activity QSAR models
involving un-interpretable many latent variables may be produced, while always remaining is
the question of correlation factor indeterminacy (i.e., the assumed descriptors can be at any
time replaced with others producing at least the same correlation performances); instead,
when restricting the analysis to search for molecular design and mechanisms throughout
performing SARs by means of special structural indicators for a given class of relevant
molecules, arises the price of limiting the use of generated models for further prediction.
The present review aims at filling this gap by deepening the modeling of inter-molecular
activity through extending the main concepts of recent developed Spectral-SAR [81-
90,94,109], developing the fully algebraic version of traditional statistically optimized QSAR
picture, targeting the quantification of the competition between molecular inter-activity and
inter-endpoints records. As such, the present review was mainly oriented in presenting and
developing the second (Q)SAR facet by rationalizing the recent introduced notion of spectral-
path-linking-endpoints and the associate least action principle to spectral path quantification,
in terms of the best fitted molecules, along the contained computed models, by means of the
introduced q(uantum)-SAR factor within the generally called Quantum-SAR (QuaSAR)
methodology.
On the other side, the so-called green chemistry stands as a priority field of research
which is approached by the research programs of United States and European Commission as
well. It has the goal of characterization, prediction and the control of the chemical structures
acting as toxicants on organisms and environment. The main reason for such research links
the economical, ecological and public health issues in a general paradigm: method data
information knowledge use. Within this epistemological chain the method relates the
involved procedure in obtaining the experimental data and is regulated by the chemical-
physical and biological scientific laws; the data represent the chemicals and their toxic or
carcinogenic values; information refers to elaboration of models through the recorded data;
the knowledge means the prediction or the final model of the molecular action mechanisms;
the use is defined by the legal boundaries for the toxic values or classes of chemicals
admitted.
In this context, the actual Spectral-to-Quantum SAR project propose an advanced study
based on the epistemological bulk data-information-knowledge of the chemicals used in green
chemistry in order to asses: a specific model of quantum characterization of concerned active
substances at the bio-, eco- and pharmaco-logic levels through unitary formulation of the
atomic-molecular indices for the effector-receptor binding degree potential of the logistic type
(including the temporal dependency); a computational consistent model aiming to minimize
the residual recorded activities in the experiments studying the enzymic, ionic liquid,
antagonists and allosteric inhibition interactions. The methodology allows pattering both the
controlling as well as the design of new compounds for synthesis this way eventually
covering also the method-and-use segments of the economical-social life in XXI.
Acknowledgments
Authors are truly indebted to Prof. Dr. Eduardo A. Castro from National University of La
Plata (UNLA) and La Plata Instituto de Investigaciones Fisicoqumicas Tericas y Aplicadas
(INIFTA), Argentina, for fruitful ideas exchanged on statistical and algebraic correlation
analysis during his visit in the summer of 2009 at the Chemistry Department of West
University of Timisoara, as well as to Dr. Francisco M. Fernndez from UNLA-INIFTA for
the follow-up useful comments on orthogonality statements of the Spectral-SAR algorithm.
Appendix: Common Poisson Integrals

+

I 0 (a ) = e ax dx =
2
the 0th order Poisson integral

a
+ ax2 + ay 2 + a (x 2 + y 2 )
Proof: I (a ) = e dx e dy = e
2
0 dxdy

2
ar 2 2
= e ar 2
rdrd = e rdr d
0 0 0 0
( ) ( )

2

2 2
= d e ar = e ar 0 =
2a 0 a a
+
I 1 (a ) = xe ax dx = 0 the 1st order Poisson integral
2

( ) ( )
+ +
1 1 ax 2 +
xe dx =
2 2
ax
Proof: I 1 ( a ) = d e ax = e =0

2a 2a
+
1
I 2 (a ) = x 2 e ax dx =
2
the 2nd order Poisson integral

2a a
( ) ( )
+ + +
1 d ax 2
x e dx = x xe
2 ax 2 ax 2
Proof: I 2 ( a) = dx = x e dx

2a dx
1 d
(
) ( )
+ + +
1 1
= xe ax 2
dx e dx =
ax 2
d xe ax 2
+
2a dx 2a 2a a
=
1
2a 14 2
(2 +
xe ax +
43
1
)
=
1
2a a 2a a
.
( l ' Hospital )0
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Chapter 22
ON PLOTS IN QSAR/QSPR METHODOLOGIES
Emili Besala,*, Jesus Vicente de Julin Ortizb

and Lionello Poglianic
a
Institute of Computational Chemistry, Universitat de Girona, Facultat de Cincies,
Avda. Montilivi s/n, 17071 Girona, Spain
b
Instituto de Tecnologa Qumica, CSIC-Universidad Politcnica de Valencia, Av. de los
Naranjos s/n, 46022 Valncia, Spain
c
Dipartimento di Chimica, Universit della Calabria, 87030 Rende (CS), Italy
Abstract
Many of the numerical and algorithmic procedures used in the QSAR/QSPR field lead to rank
or to predict activity values for virtual molecules. It is also well known that an image can give
more information than a list of numbers. This is the reason why in order to illustrate the
results obtained and its performance, several kinds of graphical representations are depicted in
many publications. Here some of these graphical representations are revisited. It is also shown
how the heuristic manipulation or interpretation of one of these graphical representations can
lead to erroneous conceptions: when using the popular ordinary multiple linear regression
technique, the graphical aspect of fitted versus experimental values scatter plot is affected by
regression towards the mean effects. As a consequence, the reverse presentation, i.e.,
experimental versus fitted plots, are not equivalent to the former ones. The underlying
properties beyond these graphs demonstrate how the point cloud is not symmetrically
distributed along the so-called ideal or desired line, that is, the bisector of the first and
third quadrants. The deviation from the ideal line is fixed, and it is related to the coefficient of
determination. Regarding classifiers, a distinction between the difficulty and the utility
concepts will be presented. Some classifier related graphs will be shown, as receiver operating
characteristics (ROC) curves or pharmacological-activiy distribution diagrams (PDD). Special
emphasis will be set on the former ones. ROC curves, despite not being extensively known in
the QSAR field, are presented here in order to promote them as a tool to qualify and compare
classifiers performance.
a
E-mail address: emili.besalu@udg.edu. (Corresponding author.)
b
E-mail address: jejuor@uv.es
c
E-mail address: lionp@unical.it
590 Emili Besal, Jesus Vicente de Julin Ortiz and Lionello Pogliani
Introduction
In many fields of Chemistry, quantitative structure or property relationships
(QSAR/QSPR) techniques are considered. There is a plethora of algorithmic procedures to be
applied in order to predict molecular properties, being physical or biological. The numerical
and algorithmic procedures lead sometimes to rank virtual molecules or to fit or predict
activity values. In order to illustrate the results obtained in the molecular modeling field,
several kinds of graphical representations are presented in the publications.
Regression towards the mean effects will be presented in situations in which multilinear
regression (MLR) technique is considered for model building. The concept is related to the
graphical aspect of some scatter plots (experimental vs fitted, and fitted vs experimental
values). These graphs demonstrate how the point cloud is not symmetrically distributed along
the so-called ideal or desired y = x line. An extrapolation of these regression effects is
also briefly discussed within the context of property predictions obtained via the leave-one-
out cross-validation technique.
Other kinds of graphs will be introduced, namely, the pharmacological distribution
diagrams (PDD) and ROC curves.
1. Plots of Fitted and Experimental Values in MLR Studies

In many scientific and chemistry-related fields it is very common to represent in a
bidimensional plot calculated and observed data. If fitted values are obtained by the ordinary
linear or MLR procedures, the two graphical representation choices, fitted vs. observed and
observed vs. fitted biplots, are not equivalent. The slopes of the bidimensional regression
lines in both plots bear distinct properties: the former representation exhibits a regression line
with a slope always equal to r2 and in the latter case, the regression line coincides exactly
with the bisector of the first and third quadrants of the representation plane. This situation is
always reproduced and can be mathematically proven [1-3]. Here it is exemplified by the aid
of a simple numerical example.
Let us consider a set of 5000 items (molecules). We choose this number of items in order
to get representative graphs having an evident visual message. Although the properties here
exposed apply for any plausible number of items, due to the general theorem that supports our
results [2], if only a few items are considered, the respective graphs may not visually exhibit
the properties in an evident manner. We will assume that our molecules bear some property of
interest in the field of QSAR, for instance, an activity which can be numerically represented
and modeled by a MLR equation. We have constructed such an artificial toy set and generated
a fitting MLR model involving three parameters. After the list of fitted values is obtained, the
well-known graphs representing fitted vs. observed values (a) and the experimental vs. fitted
ones (b) were constructed and displayed in Figure 1.
Note that in both representations the point clouds are not distributed symmetrically
around the bisector of the first and third quadrants (solid diagonal line), as many people will
presume. The distortion is related to the regression towards the mean effect anticipated by
Galton [4]. It can be mathematically demonstrated that, for the MLR case, in Figure 1a the
simple linear regression line (minimal squares) among the displayed points is a line bearing a
slope exactly equal to the subjacent MLR model coefficient of determination, r2.
On Plots in QSAR/QSPR Methodologies 591
120 120
100 100
80 80
Fitted value by MLR
Experimental value
60 60
40 40
20 20
0 0
-20 -20
-40 -40
-40 -20 0 20 40 60 80 100 120 -40 -20 0 20 40 60 80 100 120
Experimental value Fitted value by MLR
a) b)
Figure 1. Representation of fitted vs experimental values (a) and experimental vs fitted ones (b) for an
artificial set of items. The data have been adjusted by means of an ordinary MLR model involving three
descriptors slightly correlated with the dependent variable (experimental value).
In our case, this coefficient is equal to 0.62 and the line has been represented dashed in Figure
1a. The ordinate at the origin of this line is (1-r2)ymean, which in our case is 19.0. On the other
side, for the reversed graph in Figure 1b, the fitted line is always equal to the y = x line,
coinciding with the first and third quadrants bisector. Most people will anticipate that the
better the fitting ability of the MLR model (i.e., the greater the value of r2) the closer the
points cloud of Figure 1 are to be to the bisector line. Thats true and obvious, but most
people will also erroneously anticipate that the cloud is always symmetrically distributed
around the bisector. Thats false in general, as the present example shows. The situation is
that, asymptotically, as the determination coefficient r2 approaches to 1, the cloud becomes
narrower and tends to collapse to the bisector line. Simultaneously, and regarding the fitted
versus experimental representation, for r2 values lesser than 1 the points cloud becomes
spread but always clockwise rotated with respect to the bisector line. Conversely, if the
experimental vs fitted values are represented, the cloud remains to be anticlockwise rotated
respect to the bisector line. The aforementioned rotation effects are magnified if the
represented points are not the fitted ones but the ones obtained by a standard leave-one-out
(LOO) cross-validation procedure. In reference [4] this is also explained and mathematically
demonstrated. MLR-LOO and leave-many-out predictions present systematic deviations
which magnify the regression toward the mean effects. This is easily shown by recalling that
a MLR-LOO result (yi) is obtained from the following equation [5,6]:
hii yi y i
yi' = , i=1,2,,n. (1)
hii 1
where yi are experimental values, y i are the values adjusted by the overall MLR data fitting,
and each hii term is a diagonal element of the hat matrix. From (1) it can be seen that the
numerical differences between experimental, fitted and cross-validated values are related:
yi yi = (1 hii ) yi' yi ( ) (2)

and it is also known that the hii terms are bounded [7] between the values 1 and m/n (number
of descriptors divided by the number of objects). From these condition, and due to de fact that
n>m, is easy to see that the differences yi yi and yi yi appearing in (2) bear the same
'
sign and that the second difference is magnified with respect to the first one. This shows how
a cross-validated value (yi) differs from the experimental one more than the fitted one does.
Globally, this effect magnifies the rotation of the points cloud in similar graphs as those on
Figure 1 but when cross-validated property values are depicted against the experimental ones.
2. An Alternative: Orthogonal Regression

An alternative method for obtaining a symmetric graph (points cloud around a fitting
line) is orthogonal regression [1,3,8]. If orthogonal least squares (OLS) is considered, the sum
of point-line quadratic distances is minimized, whereas for the standard linear regression
method one minimizes the sum of vertical distances or differences between fitted property
and experimental one (while the distance parallel to the x-axis is not at all considered). OLS
method provides with a unique biplot regression line, that is, the distinction between abscissa
and ordinate is irrelevant. The point cloud is symmetrically distributed around the OLS line
(see Figure 2).
120 120
100 100
80 80
Fitted value by MLR
Experimental value
60 60
40 40
20 20
0 0
-20 -20
-40 -40
-40 -20 0 20 40 60 80 100 120 -40 -20 0 20 40 60 80 100 120
Experimental value Fitted value by MLR
a) b)
Figure 2. Representation of the orthogonal regression line (dashed line) for the points of the presented
example. This line corresponds to the first principal component of the represented bidimensional data
and is the same entity in both representations, fitted vs experimental (a) or experimental vs fitted (b)
values.
The method requires both series of data, {xi,yi}, to be conceptually equivalent and
expressed in the same units, if any. In fact, the obtained fitted line by OLS coincides with the
first eigenvector of the point cloud [8,9]. In Figure 2a this OLS equation line is represented
(dashed line) for our example and it has the expression Fitted=0.738Experimental+13.1. Due
to the nature of this equation and the symmetric role of x and y variables, the related formula
Experimental=1.36Fitted-17.7 (dashed line in Figure 2b) can be obtained from the former
one by isolating the required variable. Of course, this manipulation is not possible when
dealing with standard regression lines.
As it has been now stated, for the particular case of orthogonal regression, one can
properly say that the point cloud is symmetrically distributed among the fitting bidimensional
line, but always clockwise rotated respect to the bisector due to the inherent regression
towards the mean effect attached to the MLR method. If the MLR determination coefficient
tends to be the unit, the orthogonal fitting equation line also tends to collapse at the bisector
one.
3. A Distinction between Utility and Difficulty in Ranking

There are a couple of graphs the authors have found useful in order to evaluate the utility
and the difficulty of the results obtained by ranking methods. For illustrative purposes, here
we will consider the case of ranking a set of 99239 molecules taken from the Cambridge
Structural Database v5.24 (Nov. 2002) of the Cambridge Crystallographic Data Centre. In
this set, molecules were labeled as drugs or non-drugs. The molecules of interest are the 674
(0.68%) drug ones. We will not focus here on the nature of the ranking method we had used
but on the final result obtained. As it is expected, due to the application of an effective QSAR
model, the 674 compounds of interest are not uniformly distributed along the final sorted list
of compounds. As desired, the density of active compounds is greater at the beginning of the
ranked series.
3.1. Some Probability Considerations
The obtained rankings and classification results have been studied from a probabilistic
point of view. In order to estimate the quality of the obtained predictions a statistical
significance test calculation was designed [10,11]. This subsection is devoted to expose the
main ideas relative to the basic formulation.
Let us consider we have a series of m molecules (the whole database set, m=99239) and
that n (=674) of them bear a property of interest (to be a drug in our case). We randomly
select s out of the m molecules and we are asking what is the probability that r of the selected
molecules are of interest. If there are neither a priori preferences nor more information
available, this probability is equal to
n m n

r s r
P(r , n; s, m ) = with rsm; rnm. (3)
m

s
In eq. (3) the numerator accounts for the number of possible ways to take r compounds of
interest from the subset of n multiplied by the number of ways to select s-r uninteresting
compounds from the remaining database set of m-n. This product gives the total number of
ways to select r and only r molecules of interest from the whole database. The denominator
counts the total number of ways to construct sets of s structures in the database.
Within this framework, significance levels (p values) are obtained from cumulated
probabilities, that is, given fixed values of m, n and s, the p significance level value (queue on
the right) corresponds to the probability to select r or more than r structures of interest.
Compared to a random selection of structures, this datum reveals the probability to embrace r
or more active compounds when s are selected:
min( n , s ) r 1
p(r , n; s, m ) = P(i, n; s, m) = 1 P(i, n; s, m) . (4)
i= r i = max( 0 , s + n m )
In eq. 4, the first summation expresses the direct addition of probabilities for the
situations corresponding to collect r, r+1, r+2, ... active compounds. The maximal number of
active compounds will be n (all the actives) unless the size of the selected set, s, is smaller
than this number. Hence the upper limit for the first summation symbol. The last equality in
eq. 4 alternatively counts the significance probability substracting from the unit all the non
favorable cases, i. e., to collect less than r active compounds. The lower limit appearing in the
second summation is due to the fact that the minimal number of structures of interest which
can be chosen is max(0,s+n-m). This is so because there are situations for which the minimal
number of active compounds in the selected subset is zero, but if the size of the sample, s, is
greater than the number of inactive molecules, m-n, then this minimum value of active
compounds would be the difference s-(m-n). This formulation can be found in several places
of the literature [11,12] and was firstly presented by the present authors and coworkers [10].
3.2. Enrichment Factors
References [13] and [14] provide a natural and intuitive enrichment (e) factor definition:
it corresponds to the actual ratio of molecules of interest found in a selected subset divided by
the overall ratio of target molecules within the whole database. Following the notation
employed in eqs. 3 and 4, this reads
r/s r
e= = n (5)
n/ m ms
The last equality explicitly shows an equivalent and practical definition: the enrichment
is the same as the quotient between the number of active compounds found in the subset of
size s and the proportional number of active structures if a uniform distribution is being
expected.
3.3. The Result Obtained
As already seen, only 0.68% of the compounds present in the analyzed database were
drugs. After the data processing and ranking, this percentage raised up to 41% for the first
100 molecules. This corresponds to a 60-fold improvement which can be equivalently

measured with both quantities, the percentages quotient (see Table 1, column 3) or the
enrichment factor, eq. (5). Furthermore, 337 drugs (50% of the total number of drugs)
appeared in the first 10.7% (position 10569) of the sorted database (enrichment of 4.7). By
contrast, there were only 17 drugs in the last ranked decile.
The classifier performance can be checked in Table 1, which lists some ranked positions
where drug molecules are found in the sorted list. For every position, the partial cumulated
percentage of drug molecules in the selection is shown and this proportion is compared to the
global bulk one, 0.68%, giving its quotient the enrichment factor defined in eq. (5). The last
column of Table 1 gives the logarithm of the corresponding significance p-values, calculated
according to eq. (4).
160 0
140
-40
120
p-values (log)
100
Enrichment
-80
80
-120
60
40
-160
20
0 -200
1 10 100 1000 10000 100000
Number of first ranked compounds
Figure 3. Enrichment (leftmost vertical scale, thick line in graph) and p-significance values (right scale,
thin line) found along the ranked list of molecules. Note the logarithmic scaling in the abscissas axis.
Figure 3 shows the enrichment factors (leftmost vertical scale, thick line in the graph)
obtained when selecting the indicated number of first ranked molecules in the abscissas
logarithmic scale. The probabilistic formulation presented above tells us how long these
results arise from randomness: Figure 3 also displays the logarithm of the significance p-
values (scale on the right, function depicted with a thin line) versus the number of first ranked
compounds. Note that very small p values are achieved.
Despite the number attached to the first 100 ranked compounds seems to be impressive
(p10-70 and attached to a quite high enrichment), the graph reveals at once how an even
more difficult (highly improbable) result is obtained when the first 3000 compounds are
selected (significance p-value of the order of 10-160), despite the corresponding enrichment
is much lesser. For this last case, the enrichment is lesser because of the great difficulty
inherent to correctly classify all the 3000 compounds out of the whole data base.
Table 1. Ranked positions assigned to some drug molecules by the classifier. Enrichment
factors and the corresponding significance p -values (eq. 4) are given. The symbols used
in headers correspond to the ones found in the text
Ranked position Percentage

Drug molecule Enrichment p-value
in full database of drugs in
cardinal (r) factor (e) (logarithm)
(s) selection (100r/s)
1 1 100.0 147.2 -2.17
2 7 28.6 42.1 -3.02
3 8 37.5 55.2 -4.77
4 9 44.4 65.4 -6.59
5 13 38.5 56.6 -7.76
6 16 37.5 55.2 -9.14
7 17 41.2 60.6 -10.93
8 18 44.4 65.4 -12.75
9 19 47.4 69.7 -14.60
10 20 50.0 73.6 -16.47
20 42 47.6 70.1 -31.83
30 58 51.7 76.2 -48.94
40 90 44.4 65.4 -61.59
41 100 41.0 60.4 -61.28
50 133 37.6 55.4 -72.34
60 180 33.3 49.1 -83.01
70 284 24.6 36.3 -86.31
80 340 23.5 34.6 -96.95
90 419 21.5 31.6 -105.30
100 520 19.2 28.3 -111.99
133 1000 13.3 19.6 -127.60
200 2402 8.3 12.3 -154.93
217 3000 7.2 10.7 -156.32
256 5000 5.1 7.5 -151.00
300 7820 3.8 5.6 -146.57
326 10000 3.3 4.8 -141.32
337 10569? 3.2 4.7 -144.46
400 16969 2.4 3.5 -134.08
500 32519 1.5 2.3 -107.25
564 50000 1.1 1.7 -72.88
600 56961 1.1 1.6 -72.42
674 98914 0.7 1.0 -0.96
3.4. Enrichment Factors and Probability Mean: Utility and Difficulty
The enrichment factors depicted in Figure 3 reveal the utility of the obtained ranking.
That is, a molecular engineer will know from this data if the first set of ranked compounds is
enough enriched in order to be transferred to a posterior design or treatment stage. Usually, in
the literature it can be read that enrichment factors of 10-fold or more are desirable. This
seems to be a good general rule of thumb, but it has to be combined with another datum: the
number of structures which are to be collected in order to reach this enrichment factor. This is
so because it is not the same to have a 10-fold enrichment factor for a set of the first 10
molecules than for a set of the first 1000 or 10000 ranked ones. This last aspect is related to
probability: in Figure 3 the p-values tells us about the difficulty to get a particular result. All
in all, for a molecular designer it is desirable to combine both aspects: a practical utility due
to a notable enrichment factor combined with a high degree of difficulty to reach this
classification performance. This is the same to say that high enrichments are desirable, but it
is even more desirable to reproduce these enrichments in library subsets as bigger as possible.
On the other side, it can be useless to consider only the few first ranked compounds on a
ranked list, because despite of having and eventual high and impressive enrichment factor
(apparent utility), the difficulty (significance, p-value) could be easily reachable.
When a fixed database is ranked using distinct methodologies and when the goal is to
compare the classification power of the methods, both parameters (enrichment and p values)
are useful and will rank the methods in the same way. But things go different if comparisons
must be made among distinct libraries. In general, the enrichment factors are not comparable
directly and the ultimate value useful to rank the methods is the difficulty of the achieved
results, that is, the significance p value. Thus, the consideration of p-values is a general
procedure which provides with objective numerical quantifications that can be translated to
compare ranking methods (either applied over the same or distinct libraries) and ranking
results (for a fixed library using distinct methods).
In fact, enrichment factors do not provide much information by itself unless the values of
r, s, n and m are also provided (by the way, this also enables to compute significance p-
values!). If an index for the quality of the classifier is to be related to enrichment, it is better
to report the fraction of maximum enrichment which can be achieved for a given case study.
The enrichment can be evaluated relative to the maximum affordable one:
min(s, n ) / s
emax = (6)
n/m
Then, the fraction of maximal affordable enrichment is simply the quotient
e r
ef = = (7)
emax min(s , n )
Note that in this last equation the size of the database (m) does not appear.
4. ROC Curves
Receiver Operating Characteristic (ROC) curves [15] were developed in the 1940-1950's
in the context of radar signals research in order to treat noise. The research was motivated by
the Pearl Harbor Japanese attack. The question was why the US radar receiver operators had
missed the enemy signal. Later, in the 1960s ROC curves were used in psychophysics, then
in medicine and more recently for the evaluation of machine learning results. It is not still
common to see analysis of ROC curves in the QSAR or molecular design fields, but we
believe that ROC curves constitutes a good tool to be taken into account to evaluate
dichotomous classifiers.
Table 2. Confounding table obtained once the result of a classifier is known
Classification method result

Positive Negative
Positive TPF FNF
Real situation
Negative FPF TNF
A ROC curve constitutes a graphical representation of the global efficiency of a

classifier. It is a graphical representation for the frequencies of true positives and negatives
and also for false positives and negatives along all the series of ranked compounds. In Table 2
it is shown a typical confounding matrix suitable for decision-making protocols. The
nomenclature can be adapted to our example above of ranking a set of molecules: a positive
result is to being a drug compound, whereas to be a non-drug molecule it will called here to
be a negative result.
In the boxes, the relative frequencies respect to the whole populations of real positive and
negative cases are listed. These frequencies are arranged as being true positives fraction
(TPF), true negatives fraction (TNF), false positives fraction (FPF) and the false negatives
fraction (FNF). Due to the nature of these definitions, the condition FNF+TPF=1 holds. That
is the same to say that all the real positive cases (drugs) have been classified either correctly
or badly. It also holds that FPF+TNF=1, that is, the classification method has separated the
real negative cases (non-drugs) into two excluding parts, true negatives or false positives.
Threshold value
TPF
FNF
FPF
TNF
Figure 4. The four fractions of a confounding table. Upper distribution applies for the positive cases
whereas the lower one is for the negative ones. The classifier, once given a threshold value, defines the
fractions. The more distributions overlapping the worse the classifiers performance and the larger the
FNF and FPF values.
In this context, the sensitivity is defined as a parameter which shows how good the
classification method at detecting positive cases is. This corresponds to the true positive
fraction (TPF), i. e., the probability that the classification method gives a true positive result
knowing that the molecule is a real positive case. This corresponds to the conditional
probability P(C+|+). A counterpart of it is the specificity, which measures the ability of the
classifier to pick out real negative cases, the TNF. It is the same as the P(C-|-) conditional
probability. Additionally, the FNF corresponds to the probability of the method to give a case
classified as negative when de molecule is a real positive one, P(C-|+). Finally, the fraction
FPF corresponds to the P(C+|-) conditional probability.
All the above conditional probabilities, i.e., the TPF, FNF, FPF, and TNF terms can be
graphically displayed as being the respective areas under two density distribution functions
(usually it is depicted one gaussian curve for both, the real positives and the negative cases)
delimited by a critical decision point (threshold value) defined by the classification method or
by the user. This conceptual display is depicted in Figure 4.
It has to be understood that the classification method defines the horizontal scale in
Figure 4 and that it also defines the distributions for true and false cases (ROC curves are
non-parametric and are insensible to the particular probability distributions we are dealing
with). A good classification method is one able to generate two non-overlapping distributions.
If not, the FNF and FPF terms will grow dramatically. Note that if the distributions are
maintained and the threshold value (vertical line) is moved to the left (to the right), then the
proportion of false negatives decreases (increases)... but at the expense that the false positives
fraction increases (decreases) accordingly. This sort of mutual dependence vanishes if the two
distributions do not overlap and the threshold value is properly set.
0.8
Sensitivity
0.6
0.4
0.2
0
0 0.2 0.4 0.6 0.8 1
1 - Specificity
Figure 5. ROC curve attached to the example of the text relative to the classification of molecules of
being drugs or non-drugs.
Once the molecular series is ranked, inherently the false and true cases distributions are
generated. Then, in order to obtain the ROC curve it is necessary to move the threshold value
along all the ranked series. For each threshold value a ROC curve point is depicted: every
threshold defines the values of TPF, FNF, FPF, and TNF. In particular, the sensitivity and the
specificity are also defined. A ROC curve is the representation of all the (1-specificity,
sensitivity) points. Thats equivalent to depict the (1-TNF, TPF)=(FPF, TPF) values. For our
example, the corresponding ROC curve is the one of Figure 5.
Often the diagonal depicted in Figure 5 is shown and this corresponds to a random or a
neutral classifier. If the curve (or a part of it) goes below this diagonal, it means that the
classifier must have its criteria reversed (change its polarity) in order to get a proper data
dicotomization.
FNF
0.8
FPF TNF
Sensitivity
0.6
0.4
TPF
0.2
0
0 0.2 0.4 0.6 0.8 1
1 - Specificity
Figure 6. The four fractions (TPF, FNF, FPF, TNF) attached to a specific point of a ROC curve.
In many places of the literature it is represented the portion of hits (in our example drugs)
retrieved along the ranked series against the portion of the sorted database. In general, this
representation is not the same as to depict a ROC curve, but if the database is large compared
to the number of hits, then both graphical representations become almost the same.
As said above, a ROC curve shows the overall performance of the classifier, displaying
the sensitivity and the specificity obtained for each threshold value. Figure 6 shows how, at
every point of the ROC curve, all the four fractions (TPF, FNF, FPF, TNF) are depicted in the
graph.
One parameter which is extensively used in order to quantify the overall performance of a
classifier is the area under the curve (AUC). This is displayed in the shadowed zone in
Figures 5 and 6. A random classifier has an attached value of AUC=0.5, and the greater the
AUC from this value, the better the classifier performs, at least from a global perspective.
Roughly, the following intervals are assumed relative to the quality of a particular result:
AUC between 0.50 and 0.75 is fair, between 0.75 and 0.90 is good, it is very good for values
of 0.90 0.97, and it is excellent for greater values. For the example explored here, the AUC
is equal to 0.79. An ideal classifier will have an AUC equal to 1 (the ROC curve collapses to
the sensitivity axis and to the upper segment in the box represented in Figure 5 or 6).
The AUC is a universal parameter useful to compare distinct classifiers. This area can be
interpreted as a mean sensibility along all the specificity values. This is also directly related to
the Wilcoxons sum of ranks statistic [16,17]. The AUC can be also interpreted [17,18] as the
probability to correctly classify a couple of molecules, one being a drug and the other being a
non-drug.
5. Pharmacological-Activity Distribution Diagrams

The pharmacological-activity distribution diagrams (PDDs) are useful tools for the
selection of SAR equations for molecular design [19]. They are histogram-like plots in which
one or several groups of chemical structures, preferably from a test set, are distributed into
intervals of the value of the predicted property. They were initially used to visualize how a
group of active compounds was distributed with respect to a group of inactive ones, by using
a discriminant function. Galvez el al. [19] noticed that the QSAR equations could be used as
discriminant ones with the aid of PDDs. This is the reason why usually two groups (active
and inactive compounds) are usually plotted in PDDs. These QSARs, that can also model
pharmacokinetic properties, are called limiting properties.
By using simply the number of compounds in ordinates has the drawback that the two
groups must have approximately the same cardinal to reach a useful representation.
Furthermore, it is advisable including some kind of penalty in the function plotted that gives
account of the overlapping of the two groups. Thus, the function introduced was the quotient
between the fraction of molecules pertaining to one group that falls in the considered interval,
and the same fraction for the opposite group plus one, to avoid the division by zero. This
gives idea of the probability of pertaining to a group and was termed as expectancy. Thus, for
each arbitrary interval of whatever function, it can be defined the expectancy of activity as:
a
Ea = (8)
i +1
where a is the quotient between the number of active compounds in this interval and the
number of total active compounds; in the same way, i represents the ratio of inactive
compounds. It is also defined the expectancy of inactivity just as
i
Ei = (9)
a +1
For a given equation, it is easy to see the zones in which the overlapping between Ea and
Ei is minimal, and so to determine if the equation studied can be useful for the selection and
molecular design. This also allows determining the intervals of the limiting property in which
there is a good expectancy to find new active drugs: where the probability of finding new
active compounds is optimal relating to the chance of obtaining false positives.
When the groups of molecules are structurally heterogeneous, PDDs generally adopt
skew gaussian shapes or present several maxima. Let us see several examples. Figures 7 to 9
show the PDDs obtained with three QSAR equations and Figure 10 the PDD of a
discriminant function [20]. In these cases, the correlation variables are connectivity indices
(see reference 20 for its definitions), and the equations are applied to test sets. The active
group is made up of compounds that show anti-herpes simplex activity (in white in the
figures). The inactive group contains drugs that exhibit pharmacological activities different
from anti-herpes (in black in the figures).
0.6
0.4
Active
0.2
Non-active
0
-20
-5
10
25
40
55
4 4 v
Figure 7. PDD for IC50 = - 17.36 p + 41.39 pc + 21.71. Abscises: IC50 / M. Ordinates:
Expectancy of activity in white, expectancy of inactivity in black.
Figure 7 displays the PDD for the inhibitory concentration-50 against the herpes simplex
virus type 1. This is a property determined in vitro. The maximum expectancy for the active
group is between -5 and 0 and for the inactive group is between 15 and 20 M. These values
are predictions for test sets as said, and even if the predicted values are not so accurate, the
PDD reveals that this limiting property can be used for discriminating anti-herpes and
inactive compounds respectively. The interval that can be chosen depends of the purpose and
must be determined by agreement. For example, to minimize false positives, the ideal interval
should be from -10 to 0.
0 0 v 3 v 3 v 4
Figure 8. PDD for log(ID50) = - 1.42 + 4.81 - 11.41 p + 1.32 c + 4.17 pc - 8.42.
Abscises: log(ID50). ID50 expressed in M. Ordinates: Expectancy of activity in white, expectancy of
inactivity in black.
The PDD shown in Figure 8 corresponds to another microbiological property: logarithm

of the inhibitory dose-50 (ID50), determined in vivo. In this case, the limiting property is not
as discriminant as in the former case, although the absolute maxima of each distribution are
not coincident.
Figure 9 represents the PDD for a pharmacokinetic property, the percentage of

unchanged drug found in urine, in logarithmic form. The maxima for active and inactive
compounds are clearly different. This example illustrates how a property unrelated with the
activity can be limiting if modelled for a group of active compounds.
1 v 2 3 3 v 3
Figure 9. PDD for log(UDU) = - 4.67 + 8.70 - 3.64 p + 3.15 p - 8.05 c - 9.23. Abscises:
logarithm of percent of unchanged drug in urine. Ordinates: Expectancy of activity in white, expectancy
of inactivity in black.
0 v 3
Figure 10. PDD for D = - 1.17 + 2.11 p + 2.79. Abscises: Classification function obtined by
linear discriminant analysis. Ordinates: Expectancy of activity in white, expectancy of inactivity in
black.
Finally, Figure 10 shows the PDD for a linear discriminant function obtained for anti-
herpes activity. This shows the typical behaviour of a discriminant function with two
Gaussian curves partially overlapped. It is noteworthy that the PDDs can reflect the
pharmacological activity profile of a group of molecules independently that the nature of the
limiting property used. It can be a QSAR of a pharmacological property, a discriminate
function or a QSPR of a pharmacokinetic property.
PDDs are valuable tools in the validation of limiting properties, and consequently in the
search of new drugs, and give a clear picture of their quality.
Acknowledgments
E. B. acknowledges the financial support of the grant number CTQ2009-09370 of the

Spanish Ministry of Science and Innovation. J. V. de J. O. offers thanks for a grant from the
I3P program of the Spanish Consejo Superior de Investigaciones Cientificas (CSIC) and
financial support from the project MAT2007-64682 (Ministerio de Educacin y Ciencia),
Spain.
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[11] Barroso, J. M.; Besal, E. Design of experiments applied to QSAR: ranking a set of
compounds and establishing a statistical significance test Theochem 2005, 727(1-3),
89-96.
[12] Yan, S. F.; H. Asatryan; Li, J.; Zhou, J. Novel Statistical Approach for Primary High-
Throughput Screening Hit Selection J. Chem. Inf. Comput. Sci. 2005, 45, 1784-1790.
[13] Pearlman, D. A.; Charifson, P. S. Improved scoring of ligand-protein interactions
using OWFEG free energy grids J. Med. Chem. 2001, 44, 502-511.
[14] Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W.
T.; Banks, J. L. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2.
Enrichment Factors in Database Screening J. Med. Chem. 2004, 47, 1750-1759.
[15] Egan, J.P.; Signal Detection Theory and ROC Analysis; Academic Press: New York,
1975.
[16] Bamber, D.C. The area above the ordinal dominance graph and the area below the
receiver operating characteristic graph J. Math. Psychol. 1975, 12, 387-415.
[17] Hanley, J.A., McNeil, B.J. The meaning and use of the area under a receiver operating
characteristic (ROC) curve Radiology. 1982, 143, 29-36.
[18] Hanley, J.A., McNeil, B.J. A method of comparing the areas under receiver operating
characteristic curves derived from the same cases Radiology. 1983, 148, 839-843.
[19] Glvez, J.; Garca-Domenech, R.; Gregorio-Alapont, C.; de Julin-Ortiz, J. V.; Popa L.
Pharmacological distribution diagrams: a tool for de novo drug design J. Mol. Graph.
Model. 1996, 14, 272-276.
[20] de Julin-Ortiz, J. V.; Glvez, J.; Muoz-Collado, C.; Garca-Domenech, R.; Jimeno-
Cardona, C. Virtual combinatorial syntheses and computational screening of new
potential anti-herpes compounds J. Med. Chem., 1999, 42, 3308-3314.
Chapter 23
APPLICATION OF THE FUZZY LOGIC THEORY

TO QSPR-QSAR STUDIES
Pablo R. Duchowicza and Eduardo A. Castrob

Instituto de Investigaciones Fisicoqumicas Tericas y Aplicadas INIFTA (UNLP, CCT
La Plata-CONICET), Diag. 113 y 64, C.C. 16, Suc.4, (1900) La Plata, Argentina
Abstract
The Fuzzy Logic Theory has been considered a brilliant and potent revolutionary computer
technology that has received broad attention during the last decades, widely employed in the
fields of Physics, Mathematics and Chemistry, particularly for the classification and
systematization of information with applications in Theoretical Computer Science and
Artificial Intelligence. The main reason for this is that Fuzzy Logic is a system of concepts,
principles and methods for approximate ways of reasoning which are expressed in natural
language. This chapter reviews the application of Fuzzy Logic Theory to the field of the
Quantitative Structure Property-Activity Relationships Theory, describing the studies
developed by different experts in this fascinating field.
1. Introduction
The whole world of the Fuzzy Logic Theory (FLT) has a firm basis that enables it to
describe complex disciplines providing a different kind of mathematics with admiration.
Fuzzy concepts are found in Law, Medicine, Economics, Linguistics, System Theory,
Philosophy or Psychology. This sort of fuzzy Mathematics describes quantities which are not
able to be investigated by probability distributions, and this kind of reasoning parallels real-
life though patterns much better than crisp reasoning does, as is a theory of the common
sense.
a
E-mail address: pabloducho@gmail.com / prduchowicz@yahoo.com.ar. Corresponding author: Tel.: (+54) (221)
425-7430 / (+54) (221) 425-7291. FAX: (+54)(221) 4254642
b
E-mail address: castro@quimica.unlp.edu.ar / eacast@gmail.com
608 Pablo R. Duchowicz and Eduardo A. Castro
According to the founder of Fuzzy Logic Lofti A. Zadeh [1], who developed the theory in
the United States in 1964, it is a versatile theory, as it is possible to take anything in any field
and fuzzify it. Much of the logic behind human reasoning is not the traditional Boolean two-
valued or even multivalued logic, but a logic with fuzzy truths, fuzzy connectives, and fuzzy
rules of inference. Fuzzy Logic Theory is not a logic that is fuzzy but a logic that deals with
fuzzy quantities [2]. In the realms of FLT, the concept of fuzzy sets represents mathematical
objects that are able to model the vagueness present in our natural language when we describe
real phenomena that do not have sharply defined boundaries. Therefore, fuzzy sets are sets
that calibrate vagueness, and thus FLT has been suggested as a fundamental tool for carrying
out approximate reasoning processes and for automation when knowledge is uncertain,
incomplete, imprecise, or vague [3].
In ordinary Mathematics, we are used to dealing with well-defined problems admitting a
forced yes / no answer, for instance, certain subsets of a given set of objects such as the
subset of even integers in the set of integers. On the contrary, when we speak of the subset
of structurally similar compounds in a set containing various chemical families of
compounds, it may be difficult or impossible to decide whether a compound is in that subset
or not. The main drawback of applying the ordinary approach in this case is that there may be
information lost during this process, as this information is not being correctly expressed.
After Zadeh founded the FLT, the technique has evolved to become more general and
applicable to different problems of both the chemical and biological interest. Different
thinkers has recognized in the past the existing ubiquity of fuzziness: the physicist Albert
Einstein, the quantum physicist Louis de Broglie, and philosophers W. V. Quine and Ludwig
Wittgenstein. In view that fuzzy concepts need to be properly addressed in any mathematical
problem in hands, the FLT approach involves a broad number of applications in several active
fields of System Theory, whose great goal is a skeleton key for the working of systems. As it
is known, Expert Systems (ES) are software that make decisions like humans, i.e. doctors,
scientists, etc. In ES the rules expressing knowledge and facts are linguistic in nature, and the
uncertainty involved can take on various facets, such as probability, possibility, belief
functions, or fuzzy measures. Therefore, Fuzzy-based ES would reflect the way humans think
in the best manner. Complex systems are systems with a complicated and unpredictable
behavior, which defy the human comprehension, such as living organisms [4]. Control
Engineering of complex systems, where mathematical models are difficult to specify, and
Pattern Recognition, where classes of objects are more fuzzy than crisp and the variability
across objects needs to be modeled, would represent real challenges in theories other than the
one proposed in FLT [2].
In his 1965 publication [1], Zadeh noted that fuzziness plainly differs from probability,
although both of them describe uncertainty numerically and they resemble, since both of them
deal with degrees, one of truth and the other of likelihood. Probability treats yes/no
occurrences, requires ignorance, and is inherently statistical. In contrast, fuzziness deals with
degrees, does not require ignorance, and is completely nonstatistical. Consider a similar
example to that provided in ref. [2], but now applied to the chemical context, the gas phase
recombination reaction of two unknown atomic species A and B. The probabilistic question:
Is atom A more electronegative than atom B? leads to the answer of 0.5 (ignorance): A may
be more electronegative than B (value 1) or may not (value 0). Suppose now that we know
that the electronegativity of atom A is the half value to that of B (additional information). The
question now becomes: To what extent is atom A more electronegative than atom B?
Application of the Fuzzy Logic Theory to QSPR-QSAR Studies 609
which is a fuzzy question. The answer is still the same in the fuzzy case (0.5) but become
scertainty (0) for the probabilistic point of view, as we now know that A is less
electronegative than B. Unlike fuzziness, probability dissipates with increasing information,
as the more we know about the problem, the less uncertain it is. Probability vanishes, it
simply requires ignorance. On the contrary, fuzziness can coexist with total information on
the problem in hands. Fuzzy probabilities are a kind of fuzzy number, that is to say, an
approximate number like more or less 30 percent and around 30 percent. Classic
probability deals with such estimates by setting a crisp margin of error, such as plus or minus
5 percent, but fuzzy probability blurs this range. It is also possible to employ fairly low
instead of 30 percent.
The main concern of FLT is to represent, to manipulate, and to draw inferences from
imprecise statements. In the chemical context, several known properties of interest involve a
fuzzy definition, as is the case for acidity, structural similarity, aromaticity, reactivity,
Hartree-Fock molecular orbitals, molecular shape, molecular symmetry, and others. In all
these examples, the quantities are considered fuzzy in the sense that they cannot be sharply
defined, and thus involve a commonly established criterion for dealing with such vague
terms. For instance, not all the aromatic compounds are perfectly aromatic, they are aromatic
to some extent. An ideal aromatic is an aromatic compound to 1.0 extent.
The Fuzzy Logic Theory (FLT) is suitable for dealing with many real world problems,
characterized by complexities, uncertainties, and a lack of knowledge of the governing
physical laws. Fuzzy Logic provides a conceptual framework for dealing with the problem of
knowledge representation in the environment of uncertainty and imprecision. The most
important application of Fuzzy Set Theory (FST) is the fuzzy rule-based models, where the
relationships among system variables are modeled using linguistically interpretable rules.
This virtue of FLT makes it to encode expert knowledge in a direct and easy way. Another
advantage of the fuzzy approach over traditional ones lies in the fact that fuzzy system does
not require a detailed mathematical description of the system while modeling.
Among the capabilities of FST is the numerical expression of the impression that stems
from a grouping of elements into classes that do not have sharply defined boundaries. Fuzzy
set theory has been found to be a powerful mathematical tool in Artificial Intelligence
especially in the areas of knowledge representation and designing Fuzzy Expert Systems and
Artificial Neural Networks, Qualitative Reasoning, and Pattern Recognition [5]. For instance,
the Artificial Neural Networks appeared in the mid-1980s, when Artificial Intelligence efforts
started to stall. These are devices that learn and that are crudely based on the brain. If ANN
are linked to fuzzy systems, they become more powerful and reliable. It has also been widely
studied in developing intelligent fuzzy logic control and optimization systems in Engineering.
Present chapter revises in certain degree of details several Quantitative Structure
Property-Activity Relationships (QSPR-QSAR) studies developed by different experts that
apply the active area of FLT, and also include some illustrative examples in order to
illuminate non-specialist readers with a valuable insight for understanding the methodology
employed. It is not our purpose to make use of a dense mathematical treatment of fuzzy
concepts, but to concentrate more on providing a clear and transparent application of FLT to
gain a better insight of its modeling capabilities.
2. Fuzzy Sets and Rules

As it has been known for decades, a set is defined as a collection of definite,
distinguishable objects, in good agreement with our intuition [6]. The Cantors classical Set
Theory imposes a strict membership of an object to a set, that is to say, objects either belong
or do not belong to the set [1,7], and none straddle the line. One simply dictates a clear
breakpoint. FST has been developed to depart from this two valued logic scheme. A fuzzy set
(fs) A is defined by its objects x and their respective degree of memberships (dm) to the set.
The use of dm give a mathematical definition of fuzzy sets that enables to continuously
increase the number of objects encountered in human reasoning that can be subjected to the
scientific investigation. The dm of an object in the fs can range in the real closed interval
[0...1] , and is given by a defined fuzzy membership function (fmf). This fmf maps each x to
a given dm value. The space of objects X, which includes all generic elements x and A X ,
is called the Universe.
Figure 1. Examples of three fmf and their associated parameters [9].

In contrast to classical sets, an object can belong to multiple sets simultaneously by

having different dm in each set. There are several kinds of fmf which can be used, such as
triangular, trapezoidal, gaussian, bell, etc. [8] During the design of fuzzy systems if the
number of fmf is large, which leads to a great number of fuzzy rules, this may lead to the
overfitting problem which makes the system to loose predictive capability and increase the
computation time. In addition, wrong membership functions can lead to poor performance
and possibility of instability. The fmf can be optimized through learning methods [9].
Fuzzy sets include crisp sets, as a crisp set is a fuzzy one with membership values of 1
and 0. If an object is in a crisp set, it must have a value of 1; if it is not in a fuzzy set, it can
have any value except 0. It is possible to fuzzify fuzziness, as many aspects of the classic
Fuzzy Logic Theory result crisp: although a set may be fuzzy, a membership value of 0.7 is
crisp. Therefore, second-order fuzzy sets or ultra-fuzzy sets involve values like about 0.7.
Each membership is itself a fuzzy set [2].
In general, a fuzzy conditional rule is made up of a premise and a conclusion [7]:
IF premise THEN conclusion (1)
The premise term involve a number of fuzzy predicates Pi , of the type

Pi = ( X i IS Ai ) , each of them may appear negated or combined by different operators such
as AND or OR. With the purpose of applying an inference method to assess the conclusion, it
is first necessary to assess the dm of the premise. This is done by performing the respective
fuzzy operations on its Pi , leading to the dm for each of them. For instance, dm(predicate) is
calculated by assessing dm of X i in fuzzy set Ai . Two cases appear: (a) if X i is a fs, its dm
is obtained by making an intersection between both sets and choosing the maximum value of
dm; (b) if X i is a crisp value, its dm in Ai is the value that its fmf assumes for X i . The
conclusion is a result from the assessment of all the rules concerning the same output
variable. In general, after obtaining the fuzzy output set, this has to be defuzzified for
transforming the fuzzy information into numerical information. There exist various
defuzzification methods, many of which simplify calculation of the output value using a
single operation that aggregate the rules and defuzzify, without the need to calculate the fuzzy
output set [7,10].
3. Medicinal Chemistry and FLT

A research of 1998 [7] applies a new fuzzy learning technique called FuGeNeSys, that
enables both the prediction of pharmacological activity and the development of new active
compounds. This method allows a linguistic representation of the knowledge base, making it
easy for a human to understand and interpret; the analysis of rules may be of help in gaining a
theoretical understanding of the parameters and parameter ranges which affect the activity of
compounds. It also leads to a great saving in money and in time during synthesis and testing
of new compounds.
The automatic tool for learning of fuzzy rules implemented in FuGeNeSys [10,11] is an
ES that uses GA and ANN approaches and allows supervised approximation of multi-
input/multi-output systems, capable of learning and at the same time selecting the most
important structural descriptors. It generates a small number of rules, allowing obtaining
extremely compact knowledge bases which can be studied with accuracy. The study of these
rules leads to a great potential for the prediction of pharmacological activity in a highly
simplified analysis. The method only stops when it gives satisfactory results, providing a set
of rules with physical sense which are then analyzed, so one has then only to validate it for
demonstrating its predictive performance on new data.
This fuzzy approach employed for QSAR achieves 100% correct recognition of the
pharmacological activity of the compounds used in both the testing and learning phases, that
are classified into active and inactive classes. The two datasets analyzed involve compounds
inhibiting the Reverse Transcriptase enzyme of Human Immunodeficiency Virus (HIV) type
1 ( ED50 values for 44 compounds in the training set and 3 compounds in the test set) and the
antirhinovirus activity of 9-benzyl purines against Rhinovirus serotype 1B ( IC50 values for
46 compounds in the training set and 6 compounds in the test set). The results found are better
than those found in the literature and offer the great advantage of linguistic representation.
4. Fuzzy Clustering Methods

The main objective of database mining (DBM) methods is the proposal of new efficient
tools that allow designing and classifying large biochemical libraries [12,13], which is
considered an important issue in Medicinal Chemistry during the Combinatorial Chemistry
and High-Throughput Screening (HTS) research programs for selecting new leads based on
the analysis of Molecular Diversity of compounds [14]. In QSPR-QSAR studies that involve
complex datasets, an effective modeling approach can be to partition or cluster the available
data into subsets of similar (common) data and then approximate each subset by a simple
model, thus diminishing the complexity of the model [15].
Different pattern recognition approaches have been used in past years for establishing
suitable classification models, and offer different possibilities and objectives. Principal
Component Analysis (PCA) [16] is only a projective technique, while Discriminant Analysis
(DA) [17] is a really discriminate one as it is capable to find linear relations in the molecular
descriptors hyperspace able to separate different categories present in the data set. Both of
them results valuable techniques whenever clusters or classes of compounds can be visually
delineated, in other words, these are grouped in well-separated regions. In more complex
distributions their classification power diminishes and it is not possible to have knowledge
about the structure of the database. Cluster Analysis (CA) [18] provides a first approximation
to solve the problem, as instead of inspecting all compounds in the database, it is enough to
select some typical compounds representing each cluster to get a deeper knowledge of the
distribution of compounds in the involved set of descriptors. Two main problems appear in
CA based methods: a) the number of clusters and the initial positions of the cluster centers
can influence the final result, and b) a compound lying between two clusters is included only
in one of them.
Among methods based on Artificial Neural Networks, the Kohonen Self-Organizing

Maps (SOM) [19] overcome previous limitations, integrating non-linearity into the data set so
as to project the descriptor hyperspace onto a two-dimensional map as well as preserve the
original topology: points located near each other in the original space remain neighbors in
SOM. The drawback of this method is that it is an unsupervised projective procedure like
PCA [20]. The Back Propagation Neural Networks (BPNN) [21] is a supervised method
capable of discriminating any non-linearly separable class, relating continuous input and
output spaces with an arbitrary degree of accuracy, and has proven to be very efficient in
modeling complex data set relationships [22,23]. However, the employment of complex non-
linear modeling functions usually impedes a better understanding of the involved biological
mechanism that lead to the observed activities of compounds.
Patter recognition strategies, which are related to the application of human sense, could
be transferred to an algorithmic process applicable in the field of molecular recognition. The
FLT provides interesting alternatives within the context of imprecision categories, as fuzzy
classification represents the boundaries between neighboring classes as something
continuous, assigning to compounds a degree of membership of each class. Fuzzy clustering
methods allow objects to belong to multiple clusters at one time with different dm. The
degree of usefulness and complexity of different fuzzy clustering methodologies is quite vast
[24]. Some of the fuzzy clustering methods involve partitioning [25], substractive clustering
[26], fuzzy-c-means, Gustafson-Kessel, fuzzy maximum likelihood estimate clustering, fuzzy
c-verieties, fuzzy c-elliptotypes, fuzzy c-regression models, and possible clustering [24].
A previous work [20] proposes an improvement based on FLT over SOM and Bayesian
ANN [22] based methods for analyzing a set of Central Nervous System (CNS)-active
molecules, considered as good as candidates for the treatment of diffuse neurology
pathologies [27]. CNS-active compounds are classified according to the different CNS
receptors on which they could act. A hybrid system constituted by SOM and Fuzzy Clustering
[28,29] is applied on 389 active molecules, acting on eight types of receptors. The predictive
QSAR model that considers 259 compounds is able to correctly predict the experimental
activity of 130 compounds with a ratio of 81 %.
As a continuation of previous research study, in ref. [30] is developed a new and more
general DBM method called Adaptive Fuzzy Partition (AFP), which is applied on an enlarged
data set of 581 CNS compounds mainly consisting on selective agonists or antagonists, acting
on the same eight receptor types. The prediction ability of AFP is evaluated with a training set
of 377 CNS-active molecules, which are subdivided into eight receptor classes or subspaces.
The CNS data set is first distributed within a hyperspace given by 166 molecular descriptors,
including constitutional, topological, physicochemical, and electronic parameters that are
computed with ChemInter [31] and SciQSAR2D [32] programs. The structural feature
selection is performed by a procedure based on Genetic Algorithms [33], leading to the best
11 descriptors of the pool.
The AFP is based on the Fuzzy Partition algorithm [34,35] that allows generating fuzzy
rules from numerical data by developing to main steps: (a) partitioning a working space into
fuzzy subspaces ( Sk ); and (b) defining a fuzzy rule for each of these subspaces. For instance,
the rule for S k in a d-dimensional hyperspace defined by d descriptors is of the following
type:
IF d1A is associated with fmf1k ( d1 A ) AND d 2 A is associated with fmf 2 k ( d 2 A )

AND d NA is associated with fmf Nk (d NA )
THEN the score of the activity for A is Pk (2)
where diA is the value of the ith descriptor for molecule A, fmf ik is the membership function
related to descriptor i for subspace S k , and Pk is the experimental activity in the fuzzy
subspace. In the fuzzy rule given by Eq. (2), the AND is generally represented by the Min
operator [36], and the membership function can be defined by triangular, trapezoidal or
Gaussian shapes [35,37,38]. After that, AFP builds a model by establishing relationships
(rules) between the best 11 selected descriptors and the CNS activities, performing a
dynamical division of the descriptor hyperspace into a set of fuzzily partitioned subspaces. In
this case, the membership functions used are trapezoidal shapes based on the boundaries of
the created subspaces. The degree of membership of activity P for molecule A (P(A)) is
defined as follows:
nS
(Min fmf d
i ik (diA ))( Pk )
P ( A) = k =1
nS
(3)
(Min fmf
k =1
d
i ik (diA ))
where nS represents the total number of subspaces and Pk is the experimental activity in
subspace S k . For example, the following parameters are used to process the data: maximal
number of rules for each chemical activity=35, and minimal number of compounds for a
given rule=4.
Furthermore, the robustness of the technique is confirmed by predicting an external test
set of 102 compounds never used to define the AFP models. Validation ratios of about 80%
are obtained in the prediction of the experimental CNS activities. Finally, a comparison
between the results obtained by AFP and by other classic techniques, such as Learning Vector
Quantization (LVQ) [39] and BPNN, shows that AFP improved sensibly the prediction power
of the proposed QSAR models.
A main advantage of AFP is that, independent of its complexity, the test phase takes only
a few minutes to screen several thousands of molecules, as claimed by the authors of this
work. In addition, subspaces are described by simple linguistic rules, and for each compound
is calculated its degree of membership (ranging from 0.0 to 1.0) towards the different CNS
biological properties. Finally, the AFP achieves three improvements over the cited SOM/FC
hybrid method [30]: (a) the classification of the eight CNS activities is directly performed in
the original descriptor hyperspace, avoiding the loss of information contents due to the
projection into a 2D map; (b) each CNS activity is represented by a peculiar set of relevant
molecular descriptors; (c) each compound can be straight away related to a unique biological
property and not to a cluster of activities, the number of which depends on the compound
distribution in the hyperspace and on the parameters used in the FC classification.
5. Fuzzy ARTMAP Neural Networks

Non-linear QSPR models are established for the prediction of different physicochemical
properties by using the cognitive classifier fuzzy ARTMAP neural network classifier [40,41].
The fuzzy ARTMAP neural networks is an approach demonstrated to achieve greater
accuracy (in terms of lower average absolute errors) for estimating boiling temperatures [42],
critical properties [43], octanol/water partition coefficients [44], aqueous solubilities [45], and
the evaluation of toxicities [46], when compared to the BPNN approach as well as other
regression-based statistical correlations reported in the literature.
Fuzzy logic based ARTMAP neural networks have several advantages as they are able to
carry out fast but stable online recognition, learning, hypothesis testing, and prediction of rare
events, avoiding the plasticity-stability dilemma of many popular autonomous learning
systems, such as BPNN, in the case of long training is needed and that causes huge unstable
networks. The basic learning mechanism of the fuzzy ARTMAP neural system consists of
creating new categories (equivalent to hidden units in back-propagation) when dissimilar
molecular descriptors and different values of the physical property are encountered. The
fuzzy ART architecture has been designed by Carpenter et al. [47] as a classifier for
multidimensional data clustering according to a set of features.
Figure 2. Block diagram of the fuzzy ARTMAP neural network architecture [43].
In brief, the ARTMAP network consists of two fuzzy ART modules, artA and artB, that
are linked together via an inter-ART module (Figure 2). Module artA learns how to
a
categorize the input patterns (molecular descriptors) presented to layer F0 with a vigilance
parameter a , while artB develops categories of the experimental property presented to layer
F0b with a vigilance parameter b . Both vigilance parameters calibrate how well an input
pattern must match the learned prototype or cluster of input features that the category deems
to be relevant, for a category to be accepted. The two modules work together and are linked
by the map field module of Figure 2, which is an associative learning network that forms an
internal controller designed to create a minimal number of artA recognition categories or
hidden units needed to meet the accuracy criteria, by following the match tracking rule.
When the molecular descriptors are presented, the artA module attempts the prediction
through the map field of the category to which the current target belongs. The predictions of
this method are of an if-then nature, e.g., IF the molecular structure has features close
enough to a particular prototype, THEN it predicts the desired outcome. Many such rules
coexist without mutual interference because of the competitive interactions whereby each
hypothesis is compressed.
6. Ontogenic Neuro-Fuzzy Algorithm: FCID3

In a study of 1997 [48] structure-activity relationships are developed for correlating the
observed mutagenic behavior of 62 aminoazo derivatives and 12 of their reductive cleavage
products with molecular descriptors calculated by quantum-chemical semiempirical
methodology. A model consisting on 8 descriptors computed from CODESSA software and
its Best Multilinear Regression (BMLR) method [49] are shown to account for more than
70% of the variation in the relative mutagenic activity of these compounds.
The non-linear approach adopted in this analysis integrates fuzzy logic with ANNs in the
FCID3 hybrid algorithm [50]: ANN supply the computational power necessary to process
rapidly large quantities of data, while fuzzy logic provides a high level reasoning capability
that guides the overall construction of the network topology. The algorithm generates a feed-
forward network architecture for the data set and, after generating fuzzy Kosko entropies [51]
at each node of the network, it switches to fuzzy decision making based on those entropies.
The FCID3 consists on a fuzzyfication of the ontogenic CID3 algorithm [52], which
generates a neural network architecture by minimizing the Shannons entropy function by
adding new nodes arranged in layers. The initial network architecture is generated in the same
way for both CID3 and FCID3, although FCID3 subsequently defines dm for fs associated
with each of the hidden layer nodes, where the entropy is first reduced to zero. Under this
condition of zero entropy all the training examples are correctly recognized. Once fs are
defined, FCID3 switches entirely to operations on fs. This results in a simpler architecture
than the CID3 for correctly classifying data, having a drastic reduction of the number of
connections and nodes. Nodes and hidden layers are added as needed until the learning task is
accomplished.
In this study of mutagenicity, the architecture is restricted to a single hidden layer, and
the approach can account for about 95% of this variation using 8 descriptors. Furthermore, the
predictive power of this network, as assessed by the Cross-Validation technique [53], is
exceptionally good, RCV = 0.94 . The FCID3 has also been applied for modeling the
2
mutagenicity of aromatic and heteroaromatic amines and related compounds [54].

7. Prediction of Mixture Toxicities Based on a Fuzzy Set Method

A new methodology is proposed which uses molecular descriptors and the Fuzzy Set
Theory to characterize the degree of similarity and dissimilarity of mixture constituents, and
so it is able to predict the mixture toxicity regardless of whether mixture constituents possess
similar, dissimilar, or mixed similar and dissimilar acting mechanisms of action [55,56]. It
avoids the use of a two valued logic criteria which considers only mixtures comprising
constituents with either completely similar or dissimilar mechanisms, that have been
previously described through the employment of concentration addition and independent
action models, respectively. The INFCIM (INtegrated Fuzzy Concentration addition -
Independent action Model) enables an objective quantitative assessment of similarity and
dissimilarity that rely less on mechanisms of action. The INFCIM is applied in two case
studies using toxicity data of four mixtures, and its performance is compared against those of
both concentration addition and independent action models. It is demonstrated that INFCIM
performs comparably or better than the best performing existing model in the original studies
for all the mixtures tested [55].
The framework of the INFCIM applied to the analysis of toxicities is based on the
following steps:
(a) for a mixture of N components, derive the concentration response curves (CRC) for
all the pure components and the mixture at a given composition;
(b) calculate descriptors for each compound. Here are employed Dragon descriptors
[57];
(c) obtain intermolecular distances (x) using descriptors: this is done here by calculating
Euclidean distances between all pairs of molecules.
(d) use fmf to calculate binary similarity and dissimilarity between mixture components.
The proper shape choice of fmf can improve the performance of the INFCIM model,
and present work employs the Gaussian fmf of Eq. (4) for describing the degree of
similarity between mixture constituents:
dm = exp(( x c)2 2 2 ) (4)
with dm being the degree of membership, x is the binary molecular distance, c the mean,
and is the standard deviation, which is the adjustable parameter. c is set to zero so that
a binary distance of zero corresponds to a similarity of 1.
(e) calculate the overall mixture similarity and dissimilarity measures based on the
similarity/dissimilarity values of pure molecular pairs. The Z-fmf of Eq. (5) is
utilized for describing the degree of dissimilarity between constituents:
1 if x < x1
2
x x1 x1 + x0
1 2 if x1 x <
x1 x0 2
dm = 1 2
(5)
x x x1 + x0
2 0 if x < x0
x1 x0 2
0 if x > x0
where x1 and x0 are the start and end points of the slope part of the Z-fmf that are the
adjustable parameters. x1 is set to zero so that a binary distance of zero corresponds to a
dissimilarity of 0.
(f) the CRC for a mixture at a given composition is used to optimize the selection of the
fuzzy membership functions and their associated parameters.
(g) the optimized fuzzy membership functions and parameter values can be used for
future prediction of toxicity of mixtures of the same constituents but with different
compositions, through the INFCIM model:
ECx ,mix = wA (CA) + wB ( IA) (6)
In this equation, ECx , mix is the mixture toxicity, and coefficients wA and wB are
weightings for the concentration additive and independent action contributions. These
weightings are calculated using descriptors and fmf.
8. Robust Fuzzy Mappings in QSAR

An important issue in QSAR modeling is robustness: a model should not undergo
overtraining and its performance should be least sensitive to the modeling errors associated
with the chosen set of molecular descriptors and the linear / non-linear functional form of the
model. Although various fuzzy techniques have been developed using approaches such as
ANN, GA, clustering techniques, and Kalman filtering [24,58-60], most of the recursive
fuzzy identification methods use gradient-descent based algorithms (such as
Backpropagation) for calculating nonlinear fuzzy model parameters. However, in the
presence of data uncertainties and modeling errors, gradient-descent based techniques are not
suitable due to their non-robust nature, leading to errors in the identification of model
parameters.
As QSAR analyzes usually involve complexities and uncertainties due to the lack of
complete knowledge of underlying physical laws, a recent study [61] presents a new method
of clustering based fuzzy mappings (rules), establishing robust input-output mappings based
on fuzzy if-then rules. The identification of these mappings is a first-principle based
approach that minimizes the sensitivity (non-robustness) of the identification method towards
modeling errors. The sensitivity of an identification method can be assessed by measuring a

gain in energy from modeling errors to the identification errors [62]:
energy of identification errors

max min (7)
energy of modeling errors
The maximum value of energy- gain (that will be minimized) is calculated over all
possible finite disturbances without making any statistical assumptions about the nature of
signals. This is called as the energy-gain bounding approach to model identification. Such
an identification method as given by Eq. (7) will guarantee that small modeling errors cannot
lead to large identification errors.
The method of QSAR models development using Bayesian regularized neural networks
is taken as a reference method for comparing the performance of proposed robust QSAR
fuzzy models. For this task, three molecular sets of carboquinones, benzodiazepines, and
predicting the rate constant for hydroxyl radical tropospheric degradation of 460
heterogeneous organic compounds. The method based on fuzzy mappings outperforms results
of ANN due to the fact that the energy-gain bounding approach mathematically takes into
account the issue of modeling errors in a sensible manner without making any assumption
about the nature of signals. Apart of using experimental data, the better performance in
presence of disturbances of the proposed approach when compared to the Bayesian
Regularized ANN is also numerically demonstrated, in terms of the values taken by a
properly defined generalization error.
9. ANFIS: Adaptive Neuro-Fuzzy Inference System

A recent study employs for the first time the Adaptive Neuro-fuzzy Inference System
(ANFIS) [9] in QSAR for modeling a data set of 68 pyrimidines derivatives as DHFR
inhibitors, described first by Hansch et al. [63,64] and later by So and Richards [65]. This
ANFIS system is a combination of the GA technique for feature selection with FLT and
ANN, resulting in an improved tool for determining the behavior of imprecisely defined
complex systems by inducting rules from observations.
A fuzzy inference system (FIS) [1], which is a knowledge representation where each
fuzzy rule describes a local behavior of the system, can be viewed as a Feed-Forward
Network structure and thus it is possible to apply the same back-propagation principle of
ANN. Therefore, the juncture of FLT and neurocomputing leads to the formulation of neuro
fuzzy-systems. The ANFIS is a multilayer procedure that employs hybrid learning rules to
train a Sugeno-style FIS [66] with linear rule outputs, a very efficient and transparent FIS, the
system having a total of five layers. Figure 6 compares the topology of both techniques for a
simple example of two inputs and two rules. The input and output adaptive nodes represent
the descriptors and the calculated activity, respectively, and in the hidden layers there are
nodes functioning as fmf and rules. Nodes of the same layer have similar functions. The
ANFIS maps inputs through fmf and associated parameters, and then though output fmf and
associated parameters of output can be used to interpret the input/output map. This method
eliminates the disadvantage of a normal Feed Forward multilayer network, which is difficult
to an observer to understand and modify.
The ANFIS is trained using a hybrid algorithm consisting of back-propagation for
learning the premise parameters (parameters of layer 1 in Figure 3.b.), and a least-squares
estimation for learning the consequence parameters (parameters of layer 4 in Figure 3.b.). The
overall ouput is expressed as linear combinations of the consequent parameters. Here, the
optimum number and shape of fmf used are obtained through grid partition [59,67] and the
subtractive clustering algorithm [26], which are techniques that allow a proper partition of the
feature descriptors input space to decrease the number of fuzzy rules and increase the speed
of the training and testing phases.
Figure 3. (a) A two-input first-order Sugeno fuzzy model with two rules. (b) equivalent ANFIS
architecture [9].
A training set of 48 pyrimidine derivatives, a validation set of 10 compounds, and an

external test set of 10 compounds are employed in this study, which are selected by means of
D-Optimal Design and Kohonen Self-Organizing Map approaches [68]. The predictive
abilities of the resulting models are compared to those produced from classical multivariate
regression such as linear and nonlinear (quadratic) partial least squares regression (PLS). The
ANFIS method outperformed both the predictive capability of PLS models as well as
published results.
Among the strengths of the method are fast and accurate learning, deals efficiently with
imprecision and nonlinearity, good generalization capabilities, excellent explanation facilities
in the form of semantically meaningful fuzzy rules, and the ability to joint both data and
existing expert knowledge. The ANFIS technique has also been successfully applied, among
other studies, in the modeling of skin permeability coefficients of drugs [15], the prediction of
NMDA (N-methyl-D-Aspartate) receptor binding activities of phencyclidine (PCP)
derivatives [69], liquid chromatography-mass spectrometry (LC-MS) retention time of

benzodiazepines [70], prediction of respiratory motion [71], study of 1-[(2-
Hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) derivatives acting as Non-
Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) [72], or in the study of serotonin (5-
HT7) receptor inhibitors [73].
10. Fuzzy Regression in QSAR

The use of FLT based approaches to characterize imprecision has recently been
recognized in risk assessment and environmental policy applications [74]. A QSPR of 2004
[75] employs the Fuzzy Least Squares Regression (FLSR) [76,77] technique to develop a
relationship for the logarithm of the soil-water partitioning coefficient normalized to organic
carbon ( log10 K oc ), for persistent organic pollutants (POPs). The molecular structures are
represented with the octanol-water partition coefficient ( log10 K ow ) and three molecular
connectivity indices are used.
Figure 4. A triangular fuzzy number [75].
The FLSR is different from Least Squares Regression (LSR) and is used to characterize
the imprecision arising from limited data and/or incomplete model descriptions. In this study,
it is assumed that statistically based QSPR do not fully account for all the sorbate-sorbent
interactions for the partitioning of POPs for different reasons, such as: (a) the model
developed do not capture all the mechanisms of action; (b) the model functional form may
result inadequate [78]; (c) experimental artifacts that lead to vagueness in the data during the
measurement of aqueous concentrations of the highly hydrophobic POPs. This last cannot be
explained by statistical randomness, and together with previous factors, cause these
relationships to have inherent fuzziness associated with them.
The FLSR unlike LSR does not make specific assumptions regarding the distribution of
the residuals, and it is known to work well in situations where data may not be very accurate
or exhibit large variability. It has been proposed for using either fuzzy or nonfuzzy (crisp)
inputs and outputs, but the regression coefficients are treated as symmetrical fuzzy numbers.
The fuzzy number represented in Figure 4 is a fs whose fmf is convex in shape (having an
increasing and decreasing part) and normal (dm in the range 0-1). Thus, the fuzzy coefficients
define the most likely values for the input along with their range of variation. The most likely
values have dm = 1 , while the maximum and minimum values have dm = 0 .
Figure 5. Fuzzy and statistical regression between log10 K oc and log10 K ow [75].
In this study, the Fuzzy Least Squares with Minimum Fuzziness Criterion (FLSMFC)
[79] is employed. It consists on a two-step process wherein LSR is used to obtain a fit
between the input and output values. The regression coefficients using LSR are used as the
midpoints of the fuzzy regression coefficients. The halfwidths of the fuzzy coefficients are
obtained using the minimum vagueness criterion proposed by Tanaka et al. [76]
A relatively small size dataset consisting on 18 log10 K oc values of POPs having
experimental errors in their measurement suggests that FLSR is a suitable technique for
modeling purposes. A comparison between the statistical and fuzzy relationship between the
persistence of POPs and log10 K ow using a 95% confidence interval in Figure 5 indicates that
the fuzzy regression model envelopes all scatter in the data and provides a tighter and more
reliable fit around the mid-point values given by LSR estimates.
11. Conclusion
The Fuzzy Logic Theory has been successfully used in past years for modeling, control
systems, pattern recognition, or image processing. In this work we have reviewed various
applications of the Fuzzy Logic Theory to the field of QSPR-QSAR. Among the major
difficulties commonly found during the development of these applications is that the robust
methods for the automatic construction of fuzzy models remain relatively unknown, as Fuzzy
Logic can be considered an emerging theory of the last decades. Linear and non linear fuzzy
predictive models have been established and have been demonstrated to improve QSPR-
QSAR predictions in a very simple manner. This is because of the proposal of fuzzy
membership functions and the employment of rules with linguistic labels for encoding of
expert knowledge in a direct and easy fashion. The main difference between fuzzy approaches
and classical ones is that, instead of assuming an analytical model function for performing
predictions on data which severely oversimplify the problem in hands, natural rules are
developed from the data rather than imposing rules on the modeled system.
Among the objectives of QSPR-QSAR Theory for establishing good models are that the
predictions closely correlate the experimental data, involve few molecular descriptors,
enhance the understanding of the phenomenon, and it is easy to use. We believe these
objectives can be suitably accomplished by means of strategies derived from the Fuzzy Logic
Theory. During the forthcoming years, this realistic and promising tool would undoubtedly
see an increased number of applications, as Probability Theory alone is not capable of
capturing uncertainty in all of its manifestations, particularly when it arises from the
vagueness of natural language. We hope to have contributed in this respect with the present
chapter.
Acknowledgements
The authors thank the Consejo Nacional de Investigaciones Cientficas y Tcnicas

(CONICET) and the Universidad Nacional de La Plata for financial support.
List of Abbreviations
AFP Adaptive Fuzzy Partition
ANFIS Adaptive Neuro-fuzzy Inference System
ANN Artificial Neural Networks
BPNN Back Propagation Neural Networks
CA Cluster Analysis
d number of descriptors or numerical attributes
DBM Database Mining Method
d iA value of the ith descriptor for molecule A
dm degree of membership
ES Expert System
FIS Fuzzy Inference System
FLSR Fuzzy Least Squares Regression
FLT Fuzzy Logic Theory
fmf fuzzy membership function
fs fuzzy set
FST Fuzzy Set Theory
GA Genetics Algorithms
INFCIM INtegrated Fuzzy Concentration addition - Independent action Model
log10 K ow octanol-water partition coefficient
LSR Least Squares Regression
PLS Partial Least Squares
QSPR-QSAR Quantitative Structure Property-Activity Relationships
Sk fuzzy subspace
SOM Kohonen Self-Organizing Maps
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Chapter 24
MODELING THE TOXICITY OF ALCOHOLS.

TOPOLOGICAL INDICES VERSUS VAN DER WAALS
MOLECULAR DESCRIPTORS
Dan Ciubotariu1*, Vicentiu Vlaia1, Ciprian Ciubotariu2,

Tudor Olariu1 and Mihai Medeleanu3
1
Department of Organic Chemistry, Faculty of Pharmacy, Victor Babes University of
Medicine and Pharmacy, P-ta Eftimie Murgu No. 2, 300041 Timisoara, Romania
2
Department of Computer Sciences, University Politehnica, Timisoara, Romania
3
Department of Organic Chemistry, University Politehnica Timisoara, Romania
Abstract
In this chapter we present three molecular size (CiD, i=1,2,3) and three molecular shape
( iD , i=1,2,3) descriptors developed on the basis of molecular vdW space supposed isotropic,
homogeneous, and compressible to some extent, and sixteen generalized topological
descriptors based on the reciprocal distance matrix, GTRDIs (
k
). Thus, assuming that a
given molecule can be characterized by the vdW surface area and volume, we developed the
compressibility measures of molecular vdW space, CiD, and we extend the ovality concept
as ovality molecular descriptors, iD ; the subscript i refers to the dimensionality of vdW
space. The GTRDIs were built starting from the idea that each vertex i of a chemical graph
supports a topological distance strain (TDS) of order k, k=1,2,3, from all other vertices of
the molecular graph. Consequently, the GTRDIs may be considered as form of an internal
topological strain of chemical graphs. The GTDRIs and the vdW measures of molecular
compressibility and ovality, together with intrinsic density ID (defined by the ratio
ID=MW/VW, where MW is molecular weight), have been tested as molecular vdW descriptors
for correlating toxicity of aliphatic alcohols on simple organisms like larvae and tadpoles and
on Tetrahymena pyriformis and Pimephales promelas. The obtained QSAR results prove that
these vdW indices offer an appropriate description of chemical structure of aliphatic alcohols
for the modeled properties.
*
E-mail address: dciubotariu@mail.dnttm.ro
630 Dan Ciubotariu, Vicentiu Vlaia, Ciprian Ciubotariu et al.
1. Introduction
Our society is confronting challenges such as continuous degradation of the environment
due to aggressive agricultural pest control processes and to various chemicals produced by
chemical, pharmaceutical and other industries. Thus, there is an imperative need for
predictive models for health hazard purposes, that is, to design new chemicals with improved
properties and diminished side-effects, and to assess the safety of some chemical compounds.
In addition, the consideration of the risk of chemicals released to the environment and the
evolvement of environmentally benign synthetic methods is strongly required [1].
Among the most prevalent organic chemicals in the world, as defined by the high
production volume chemical list, are a variety of aliphatic alcohols, acids, esters, saturated
and unsaturated alkanes, and halogenated alkanes [2]. There is an increased emphasis in
predicting the hazardous effects of these chemicals from molecular structure [3]. The ability
to use a quantitative structure activity relationship (QSAR) to estimate accurately the
relative toxicity of chemical compounds would be of value to industry and regulatory bodies
alike. Strictly speaking, the term QSAR refers to the mathematical relationship between the
biological activities of a set of chemical compounds and their structural parameters, called
molecular descriptors (MDs).
Generally, quantitative structure property relationships (QSPRs) correlate chemical
structure to a wide variety of physical, chemical, biological (including biomedical,
toxicological, ecotoxicological), and technological (glass transition temperatures of polymers,
critical micelle concentrations of surfactants, rubber vulcanization rates) properties. It is
widely recognized that QSPR equations, whether they be derived in a purely empirical
fashion from an arbitrary set of molecular descriptors or from a preselected set of descriptors
chosen on theoretical grounds for a connection with a particular property, can give
considerable insight into the manner by which chemical structure controls physical and
biological properties of compounds [4].
The properties of a molecule, including its toxicological effect, are a consequence of a
complicated interplay of its topology (atomic connectivity), metric characteristics (bond
lengths, valence and torsional angles) and dynamics of electrons and nuclei. Finding out how
various molecular features (quantified by topological, geometrical, and quantum-mechanical
molecular descriptors, respectively) depend on molecular structure is one of the central fields
of research in chemistry and particularly the main subject of QSTR (quantitative structure
toxicological properties relationship). To develop such a QSTR requires the following three
components: a data set, which provides a uniform and relative measure of toxicity for a group
of chemicals, molecular structure/property data (i.e., MDs) for each chemical compound
within the group, and a statistical method to develop a linear (usually) or nonlinear
relationship between toxicity and structure [5].
The compounds used in developing a QSTR (the training set) should preferably all act by
the same mechanism. Otherwise, the QSTR will be less accurate and there will be compounds
that are not modeled well (outliers). Therefore, the QSTR analysis is commonly carried out
on congeneric series of compounds. The experimental data should be as accurate and precise
as possible and should have been determined with the same protocol and, if possible, in the
same laboratory. For best results, they must represent the molar concentration (or dose) that
produces a given observed effect (e.g., the dose required to kill 50% of the organisms, LD50,
Modeling the Toxicity of Alcohols 631
etc.). The compounds should cover as wide as possible the range of chemical (MD) space and
the range of end point values. For details about the design of series of compounds one may
consult the ref. [6].
At present there are many MDs available hydrophobic, electronic, steric, geometric,
quantum chemical, topological and there are a number of commercially available software
packages (IRS [7], Dragon [8], CODESSA [9], etc.) that will each generate many structural
descriptors. For the selection [10] of relevant MDs for the series under QSTR study one can
use two ways. The first is to choose only those descriptors that are relevant to a presumed
mechanism of action. In this case the number of MDs is usually small, but the method has the
disadvantage that, if the chosen descriptors are irrelevant, a good QSTR will not be obtained.
The second approach consists in generating a large number of descriptors by means of a
software package. The selection of those MDs that form the best model of the toxic activity is
made by appropriate statistical methods.
QSTR models can be generated using a wide variety of mathematical models ranging
from linear methods (e.g., linear correlation and regression and linear discriminant analysis)
to nonlinear methods (e.g., random forests and neural networks). The multiple linear
regression (MLR) method remains the most widely used type of statistical method used in
QSTR. This method has the advantage that it is simple to use and the MDs that best model the
toxicological activity can be seen and easily understood. Its disadvantage is related to the fact
that it works best with the congeneric series of compounds and, also, it can suffer from a high
risk of chance correlation, especially when a large pool of descriptors is used. To minimize
this risk the ratio between the number of compounds (data points) and the number of MDs
have to be at least five [11].
Once a QSTR model has been built for a series of chemicals (the training set or test set),
it must be validated. In all cases the predictive ability of the models are the tested with a set of
molecules (the prediction set or validation set), which were not used during the model
building process [12, 13].
In conclusion, a QSTR has two main uses. Its foremost use is predictive, to estimate the
toxicity of a compound not used to develop the QSAR. Second, the molecular descriptors
used in QSTR analysis should be related to the process by which the toxicological activity is
manifested. Thus, the MDs could offer some insights on the mechanism of action. However,
it should always be remembered that the existence of a correlation between structure and
activity is not proof of causality.
Among different approaches to develop MDs used in QSTR analysis, we present in this
chapter our own structural approaches based on molecular topology and molecular van der
Waals (vdW) space.
Molecular topology is conventionally represented by a molecular graph being essentially
a non-numerical mathematical object. To quantifying the structural information, a graph G is
transformed into a more convenient mathematical representation (matrix, polynomial, etc.)
and then, using an algorithm, the structural information contained in G is converted into a
graph invariant. These invariants are usually called topological indices. Among the
topological invariants we used the reciprocal distance (RD) matrix to generate a set of
generalized topological reciprocal distance indices (GTRDIs), k ( = 1,2,3,;
k = 1,2,3,), which seems to be a good mathematical representation of chemical structure in
numerical form, with a priori physicochemical meaning.
The space occupied by a molecule exhibiting a toxicological action can be described by

the approximation of hard spheres: each atom of that molecule is represented by an
isotropic sphere having the centre in the equilibrium position of the corresponding atom and a
radius equal to its vdW radius. Consequently, one can define a molecular vdW envelope as
the external surface resulted from the intersection of all vdW spheres. This envelope embeds
a 3D space of volume VW and surface SW. VW and SW were computed by means of the Monte
Carlo method. They are used to calculate three vdW compressibility (CiD, i=1,2,3) descriptors
and three vdW ovality ( iD , i=1,2,3) descriptors, which have a clear physical meaning.
These MDs are used to model the QSTR of aliphatic alcohol toxicological effects on
simple organisms like larvae and tadpoles and on Tetrahymena pyriformis and Pimephales
promelas. The obtained QSAR results prove that these two types of MDs are inter-related and
offer an appropriate description of chemical structure of aliphatic alcohols.
2. Statistical Methods
No general theory of the quantitative relationship between molecular structure and
toxicological properties of organic chemical compounds (QSTR) can reasonably be regarded
as satisfactory unless provided a sound basis for predicting and interpreting linear
relationships among molecular quantities. A satisfactory theoretical model for linear
correlations in toxicology should allow reliable predictions to be made as easily as possible
concerning both the circumstances in which correlations should occur (e.g., between which
toxicological action and for which compounds) and the magnitudes of the regression
coefficients. An important factor to be considered in the development of a model is the degree
of parameterization required. An under-parameterized model will fail to predict the existence
of certain significant experimentally detectable features in the pattern of toxic behavior. An
over-parameterized model will suggest that a more complex pattern of toxic behavior exists;
the more parameters are involved in a model, the harder it is to apply that model in making
predictions. Statistical analyses of experimental data are a valuable guide when searching for
the optimum degree of parameterization [14].
Modern approaches to the QSTR analysis of organic molecules such as drugs,
insecticides, herbicides, fungicides etc., are based on the quantification of toxicity as a
function of molecular structure [15]. These are generally carried out by means of the MLR
method using a correlation equation of the type [16]:
y n = 1 x n1 + 2 x n 2 + + p x np + z n = (x n1 , , x np ) + z n (1)
where yn are toxicological activities and the matrix X=(xn1,,xnp) contains the predictor
variables, i.e., the structural parameters (MDs) of the compounds from studied series.
Linear regression provides estimates and other inferential results for the (statistical)
parameters =(1,2,,p)T in the model (1). In this model, the random variable yn, which
represents the response for case n, n=1,2,,N, has a deterministic part and a stochastic part.
The deterministic part, (xn1,,xnp) , depends upon the parameters and upon the predictor
or regressor variables xnp, p=1,2,,P. The stochastic part, represented by the random variable
T
zn is a disturbance that perturbs the response for that case. The superscript denotes the
transpose of a matrix.
The model for N cases can be written
Y = X + Z (2)
where Y is the vector of random variables represented the experimental data we may get, X is
the NP matrix of regressor variables, i.e., the molecular structural parameters and/or the
physical and chemical properties (especially for QSAR studies) and Z is the vector of
variables representing the disturbances; one assumes that Z is normally distributed. The
maximum likelihood estimate is the value of which minimizes S():
2

N
P
S( ) = Y X = y n x np p
2
(3)
n =1
p=1
This is called the least squares estimate and can be written:
= (X T X ) X T Y
1
Least squares estimates can also be derived using sampling theory or by using a Bayesian
approach [17].
All three of these methods of inference, the likelihood approach, the sampling theory
approach, and the Bayesian approach, produce the same point estimates for and, also,
similar regions of reasonable parameter values. In using the least squares estimates one
assumes [18]:
(1) The expectation function X is correct.

(2) The response is expectation function plus disturbance (relation 2).
(3) The disturbance is independent of the expectation function.
(4) Each disturbance is of zero mean and has a normal distribution.
(5) The disturbances are independently distributed and have equal variances.
The condition for existence of the least squares solution is that the reciprocal product of
( T
)
matrices X X exists, so that it is non-singular. This, in turn, requires that X is non-
singular. In this case no column of X may be written as a linear combination of other columns
of X, the system of equations is of fully rank, (n>p), and there is a unique solution. If the
number of descriptors, p, is close or greater than the number of data points (chemical
compounds), np or n<p, cannot be estimated by MLR because |XTX| determinant is null,
(
and X X
T
)
1
is not defined; the predictor variables (MDs) are linearly dependent. The
problem of colinearity can be solved by suppressing descriptors or by using other multivariate
methods, e.g. PLS (projection of latent variables) method [19]. For a detailed presentation of
MLR models one may consult refs. [16] and [17].
Once the QSTR model is built, its goodness of fit is evaluated by means of the following
statistics: the correlation coefficient (r) and the coefficient of determination (r2), adjusted for
2
the degree of freedom ( radj ), which is also called explained variance, (EV). The uncertainty in
the model was noted as the standard error (s), and the reliability in the model was expressed
by F (Fisher) and t (Student) statistics. The t-test was used to determine the 95% confidence
limits of that QSTR model.
Statistical fit should not be confused with the ability of a model to make predictions.
Therefore, one use the leave-one-out (LOO) and the leave-n-out (L-n-O) cross-validation
method to estimate the predictive ability of the obtained QSTR model, using the cross-
validation coefficient (also called coefficient of predictions), q2, and the squared correlation
2
coefficient between predicted and experimental activities, rPE .
In the LOO procedure one compound is removed from the training set, the QSTR is
reconstructed using the remaining compounds, and the toxicological activity of the deleted
compound is then predicted with the new QSTR model. The deleted compound is then
reinstated and the procedure is repeated until each compound in turn has been left out. A
cross-validated q2 value is obtained that is a guide to the predictive ability of the QSTR. A q2
value of >0.5 is acceptable [19]. However, the LOO technique has come in for criticism [20,
21]. A better procedure, if one has sufficient data, is to leave an appreciable proportion (20-
50%) of compounds out of the training set and to use them as an external test set. This L-n-O
procedure may be viewed as an external method for validation: the chemical structures
selected for inclusion in the validation set
Finally, whether or not the developed QSAR is a chance correlation can be checked by
scrambling the toxicological response values (Y-scrambling) [8] and trying to build a model
using the scrambled data. This procedure is then repeated, say, 100 times and the r2 values are
checked against that for the real QSTR: if only one of the r2 values from the scrambled data is
as high as that from real QSTR, then there is 1% risk that the real QSAR is a chance
correlation [22].
Nonlinear relationships are accommodated by transforming the data and/or descriptors
using mathematical functions such as square, square root, logarithm, and inverse. Less
frequently, combinations of descriptors such as products of two descriptors are made to
account for nonlinear cross-dependencies [23].
3. Van Der Waals Molecular Descriptors

3.1. Introduction
The recent interest in the van der Waals (vdW) volume and surface affords an adequate
reason for introducing new vdW molecular descriptors in the treatment of steric effects in the
analysis of chemical reactivity or in QSAR studies [18]. The molecular volume and the
surface area were used as molecular structural parameters in QSAR studies of Hansch type
[24-26]. They were also used as a starting point for deriving other QSAR parameters, e.g.
lipophilicity/hydrophilicity [27], surface tension parameters [28], Weighted Holistic Invariant

Molecular (WHIM) descriptors [29] and so on.
Both numerical and analytical algorithms were devised for the calculation of the volume
and surface area of molecules. The molecular volume is a measure of the space around atomic
nuclei filled by electrons [30, 31] and is defined geometrically as the combined volume of
overlapping spheres centered on the nuclei, similar in shape to a space-filling molecular
model. The van der Waals radii are used for the radii of the atomic spheres. The molecular
surface area is the area of the surface, which wraps the molecular volume. Exact calculation
of the molecular volume and surface area is, however, a formidable task due to multiple
overlap of spheres of different radii.
The first methods for calculating the molecular volume and surface area used molecular
fragments [30]. The additive technique is particularly suited for QSAR because many of its
parameters are obtained from molecular fragments (e.g. octanol/water partition coefficients).
Recently, Govers and de Voogt proposed a quantum definition of the molecular volume in
terms of molecular fragments via electron indices [32].
Because the volume of overlapping spheres (solvent excluded volume) is a quantity of
interest in solution chemistry, attempts were made decades ago to find an analytical
expression for it. Thus, Rowlinson performed the first analytical calculation of the volume
occupied by three and more overlapping spheres [33] and used it to give an analytical
expression for the triplet radial distribution function g(3) in terms of the intersecting volume of
three simultaneously overlapping spheres [34]. But Connolly was the first to obtain a general
solution for the analytical computation of the volume and surface area for an ensemble of
overlapping spheres with unequal radii [35, 36]. At about the same time, Richmond proposed
another method to solve the same problem [37], this time by analytical integration of surface
area obtained from Gauss-Bonnet theorem [38]. Finally, Gibson and Scheraga obtained an
analytical expression of the volume in terms of the inclusion-exclusion principle [39].
Gavezzotti [40], Meyer [41] and Ciubotariu et al. [42, 43] developed, among others,
numerical algorithms for calculating the volume and surface area of overlapping spheres,
which use either three dimensional grids or Monte Carlo integration techniques. The grid
methods are quite expensive computationally, as a very large number of grid points are
necessary to obtain acceptable accuracy. Optimized algorithms were also proposed (based on
Lebesgue integral) which eliminate large part of the grid points by focusing the grid near the
molecular surface. The method based on the Monte Carlo integration is similar in
performance with the grid method. In addition, its results are dependent on the quality of the
random number generator. A relative recent review by Mezey [44] gives an account of the
methods used to calculate molecular volume and surface area and their use in defining the
molecular shape and similarity.
In the last years, we have developed some new models for quantitative treatment of steric
effects, on the basis of standard and optimized geometry of molecules and their vdW space,
supposed to be homogeneous and isotropic [18, 24-26, 42, 43]. For this purpose we
investigated the way in which the vdW volume and the vdW surface of substituents, as well
as different directions in the van der Waals space of a molecule are responsible for the steric
effects manifested during chemical reactions. In this section we present two types of vdW
molecular descriptors developed to measure the size (compressibility MDs, CiD, i=1,2,3) and
the shape (ovality MDs, iD, i=1,2,3) of molecules. They describe the steric aspects of a
molecule, as they are manifested by its vdW space on one dimension (C1D and 1D), two
dimensions (C2D and 2D), and three dimensions (C3D and 3D). The purpose is to model
quantitatively their interaction with biological targets responsible of various biological
responses, including here the toxicological activity of aliphatic alcohols. The development of
these MDs is made on the basis of vdW molecular volume, VW, and surface, SW. VW and SW
were calculated with the aid of original algorithms[24, 26] developed on the basis of Monte
Carlo methods [45] and implemented in the IRS computer package [7, 47].
The necessity to define such numerical molecular descriptors, in order to quantify in a
proper mode both the shape and size of substituents and molecules, comes out from the
theoretical considerations regarding the nature of steric effects and the practical conditions
imposed by such parameters.
The fundamentals and the derivation of CiD and iD (i=1,2,3) MDs and their application
in QSTR modeling of toxic activity of aliphatic alcohols is presented on in this section.
3.2. Van Der Waals Radii
The distance where attractive forces between the unbound atoms of a molecule, or
between atoms of different molecules, are in equilibrium with repulsive forces is known as
the van der Waals distance. One may define the van der Waals radius (rw) as the half of the
vdW distance. The van der Waals radii have long been considered a measure of atomic size
[48].
The space occupied by molecules can be described suitable in the approximation of hard
spheres: each atom of the molecule M is represented by an isotropic sphere having the center
in the equilibrium position (Xi, Yi, Zi) of atoms of a molecule and the radius equal with its
w
van der Waals radius ri . There are several methods to compute the vdW radii [49]. The best
extant values of rW for atoms are those of Bondi [30], listed in Table 1.
Table 1. Bondi vdW radii
Atom H C O N F Cl Br I S P
rw 1.20 1.70 1.52 1.55 1.47 1.75 1.85 1.98 1.80 1.80
These values were obtained from a careful comparison of various types of physical
properties and are quite reliable. Unfortunately, values for groups are limited to the methyl
group and to the half thickness of the benzene ring.
3.3. Molecular Van Der Waals Volume
The molecular van der Waals envelope, , can be defined in the hard-spheres
approximation as the outer surface resulted from the intersection of all vdW spheres
corresponding to the atoms of molecule M. The points (x,y,z) inside the envelope satisfy at
least one of the following inequalities:
(X i x) 2 + (Yi y)2 + (Zi z) 2 (riw ) 2 i = 1, m (4)

where m represents the number of atoms from a molecule, M, and (Xi,Yi,Zi) are the
coordinates of these atoms. Consequently, the total volume embedded by the envelope is the
w
molecular vdW volume ( VM ) of the molecule M.
w
To compute the vdW volume, VM , the molecule is inserted into a bounding
parallelepiped with the volume Vp. The random points (x,y,z) are generated into the
parallelepiped, which includes the domain M. If nt is the total number of generated points and
ns the number of points that satisfy the inequalities in (4), than the van der Waals volume is
[18,24,42,43]:
ns
VMw = Vp (5)
nt
The accuracy of the estimate (5) for a given maximum probability is inversely
proportional to the square root of the number of trials [45]:
1
= (6)
2 N
This circumstance causes the relatively slow convergence of the Monte Carlo methods.
For example, in order to reduce the error of the result 10-fold, the number of trials must be
increased 100-fold. If the accuracy of the estimate and the guarantee probability 1- are
given, then from formula (6) one derives the necessary number of trials:
1
N= (7)
4 2
Taking into consideration the precision and the accuracy of chemical and biological
experiments, for =0.05 and =0.01 the number of necessary points is N=10,000. This makes
the Monte Carlo method not difficult to apply, due to the performances of nowadays
computers. In order to increase the accuracy of the method the calculus must be repeated at
least 10 to 20 times for each volume. The final result, i.e., the mean value of the computed
volume of each alcohol from the series under study, is validated by statistical method [47].
The vdW values of the volumes of the 35 alcohols are systematized in Table 2.
3.4. Molecular Van Der Waals Surface
The molecular van der Waals envelope, , defined by relation 4, is a surface. We used
also the Monte Carlo integration method for computing the area of molecular vdW surface of
the studied aliphatic alcohols [18, 24].
Table 2. Values of vdW molecular volumes (VW) and surface areas (SW)
of aliphatic alcohols
No. Name of alcohol VW SW ID* log KOW#

1 1-tridecanol 322.559 239.890 0.836 5.58
2 1-dodecanol 300.620 222.535 0.838 5.13
3 1-undecanol 278.841 205.877 0.837 4.53
4 1-decanol 256.950 188.936 0.838 4.57
5 1-nonanol 235.136 172.136 0.839 3.77
6 4-decanol 253.550 188.490 0.840 3.78
7 2-nonanol 233.761 172.282 0.837 3.77
8 1-octanol 213.176 155.162 0.840 3.00
9 3,7-dimethyl-3-octanol 244.976 187.985 0.841 3.52
10 2-ethyl-1-hexanol 206.057 154.983 0.841 2.81
11 1-heptanol 191.197 138.127 0.839 2.72
12 3-octanol 209.923 154.924 0.840 2.72
13 2-octanol 211.027 155.002 0.842 2.90
14 2-propyl-1-pentanol 206.302 154.953 0.843 2.81
15 3-ethyl-2,2-dimethyl-3-pentanol 207.862 169.338 0.851 2.86
16 1-hexanol 169.464 121.686 0.843 2.03
17 4-methyl-1-pentanol 166.775 121.506 0.841 1.75
18 2,4-dimethyl-3-pentanol 178.716 137.232 0.847 1.93
19 3,3-dimethyl-1-butanol 162.967 120.937 0.848 1.62
20 2,2-dimethyl-1-propanol 143.337 104.097 0.846 1.31
21 2-methyl-1-butanol 141.195 102.994 0.855 1.22
22 3-methyl-2-butanol 142.242 104.075 0.846 1.28
23 1-Pentanol 147.495 104.533 0.844 1.56
24 3-Methyl-1-butanol 145.178 104.375 0.843 1.16
25 2-pentanol 145.351 104.643 0.845 1.19
26 tert-amylalcohol 137.741 102.532 0.858 0.89
27 3-pentanol 144.562 104.550 0.844 1.21
28 2-Methyl-1-propanol 124.510 87.537 0.847 0.76
29 1-Butanol 125.736 87.761 0.843 0.88
30 2-Butanol 124.709 87.631 0.848 0.61
31 1-Propanol 103.855 70.947 0.847 0.25
32 2-Methyl-2-propanol 124.252 87.465 0.846 0.35
33 2-Propanol 103.470 70.559 0.849 0.05
34 ethanol 82.003 53.917 0.854 -0.31
35 methanol 59.917 37.049 0.865 -0.77
*
ID is the intrinsic density [24], defined as follows: ID=/VW; is the molecular weight.
#
log KOW is the coefficient of partition octanol-water; the data are from ref. [5].
The Monte Carlo algorithm [24,46] implies the generation of a random uniform grid on
each sphere of the molecule, followed by the detection of the number of points generated on
the surface (nt) and of those (ne) that do not satisfy the inequalities in (4). For every hard
W
sphere i, one computes the outer part of each spheres surface, S i :
(n e ) i
Siw = 4 (riw ) 2 (8)
nt
W
The final surface is computed as a sum of exterior surface of each sphere, Si :
m
S = Siw
w
(9)
i =1
As we have seen, the vdW radius is a successful concept for the computation of
molecular size and shape descriptors, even if in a quantum chemical description the electron
cloud has no well-defined boundary surface. In the hard-spheres theory, each atom of the
molecule is represented as an impenetrable sphere, i, centered at the equilibrium position of
the atomic nucleus and having a radius equal to the vdW radius of the corresponding atom,
riW (see Table 1 from Section 3.2). The exterior surface of all atomic spheres defines the vdW
surface of area SW, which delimits the vdW volume of the molecule. The corresponding
values of the surface area of aliphatic alcohols are also presented in Table 1. These VW and
SW values were used for the computation of the compressibility and ovality MDs.
3.5. Molecular Van Der Waals Compressibility Descriptors
Assuming that a molecule can be characterized by two spheres, corresponding to the vdW
volume, V w , and to the vdW surface, S w , respectively, we developed three compressibility
measures of molecular vdW space, CiD, i=1,2,3. This hypothesis is based on the known
conformational flexibility of the molecules and on the fact that the molecules are relatively
compressible [24, 25]. Therefore, one may suppose that a molecule should be compressed
w
from the greatest sphere (SG), corresponding to the vdW surface area of , equal to S , to the
w
smallest sphere (SS), concordant to the vdW volume embedded by , equal to V [50].
w w
The vdW radius, r , and the vdW volume, V
S S , of the molecular SG sphere are
calculated as follows
rSw = [ S w / 4 ]1 / 2 (10)
VSw = 4 (rSw )3 / 3 (11)

The molecular SG sphere can be compressed to a molecular SS sphere, which has a

w w
volume equal to the molecular van der Waals volume, V . The vdW radius, rV , and the
w
vdW surface area SV of this molecular SS sphere are calculated with the following relations:
rVw = [3V w / 4 ]1 / 3 (12)
SVw = 4 (rVw ) 2 (13)
In this way, the molecular SG and SS spheres are characterized by the following two
triplets:
{SG }: (rSw , S w ,VSw ) (14)
{S S } : (rVw , SVw ,V w ) (15)
The molecular vdW compressibility measures, CiD, can be easily defined from the triplets
(14) and (15), as the difference between the corresponding values of vdW radius, surface
area, and volume of SG sphere and SS sphere, as follows,
C1D = rSw rVw (16)
C2 D = S w SVw (17)
C3 D = VSw V w (18)
Figure 1. The physical model of the molecular compressibility measures CiD, i=1,2,3.
The molecular descriptors considered in this QSTR analysis were those for molecular
compressibility, which have been evaluated by relations (16), (17), and (18), corresponding to
mono-, bi-, and tri-dimensional compressibility measures C1D, C2D, and C3D, respectively,
w
and the alcohol hydrophobicity, logP. The vdW volume ( V ), and the area of vdW surface
w
( S ) were calculated with an in house algorithm, IRS (Investigation of Receptor Space)
developed on the basis of the Monte Carlo method [7]. The geometry of molecules was
optimized with MM+ and AM1 algorithms from the HyperChem software package [51]. The
values of C1D, C2D, C3D for the series of 35 alcohols are presented in Table 3. For physical
meaning see Figure 1.
The compressibility descriptors CiD have a clear physical meaning. Thus, supposing an
isotropic and homogeneous molecular vdW space, C1D measure the quantity (in ) with that a
molecule may be compressed into hydrophobic pocket, in the solvation process or in various
biological environments. The packed capacity of a molecule is estimated by means of C2D
the molecular vdW surface, in 2, and C3D the molecular vdW volume, in 3. These facts
are well understood from Figure 1.
3.6. Molecular Van Der Waals Ovality Descriptors
Central to the creation of a QSTR is the choice of structural descriptors [52]. The purpose
of a molecular descriptor in a QSTR application is to provide a measure of a particular feature
of the structures of the compounds being studied. The goal is simply to measure the feature in
question as accurately and unambiguously as possible. At present, many structural descriptors
are available, ranging from simple whole-molecule properties to quantum mechanical indices
[53].
Taking into account the fact that for a given volume the spherical shape presents the
minimum surface, the ovality index, O, was introduced [54] as a measure of the deviation of a
molecule from the spherical shape. It was calculated from the ratio between the actual
molecular surface area, Sw, and the minimum surface area, SV, corresponding to the actual
van der Waals (vdW) volume, Vw, of that molecule [53, 55]:
Sw Sw Sw
O= = = (19)
SV 4 ( r w )2 3 V w
2/3
4
4
In relation (19) rw represents the vdW radius of the given molecule, calculated from its
actual vdW volume. The ovality index is equal to 1 for spherical top molecules and increases
with increasing linearity of the molecule.
In fact, the reciprocal of the ovality index, = O , was introduced [56] before, in
1
1935, as sphericity index, to measure how spherical (or round) an object is. The sphericity,
, is the ratio of the surface area of a sphere (with the same volume as the given object) to
the surface area of the object.
Table 3. Values of compressibility (CiD,i=1,3) and ovality ( iD ,i = 1,3 ) molecular

descriptors for the alcohols of Table 2
No. C1D C2D C3D 1 D 2D 3D

1 1.218 136.419 305.980 1.316 1.734 2.279
2 1.134 123.275 268.036 1.302 1.694 2.193
3 1.050 110.499 232.306 1.287 1.656 2.128
4 0.964 97.888 159.580 1.271 1.615 2.052
5 0.877 85.650 167.202 1.254 1.572 1.972
6 0.934 94.509 191.080 1.263 1.595 2.015
7 0.864 84.307 164.253 1.251 1.565 1.951
8 0.783 73.794 137.197 1.235 1.525 1.883
9 0.862 86.326 172.646 1.243 1.544 1.927
10 0.719 66.690 123.467 1.216 1.478 1.802
11 0.695 61.955 110.712 1.217 1.480 1.803
12 0.751 70.055 130.485 1.225 1.500 1.845
13 0.770 71.842 133.884 1.231 1.516 1.857
14 0.717 66.554 123.269 1.215 1.478 1.804
15 0.639 60.183 113.040 1.186 1.409 1.664
16 0.600 51.015 85.973 1.195 1.428 1.710
17 0.567 47.911 80.669 1.185 1.404 1.671
18 0.573 50.206 87.668 1.179 1.391 1.638
19 0.535 44.845 74.899 1.175 1.382 1.615
20 0.461 36.412 57.361 1.158 1.342 1.545
21 0.440 34.638 54.332 1.151 1.326 1.531
22 0.446 35.205 55.410 1.153 1.328 1.531
23 0.506 40.316 64.117 1.173 1.376 1.613
24 0.477 37.898 59.936 1.163 1.352 1.574
25 0.476 37.790 59.847 1.163 1.354 1.575
26 0.404 31.548 49.123 1.139 1.297 1.483
27 0.471 37.374 59.083 1.161 1.349 1.559
28 0.394 28.931 43.164 1.143 1.305 1.489
29 0.408 30.270 44.953 1.148 1.317 1.510
30 0.395 29.121 43.366 1.143 1.308 1.494
31 0.306 21.157 28.494 1.119 1.254 1.403
32 0.388 29.084 42.555 1.141 1.304 1.483
33 0.302 20.505 28.094 1.118 1.250 1.398
34 0.211 13.010 15.919 1.090 1.188 1.297
35 0.117 6.263 6.660 1.057 1.116 1.181
Here we present our extension [50] of the ovality molecular descriptor defined by relation
(19) to three molecular vdW ovality measures, denoted by iD, i=1,2,3. Thus, taking into
account the characteristics of the greatest and the smallest molecular sphere, SG (relation 14),
and SS (relation 15), respectively, evaluated with relations (10)-(13), the ovality descriptors
have been defined as follows [50]
rSw
1D = (20)
rVw
SW
2D = W (21)
SV
VSW
3D = (22)
VW
One may observe that the relations (19) and (21) are the same. Consequently, the two-
dimensional (2D) ovality molecular vdW descriptor, 2 D , is identical with the ovality index,
O [54, 55]. The relations (20) and (22) extend the index O so that one can also measure the
deviation of a molecule from the spherical shape on one- (1D) and on three-dimensions (3D)
of the vdW space. In addition, for the series of alcohols from Tables 2 and 3 the domain of
3 D values is greater than those of 2 D values. Consequently, one may expect that the
discrimination capability between the molecular shapes of the congeners decreases as
follows 3 D > 2 D > 3 D .
While the compressibility descriptors CiD (i=1,2,3) are dimensional measures of the
molecular size (in , 2, and 3, respectively), the ovality descriptors are dimensionless
measures of the molecular shape. The ability to discriminate among the molecules of aliphatic
alcohols from Table 1 is higher for the compressibility than the ovality molecular descriptors,
as we can see in Table 3.
4. Topological Descriptors from Reciprocal Distance Matrix

4.1. Introduction
Quantitative structure property (QSPR) and structure activity (QSAR) relationships

are valuable tools now used in analyzing and predicting various physicochemical and
biological properties of organic chemical compounds. QSARs are also used as scientifically
credible tools (QSTRs) for predicting the acute toxicity of chemicals when few or no
empirical data are available [57].
Many QSTR studies use graph theoretical indices that are based on the topological
properties of a molecule viewed as a graph. The application of graph theory to this field
implies the representation of molecules by selected molecular descriptors, often referred to as
topological indices (TIs). TIs are numerical quantities based on various invariants or
characteristics of the molecular graph such as the adjacency matrix, the distance matrix, or
centric topological indices and TIs based on information theory [58]. Among various
invariants, more detailed topological information is provided by the distance matrix of

chemical graphs, D, whose entries dij represent the topological distances between vertices i
and j that is the number of edges (bonds) along the shortest path between vertices (atoms)
[59]. Therefore, many TIs used in QSTR studies have been developed on the basis of D.
Based on their definition one proposed that many TIs derived from D may code two structural
steric factors, namely the size and the shape of the molecule [58, 60]. Although TIs do not
have a precise physical meaning, they are measures for topological shape, i.e. the degree of
branching or cyclicity and they correlate well with molecular volume or surface [61].
However, extensive studies on this topic do not yet exist.
The success of the connectivity indices [62, 63] and of the Wiener index [64] as graph
descriptors in QSAR/QSPR models stimulated the research in the field of molecular
descriptors based on graph distances, Wiener-like indices [65] and various molecular matrices
1
[59]. The idea to use as LOVIs the sum of the reciprocal values of D matrix ( d ij ) was
adopted [24] in the definition of three distance connectivity indices (DCIs), , =1-3 [24, 66,
67]. These LOVIs are in fact the elements of the reciprocal distance (RD) matrix,
{ }
RD = d ij1 [68-73].
In this section we present several topological distance indices and the set of generalized
topological distance indices (GTRDIs),
k
( = 0,1,2,3,...; k = 1,2,3,4 ,...) developed earlier
by extending the definition of DCIs . In the construction of these indices we used as LOVIs
the k power of the row sum of the values of the RD matrix, d ij k [73]. In a tentative to offer a
physical meaning of GTRDIs in the frame of molecular graphs we consider these LOVIs as
measures of the local topological distance strain (LTDS). Thus, one may define the internal
topological distance strain (ITDS) of order k as a part of the topological energy (TE) of a
molecule structurally described by its molecular graph. These GTRDIs are even measures of
the internal topological distance strain of order k. Introducing the corresponding bond lengths
as a metric on the topological molecular graph, we developed a new set of GTRDIs, k (=0-
3, k=1-4), which can discriminate between the (hetero)atoms. The subscript represent all
possible paths of length .
4.2. Brief Review of Several Topological Distance Indices
The distance matrix D() = {dij} of a graph is an important graph-invariant. Its entries
dij, called distances, are equal to the number of edges connecting the vertices i and j on the
shortest path between them. Thus all dij are integers, and dij =1 for nearest neighbors; by
definition, dii = 0. Therefore, the distance matrix D = D() of a labeled connected graph is
a real symmetric matrix NxN whose elements dij are defined as [74,75]:
lij if i j

D = {dij} and d ij = (23)
0 otherwise
where lij is the topological length of the shortest path, i. e. the minimum number of edges
between the vertices i and j in . The length of the shortest path lij is also called [75] the
distance between the vertices i and j in , hence the name distance matrix for D.
Many TDIs have been developed on the basis of D. We selected some of these for the
present study, in which we analyze the relationship between TDIs and molecular vdW space.
Among the TDIs that can be derived from D, the most popular investigated and applied is the
Wiener number [76]. Besides the Wiener number [64, 77] we will briefly present the
following TDIs used in our analysis: the polarity number [64, 77, 78], the Platt index [77], the
Balaban J index [79, 80]. The values of these TIs for the aliphatic alcohols of Table 1 are
systematized in Table 4.
(A) Wiener Index
The Wiener index, W, [64, 77] was defined as the sum of the number of bonds separating
all pairs of atoms in an acyclic molecule. It is easy to shown that this index is equal to the
half-sum of the off-diagonal elements of D [81]:
N N
2 d
W=1 ij ; ij (24)
i =1 j =1
where N is the total number of vertices (atoms) in .
(B) Polarity Number
Wiener has also introduced the so-called polarity number, P. P is the number of pairs of
vertices separated by three edges, that is half of the number of distances of length three:
N N
P= 1
2
(i + j ) ; i, j where d ij =3 (25)
i =1 j =1
In relation (25) N represents the total number of vertices in .

The factor before the sums in (25) compensates for the fact that the three edges
between the vertices i and j in are accounted for two times (both ways). W and P have been
applied to correlations with boiling points, heat of formation and vaporization and other
physical properties of alkanes [64, 77, 78].
(C) Platt Index
Platt (nearest-neighbor edges) index F is calculated by summing for each edge the
number of its adjacent edges [78]:
N N
2
F=1 d ij ; i, j where d ij = 1 (26)
i =1 j =1
Table 4. Values of Wiener, Polarity, Platt, and Balaban TIs corresponding to aliphatic
alcohols in Table 2
No. W P F J No. W P F J
1 455 24 11 2.785 18 65 18 8 3.464
2 364 22 10 2.758 19 46 16 4 3.155
3 286 20 9 2.727 20 28 14 3 3.169
4 220 18 8 2.691 21 29 12 4 2.994
5 165 16 7 2.648 22 35 8 3 2.339
6 202 20 9 2.973 23 32 10 3 2.627
7 158 18 7 2.773 24 32 10 3 2.627
8 120 14 6 2.595 25 31 10 4 2.754
9 180 26 10 3.376 26 18 8 2 2.540
10 104 16 8 3.092 27 20 6 2 2.191
11 84 12 5 2.530 28 18 8 2 2.540
12 110 16 7 2.877 29 10 4 1 1.975
13 114 16 6 2.747 30 16 12 0 3.024
14 102 16 8 3.175 31 9 6 0 2.324
15 110 28 15 4.328 32 4 2 0 1.633
16 56 10 4 2.448 33 1 0 0 1.000
17 52 12 4 2.678
(D) Balaban Index
Balaban [79, 80] has proposed a topological index, which can be described as the average
distance sum connectivity. The Balaban topological index J of a molecular graph is defined
as [79]:
m N 1 N 1
J=
+ 1 i =1 j =i +1
(d i d j ) 2 ; i, j where d ij = 1 (27)
where m is the number of edges in , is the cyclomatic number, and the vertices i and j are
adjacent.
The average distance sum d k for a vertex k in represents the sum of all entries of the
th
k row or column in the distance matrix, D [79]:
N
d k = d ki ; k = 1, N , k i (28)
i =1
The cyclomatic number = (), i.e. the number of cycles in , is given by [80]
= m n +1 (29)
where N is the number of vertices in . Relation (29) is the known Euler equation connecting
the number of vertices (N), edges (m) and cycles () in a planar graph. Average distance sums
were used in relation (27) instead of distance sums because distance sums increase
approximately parallel with m for the same type of branching. The cyclomatic number ,
defined in relation (29), was introduced in the definition of J because the presence of cycles
markedly reduces the distance sums [58].
4.3. Generalized Topological Distance Indices
Another graph-invariant is the reciprocal distance matrix RD = d ij { } , i,j = 1,N, where N

1
is the total number of graph vertices. This is a symmetrical matrix whose elements are
reciprocal of the topological distance [24, 71, 82, 83]. The first TDIs proposed on the basis of
RD have been developed by a two-steps process as follows [24, 82, 83].
(i) The LOVI of each vertex in a molecular graph , denoted later by i, was defined
from the RD using the following relation [24, 82]:
N
i = d ij1 ; i = 1, N , i j (30)
j =1
In relation (30) dij is the topological distance between the vertices i and j, N
represents the total number of vertices (i.e. non-hydrogen atoms) in , and summation is
made over all possible paths, from dij = 1 to dij = max(dij). Thus, each vertex is well
characterized; it contains global information of the topological structure of , the
topological interaction between vertices i and j decreasing as distance dij is increasing.
That is, for each vertex i, the quantity i may be viewed as a measure of the influence of
all others vertices in a given graph on the vertex i.
(ii) The LOVIs i were condensed into a TDI, h, with the aid of the Randi-type
formula [84], namely the generalized molecular connectivity [85], as follows
[24, 82]:
=
h
(
paths
i j ... h )
1
2 (31)
These topological distances connectivity indices (TDCIs) [24, 82], also called topological
distance measure connectivity indices (TDMCIs) [83], of order higher than three, have not
been used in correlation due to the expected small contributions to the molecular properties.
The TDCIs of order one (1), two (2) and three (3) have been calculated by the
following relations [24, 82]:
N 1
1
= j 2 (32)
j =1
= ( i j )
1
2 2 ; i j ; i, j where d ij = 1 (33)
i, j
= ( i j k )
1
3 2 ; i, j , k = 1, N ; i j k; i, j , k where d ijk = 2 (34)
i , j ,k
Monoparametric correlations with molecular properties such as boiling temperatures (at

normal pressure), gas chromatographic retention indices, atomization enthalpies, and molar
refractions for alkanes were performed. The reported results for 2 are very good, the
correlation coefficients r being in the range 0.983 0.991 [24, 82].
We extended the TDCIs by generalization of relation (30) as follows [73]:
N
k
= d ij k ; k = 1,2,3,4,... ; i, j = 1, N ; i j (35)
j =1
Thus, we obtain a set of generalized topological distance indices based on the reciprocal
distance matrix (GTRDIs), k, where k is the same as in relation (35), which can be
calculated with the following formulas:
N
k
0 = k i ; k = 1,2,3,4,... (36)
i =1
N
1
k
1 = ( k i ) 2
; k = 1,2,3,4,... (37)
i =1
1
k
2 = ( k i k j ) 2
; k = 1,2,3,4,... ; i, j = 1, N ; i j; where d ij = 1 (38)
i , j ,k
1
k
3 = ( k i k j k l ) 2
; k = 1,2,3,4,... ; i, j , l = 1, N ; i j l ; where d ij = d jl = 1 (39)
i , j ,l
One may easily observe that the TDMCIs in relations (32)-(34) are included in GTRDIs
in relations (36)-(39), and there exists a formal identity between and 1 (=1,3).
The sixteen GTRDIs corresponding to k = 1,4 in relations (36)-(39) have been
calculated with the IRS computer program [7, 47, 86] for 72 alkanes with N = 2,9 carbon
atoms. GTRDIs have been used with good results for correlation the boiling points of these
alkanes [73]. The values of GTRDIs for the series of 35 aliphatic alcohols in Table 1 are
given below in Table 5. In computation of GTRDIs the oxygen atom is treated as the carbon
atom. Consequently, the k values are quantitative measures of topological structure of the
equivalent graphs of alkane molecules.
Table 5. Values of generalized topological reciprocal distance indices (GTRDIs)

corresponding to the alcohols in Table 2
1 2 3 4 1 2 3 4
No. 1 1 1 1
1 63.044 37.625 30.439 27.903 6.653 8.683 9.679 10.117
2 56.684 34.483 28.041 25.738 6.280 8.122 9.033 9.437
3 50.477 31.353 25.643 23.574 5.903 7.560 8.388 8.757
4 44.437 28.237 23.246 21.410 5.523 6.998 7.742 8.078
5 38.579 25.137 20.851 19.246 5.138 6.435 7.097 7.398
6 45.932 29.008 23.593 21.566 5.444 6.962 7.790 8.182
7 39.357 25.613 21.098 19.370 5.090 6.407 7.134 7.490
8 32.921 22.058 18.458 17.082 4.750 5.871 6.451 6.718
9 48.471 30.548 24.382 21.958 5.305 6.854 7.840 8.374
10 34.600 22.959 18.863 17.260 4.652 5.832 6.510 6.835
11 27.486 19.003 16.068 14.918 4.358 5.306 5.806 6.039
12 34.052 22.708 18.772 17.230 4.681 5.839 6.498 6.821
13 33.671 22.527 18.704 17.206 4.701 5.844 6.489 6.811
14 34.767 23.028 18.885 17.267 4.644 5.830 6.512 6.836
15 45.500 29.208 22.830 20.175 4.764 6.158 7.189 7.797
16 22.300 15.979 13.681 12.755 3.960 4.741 5.160 5.359
17 22.967 16.424 13.922 12.879 3.909 4.715 5.198 5.451
18 30.333 20.778 16.968 15.354 4.169 5.197 5.913 6.322
19 24.167 17.264 14.390 13.122 3.820 4.645 5.212 5.546
20 19.000 14.167 11.972 10.949 3.421 4.082 4.565 4.865
21 18.167 13.514 11.578 10.732 3.494 4.149 4.561 4.781
22 18.667 13.889 11.796 10.849 3.450 4.117 4.586 4.862
23 17.400 12.997 11.301 10.593 3.558 4.176 4.515 4.679
24 18.000 13.417 11.535 10.715 3.506 4.151 4.553 4.772
25 18.000 13.417 11.535 10.715 3.506 4.151 4.553 4.772
26 19.000 14.167 11.972 10.949 3.421 4.082 4.565 4.865
27 18.167 13.514 11.578 10.732 3.494 4.149 4.561 4.781
28 13.333 10.444 9.148 8.549 3.101 3.587 3.909 4.092
29 12.833 10.069 8.929 8.432 3.151 3.610 3.870 4.000
30 13.333 10.444 9.148 8.549 3.101 3.587 3.909 4.092
31 8.667 7.222 6.574 6.275 2.742 3.048 3.227 3.322
32 14.000 11.000 9.500 8.750 3.030 3.524 3.911 4.171
33 9.000 7.500 6.750 6.375 2.699 3.027 3.261 3.406
34 5.000 4.500 4.250 4.125 2.340 2.496 2.593 2.647
35 2.000 2.000 2.000 2.000 2.000 2.000 2.000 2.000
Table 5. Continued
1 2 3 4 1 2 3 4 1
No. 2 2 2 2 3 3 3 3 2
1 2.863 4.794 5.916 6.448 1.210 2.604 3.575 4.075 2.863
2 2.726 4.479 5.499 5.986 1.160 2.426 3.306 3.761 2.726
3 2.586 4.162 5.083 5.524 1.109 2.248 3.036 3.447 2.586
4 2.444 3.845 4.666 5.062 1.057 2.068 2.767 3.133 2.444
5 2.299 3.527 4.249 4.600 1.002 1.888 2.498 2.819 2.299
6 2.334 3.677 4.511 4.928 1.085 2.122 2.894 3.323 2.334
7 2.220 3.374 4.078 4.436 1.099 2.078 2.794 3.195 2.220
8 2.150 3.207 3.831 4.138 0.946 1.706 2.228 2.505 2.150
9 2.137 3.296 4.091 4.534 1.285 2.491 3.491 4.115 2.137
10 2.005 3.018 3.683 4.029 0.938 1.664 2.211 2.520 2.005
11 1.997 2.886 3.414 3.676 0.886 1.523 1.957 2.190 1.997
12 2.042 3.040 3.673 4.001 0.995 1.778 2.356 2.683 2.042
13 2.067 3.053 3.661 3.974 1.047 1.899 2.525 2.881 2.067
14 1.995 3.014 3.685 4.032 0.925 1.651 2.211 2.532 1.995
15 1.797 2.703 3.438 3.893 1.207 2.171 3.095 3.745 1.797
16 1.840 2.564 2.996 3.213 0.823 1.337 1.687 1.876 1.840
17 1.746 2.405 2.825 3.049 0.940 1.538 1.987 2.253 1.746
18 1.700 2.402 2.923 3.232 1.080 1.830 2.473 2.889 1.700
19 1.604 2.171 2.572 2.807 1.119 1.806 2.400 2.807 1.604
20 1.430 1.838 2.146 2.339 1.108 1.658 2.140 2.479 1.430
21 1.559 2.068 2.416 2.611 0.838 1.243 1.546 1.727 1.559
22 1.475 1.915 2.236 2.430 0.987 1.492 1.908 2.178 1.475
23 1.678 2.240 2.578 2.751 0.755 1.149 1.416 1.562 1.678
24 1.577 2.077 2.405 2.587 0.888 1.358 1.718 1.938 1.577
25 1.577 2.077 2.405 2.587 0.888 1.358 1.718 1.938 1.577
26 1.430 1.838 2.146 2.339 1.108 1.658 2.140 2.479 1.430
27 1.559 2.068 2.416 2.611 0.838 1.243 1.546 1.727 1.559
28 1.401 1.746 1.983 2.122 0.843 1.186 1.449 1.614 1.401
29 1.509 1.914 2.160 2.289 0.679 0.958 1.144 1.248 1.509
30 1.401 1.746 1.983 2.122 0.843 1.186 1.449 1.614 1.401
31 1.334 1.587 1.743 1.828 0.591 0.762 0.873 0.935 1.334
32 1.265 1.512 1.706 1.835 1.200 1.714 2.182 2.526 1.265
33 1.225 1.414 1.549 1.633 0.866 1.155 1.386 1.540 1.225
34 1.155 1.265 1.333 1.372 0.471 0.566 0.629 0.666 1.155
35 1.000 1.000 1.000 1.000 0.000 0.000 0.000 0.000 1.000
We supposed that the relations (30) and (35) describe the topological interactions k
i
between all the vertices j and the vertex i; i,j=1,N, ji; N is the number of vertices (non-
hydrogen atoms) in the molecular graph . This interaction depends on the distance between
the vertices i and j, dij, that is on the number of edges separating the vertices i and j. Paths of
length one (dij=1) represents bonds, and paths of length two (dij=2) signify two consecutive
bonds. Longer paths represent a string of consecutive bonds. One proposed that paths are to
be viewed as one of the elementary structural concepts which are well understood and need
no explanation [63].
One may consider that the molecules contain an internal topological energy, due to the
strains appearing among the vertices of the corresponding chemical graphs. This is an internal
topological strain, which decreases when the distance between the vertices increases. Thus,
the contribution of the adjacent vertices to the internal topological strain (ITS) is highest; it is
equal to 1 for all the powers of k. It diminishes with the growth of the topological distances
between two vertices.
Thus, from the definition of the local topological distance strain (LTDS) see relation
(30), the contribution of the vertices in molecular graphs n decreases as the corresponding
distance between them increases, and the power k also increases. The individual LTDS (local
topological distance strain) value of order k associated to a given vertex j, j, is a measure of
the topological strain due to all other adjacent vertices i of the molecular graph, with the
condition ji. The topological strain exercised by each node of on a given node depends on
the reciprocal distance between these nodes, raised at power k. In this way, we have obtained
a variable value for the local topological distance strain, depending of the values of k. In this
study the value of k was limited to integers k=1, 2, 3, 4. The value of refers to the path of
chemical graphs see relations (36) (39). It corresponds to the generalized molecular
connectivity [85].
5. QSTR Models of the Toxicity of Aliphatic Alcohols

5.1. Introduction
There is an increased emphasis in predicting the toxic effects of the chemical compounds
from molecular structure. The ability to use a QSTR analysis to estimate accurately the
relative toxicity of chemicals would be of value to chemical and pharmaceutical industry. A
variety of toxicity data sets have been compiled for QSTR studies. Of these, the population
growth inhibition of the freshwater ciliate Tetrahymena pyriformis is among the largest.
These toxicity data have been derived for the express purposes of the QSTR development and
validation [5, 87].
Among the most widespread industrial organic chemicals in the world are the aliphatic
alcohols, as indicated by the high production volume chemical list [88]. The alcohols exhibit
their toxic effect by means of narcosis, which is a general term that describes non-covalent
interactions between xenobiotics and cellular membranes. When accumulating, they disturb
the function of cellular membranes, and over a certain concentration they may cause the death
[5, 87]. The toxicant molecule partitions into the lipid bilayer, and if a critical volume is
reached death occurs. The toxicity of substances is governed by their properties, which in turn
are determined by their chemical structure. Therefore, there are interrelationships between
structure, properties, and toxicity [57].
The most important problem in QSTR analysis is to convert chemical structure into
molecular descriptors (MDs) with good predictive ability and that are relevant to the physical,
chemical or biological properties [89]. Unfortunately, there are many molecular descriptors
that are not so easy to interpret. Such descriptors include the topological indices, of which the
molecular connectivity descriptors are the most frequently used [58, 63, 84, 85].
During recent years our research is concerned mainly to develop topological and van der
Waals (vdW) descriptors and to investigate their use in QSAR (Quantitative Structure-
Activity Relationship) and QSTR studies [18, 50, 66-68, 73, 82, 83, 90].
In this chapter we also present some QSTR studies on a series of 33 aliphatic alcohols,
which exhibit toxic effects on ciliate protozoa Tetrahymena pyriformis. These studies have
been performed using the compressibility (CiD) and ovality ( i ) vdW molecular descriptors
[91] and topological descriptors GTRDIs [92] presented above.
5.2. Modeling of Alcohol Toxicity with Van Der Waals Molecular Descriptors
The data set was collected from literature [5, 93]. Each alcohol was tested in three
replicate assays to ciliate Tetrahymena pyriformis. Each test replicate consisted of six to ten
different concentrations. The reported toxic activity was the 50% growth inhibitory
concentration (IGC50), expressed millimolar [5]. We used as experimental biological activity,
A, the logarithm of the inverse of concentration that produces 50% growth inhibition to T.
pyriformis. The values of A=log(1/IGC50) for a series of 33 alcohols used in this QSTR study
are presented in Table 6. The T. pyriformis toxicity data for various chemicals are available at
the Tetratox database Web site [93]. Molecular descriptors used in correlations are
experimental and calculated 1-octanol/water partition coefficient (log KOW), and
compressibility molecular descriptors C1D (in ), C2D (in 2), and C3D (in 3). The linear
QSTR models obtained by correlating toxicity (A) versus compressibility descriptors CiD, i=1-
3, are the following:
A = 3.2635( 0.0832) + 4.6399( 0.1228) C1D

n = 33,s = 0.185;r = 0.989;radj
2
= 0.978;F = 1428;qLOO
2
= 0.976 (40)
A = 2.5692( 0.0698) + 0.0385( 0.0011) C2 D

n = 33,s = 0.193,r = 0.988,radj
2
= 0.976;F = 1301;qLOO
2
= 0.973 (41)
A = 2.1282( 0.0898) + 0.0168( 0.0007 ) C3 D

n = 33, s = 0.290, r = 0.974, radj
2
= 0.946, F = 562, qLOO
2
= 0.936 (42)
A = 2.0298( 0.0561) + 0.7699( 0.0210) log P

n = 33, s = 0.190, r = 0.989, radj
2
= 0.977, F = 1351, qLOO
2
= 0.974 (43)
where A stands for the calculated value of experimental inhibitory activity, n represents the
2 2
number of data, s is the standard error, and r, radj , and q LOO are the correlation coefficient,
coefficient of determination adjusted for the degree of freedom, and the cross-validation
coefficient of the leave-one-out method, respectively. The statistical tests F and t are used at
the 95% reliability degree. The Student (t-) test was used for calculating the confidence limits
of the parameters of the linear models (40)-(43).
Table 6. Data used in QSTR analysis; the toxic activity of alcohols to Tetrahymena
pyriformis is expressed by A=log(1/IGC50), where IGC50 is the concentration that
produces a 50% inhibition of Tetrahymena pyriformis growth (in mM)#
No. Name of alcohol A A( 40 ) A( 41 ) A( 42 ) A( 43 )

1. 1-tridecanol 2.450 2.388 2.683 3.012 2.266
2. 1-dodecanol 2.161 1.998 2.177 2.375 1.920
3. 1-undecanol 1.955 1.608 1.685 1.775 1.458
4. 1-decanol 1.335 1.209 1.199 0.553 1.489
5. 1-nonanol 0.855 0.806 0.728 0.681 0.873
6. 4-decanol 0.850 1.070 1.069 1.082 0.880
7. 2-nonanol 0.618 0.745 0.677 0.631 0.873
8. 1-octanol 0.583 0.370 0.272 0.177 0.280
9. 3,7-dimethyl-3-octanol 0.340 0.736 0.754 0.772 0.680
10. 2-ethyl-1-hexanol 0.167 0.073 -0.002 -0.054 0.134
11. 1-heptanol 0.105 -0.039 -0.184 -0.268 0.064
12. 3-octanol 0.031 0.221 0.128 0.064 0.064
13. 2-octanol 0.001 0.309 0.197 0.121 0.203
14. 2-propyl-1-pentanol -0.134 0.063 -0.007 -0.057 0.134
15. 3-ethyl-2,2-dimethyl-3-pentanol -0.169 -0.299 -0.252 -0.229 0.172
16. 1-hexanol -0.379 -0.480 -0.605 -0.684 -0.467
17. 4-methyl-1-pentanol -0.637 -0.633 -0.725 -0.773 -0.682
18. 2,4-dimethyl-3-pentanol -0.705 -0.605 -0.636 -0.655 -0.544
19. 3,3-dimethyl-1-butanol -0.737 -0.781 -0.843 -0.870 -0.783
20. 2,2-dimethyl-1-propanol -0.870 -1.125 -1.167 -1.165 -1.021
21. 3-methyl-2-butanol -0.996 -1.194 -1.214 -1.197 -1.044
22. 1-pentanol -1.030 -0.916 -1.017 -1.051 -0.829
23. 3- methyl-1-butanol -1.036 -1.050 -1.110 -1.121 -1.137
24. 2-pentanol -1.160 -1.055 -1.114 -1.123 -1.114
25. 3-pentanol -1.244 -1.078 -1.130 -1.136 -1.098
26. 2- methyl-1-propanol -1.372 -1.435 -1.455 -1.403 -1.445
27. 1-butanol -1.431 -1.370 -1.404 -1.373 -1.352
28. 2-butanol -1.542 -1.431 -1.448 -1.400 -1.560
29. 1-propanol -1.746 -1.844 -1.755 -1.650 -1.837
30. 2- methyl-2-propanol -1.791 -1.463 -1.449 -1.413 -1.760
31. 2-propanol -1.882 -1.862 -1.780 -1.656 -1.991
32. Ethanol -1.991 -2.284 -2.068 -1.861 -2.268
33. Methanol -2.666 -2.721 -2.328 -2.016 -2.623
#
The compounds were sorted by activity, in its decreasing order; A( n ) are the calculated values of toxicity
A with eqs. n = 40, 41, 42, 43, respectively.
The correlation results are very good, as expressed by correlation coefficients; r varied
from 0.989 for the model (40), corresponding to the predictor variable C1D, to 0.974 for the
model (42), with C3D as predictor variable. The 95% confidence limits of the parameters of
linear models are about 5% of the statistical parameter values for C1D (see value in relation
40), slightly greater than 5% for C2D (relation 41), and over 8% for C3D (relation 42). The
standard error is less than 4% of the range of experimental values, A, for the linear models
(40) and (41), corresponding to C1D, and C2D descriptors, and about 6% for the model (42),
with C3D as the independent variable. The variance of experimental data is explained better by
2
the compressibility descriptors C1D and C2D (about 98% of variance) see the values of radj
from equations (40) and (41); C3D explains only 95% of the variance of log (IGC50)-1 values.
The reliability in the models (40) and (41) is very good see the values of F, 1428 and 1301,
2
respectively, and, also, their predictive ability see the values of q LOO , 0,976 and 0.973,
respectively. Consequently, the predictive power (or goodness of prediction) of these models
are very good, taking into account the commonly accepted values for a satisfactory QSTR
model, q > 0.500 . The statistical quality of the QSTR models using C1D and logP
2
2
descriptors is similar see the values of s, r, radj from equations (40) and (43); the F statistic
is an indication that C1D works slightly better than logP for the series of alcohols from
Table 6.
Several QSTR models predicting chemical toxicity to T. Pyriformis have been published
[5, 87, 89, 94]. They were mainly based on the algorithm of the octanolwater coefficient
(logP, also referred to as log KOW) as this hydrophobicity term reproduces the ability of a
molecule to enter cells through the lipid membranes and indicates both toxicant uptake and
baseline toxicity. Nevertheless, the experimental determination of logP values can be a
complex matter, and experimental values can differ greatly even when referred to the same
compound. Thus, several approaches have been developed for the theoretical calculation of
logP [95] but also in these calculations it is not uncommon to have differences of several
orders of magnitude [96]. Therefore, the CiD compressibility measures of molecular vdW
space can be used in QSTR studies as predictor variables, in place of log KOW. These
structural descriptors are easy to calculate for any molecule with whatever geometry. They
describe the compression ability of molecules of chemical compounds in their specific
environments.
To assess the predictive ability of the statistical QSTR model (40), we split the data set
from Table 1 into test set and training set, using the rule [24, 97, 98] described below. With
this end in view the data were sorted by toxicity values, Ai, i=1,33, in its decreasing order (see
Table 6), and the compounds were alternately assigned to test (validation) set and training
(calibration) set, and vice versa. Thus, 50% of the compounds were used for training and 50%
for testing. That is, the QSTR model obtained for the subset composed of odd ranking
p
compounds was used to calculate toxic activities, Ai , of the pair ranking subset, i=2n,
n=1,16, and, reciprocally, the QSTR model developed for the pair ranking subset was used to
p
estimate the toxic activities, Ai , of the compounds belonging to odd ranking subset, i=2n-1,
n=1,17. Finally, the correlation between experimental toxicities, Ai, and predicted
p
toxicities, Ai , for all alcohols i=1,33 from Table 6 was done (see eq. 44) and the
corresponding statistics were estimated. The procedure described above is a LHO-type cross-
validation method; it will be referred to below as the Leave odd-pair Out (Lo-p-O) cross-
validation technique.
A p = 0.0064 + 0.9801 A
n = 33, RMSE = 0.181, rPE
2
= 0.979, q Lo
2
pO = 0.979 (44)
p
The plot of the predicted toxicity values, Ai , i=1,33, with Lo-p-O cross-validation
method, against the experimental toxicity values, Ai, i=1,33 is presented in Figure 2. One can
see from this Figure that the data points are very close to the correlation line. The slope of the
line is about 1 (0.980), corresponding to an angle of 45 degree, and the intercept is near to 0 (-
0.0064).
Figure 2 The plot of predicted toxicity versus experimental toxicity, Ap vs. A. [ A = log (IGC )].
1
50
The quality of the predictions was assessed by three statistical measures (see eq. 44). The
2
coefficient of prediction, qLo 2
pO , was used as a first statistical measure. The value of q can
range between 1 and [98]. The closer to the unity, the better predictiveness is achieved.
The second statistical measure is the squared correlation coefficient between the predicted
A p and the experimental A toxic activities, which is reported in this paper by rPE
2
. The
2 2
squared correlation coefficient rPE can vary between 1 and 0. The main difference to q is
2 p 2
that correlation rPE measures the association between the variables A and A, whereas q
requires the magnitude of predicted and experimental data to be the same. rPE is defined
within the interval [-1,1], and it is calculated as the correlation coefficient but replacing the
fitted toxicity with the by predicted toxicity. The commonly accepted reference values for a
satisfactory QSTR model are rPE > 0.800 , and q > 0.500 . The root-mean-square error
2 2
(RMSE) of the prediction is the third statistical measure used to assess the quality of eq. (44)
and the predictive ability of the QSTR model (40).
This cross validation procedure, Lo-p-O, can be considered a pseudorandom division of
data sets because the actual values of activities, A, are scattered by measurement errors. The
method has the advantage that the activity distributions of corresponding training sets and test
sets are very similar, and it should allow assessing the ability of the model to interpolate [98].
The mono-dimensional C1D compressibility descriptor models very well the toxicity of
aliphatic alcohols to T. pyriformis. The goodness of fit and the predictive ability are described
above by means of statistics of eqs. (40) and (44), respectively. The obtained results suggest
that C1D can be used in QSTRs for other series of toxic compounds, and, also, that it can
replace the hydrophobicity descriptor log KOW [91].
The results obtained by statistical analysis of the aliphatic alcohol toxicity by means of
ovality molecular descriptors are summarized in eqs. (45), (46), and (47).
A = 24.3317 ( 0.8433 )+ 20.0853( 0.7059 ) 1D

n= 33 ,s= 0 .243 ;r = 0 .981 ;r 2adj = 0 . 962 ;F = 810 ;q 2LOO = 0 .955 (45)
A = 12.4069( 0.3856 ) + 8.4349( 0.2688 ) 2D

n= 33 ,s= 0 .221 ;r = 0 .985 ;r 2adj = 0 . 969 ;F = 985 ;q 2LOO = 0 .964 (46)
A = 8.4197 ( 0.2429 )+ 4.7074 ( 0.1404 ) 3D

n= 33 ,s= 0 .208 ;r = 0 .987 ;r 2adj = 0 . 972 ;F = 1124 ;q 2LOO = 0. 969 (47)
The correlation coefficients are r>0.930 and the LOO-cross-validation coefficients are
2
q LOO >0.960. The QSTR models (45)-(47) explain more than 96% of the variance of
experimental toxicity values, A=logIGC50. They are reliable models in predicting the toxicity
of other aliphatic alcohols. Our studies [50, 91] prove that the vdW molecular descriptors
presented in this chapter work well in QSTR analysis of the toxicity of this series of aliphatic
alcohols. These compressibility and ovality descriptors are valuable tools in predicting the
toxicity at least in the series of congener molecules.
5.3. Alcohol Toxicity Modeling with the Topological Descriptors GTRDIs
Most of industrial organic chemicals present acute toxicity, exhibited by a narcosis mode
of toxic action. This is a non-receptor-mediated toxic effect that is most often quantified as
individual lethality, population-based endpoints such as growth or reproduction, or a
biochemical/physiological measurement. Thus, QSARs for acute toxicity typically deal with
aquatic and ecological endpoints [5].
The emphasis in the present study was placed on the physical meaning of generalized
topological reciprocal distance indices (GTRDIs). Previous studies have analyzed the ability
of these topological molecular descriptors in correlations with boiling points of alkanes, and
the informational content in terms of molecular van der Waals space [18, 24]. Therefore, the
aim of this example study is also to asses the use of GTRDIs for development of toxicological
QSARs. The data set is chemically homogeneous, including only aliphatic alcohols. The
values of toxicological activities are collected in Table 7.
Table 7. Toxicity of alcohols against Arenicola Larvae (A1), frog tadpoles (A2), Barnacle
Larvae (A3), Tetrahymena pyriformis (A4) and Pimephales promelas (A5)*
No. Alcohol A1 A2 A3 A4 A5
1 Methanol -0.40 0.24 -0.14 -2.77 -2.96
2 Ethanol -0.01 0.54 0.28 -2.41 -2.51
3 1-Propanol 0.47 0.96 0.79 -1.84 -1.88
4 2-Propanol 0.41 0.89 0.92 -1.99 -2.22
5 1-Butanol 1.06 1.42 1.46 -1.52 -1.37
6 1-Pentanol 1.64 - 1.84 -1.12 -0.73
7 1-Hexanol - - 2.41 -0.47 0.02
8 1-Heptanol - - 3.02 0.02 0.53
9 1-Octanol 3.00 3.40 3.62 0.51 0.98
10 Isobutanol - 1.35 1.54 -1.47 -1.29
11 sec-Butanol - - 1.16 -1.64 -1.69
12 tert-Butanol - 0.89 0.98 - -
13 Isoamyl alcohol - 1.64 1.86 - -
14 tert-Amyl alcohol - 1.24 1.34 - -
15 1-Nonanol - - - 0.77 1.40
16 1-Decanol - - - 1.10 1.82
17 1-Undecanol - - - 1.87 2.22
18 1-Dodecanol - - - 2.07 2.27
*
The toxicological data represent: A1 is narcotic concentration, pC, against Arenicola Larvae [62]; The
original data are from R. S. Lillie, J. Physiol. 1913, 31, 255; A2 is log (1/C), where C is the effective
concentration that produces narcosis of frog tadpole [62]; The original data are from E. Overton. Studies
of Narcosis, Fischer, Jena, Germany, 1901; A3 is narcotic concentration, pC, against Barnacle Larvae
[62]; The original data are from D. J. Crisp; D. Marr, Proc. Int. Congr. Surface Activity, 2nd, 1975, p.
310; A4 is log (1/C), C is ciliate toxicity, in (mmol/L)-1 [99]; A5 is log (1/C); C is fish toxicity,
(mmol/L)-1 [99].
Narcotic chemicals such as alcohols act at the level of cellular membrane, which is
considered the theoretical site of action. The interactions are supposed to be non-covalent and
reversible. Consequently, one expects that the measured toxicological effect may be modeled
by the octanol/water partition coefficient; log Kow (see, also, Table 2 for the values of log Kow
for the alcohols from this chapter). The values of this partition coefficient were computer-
estimated CLOGP values (version 3.51) or retrieved as measured values from the same
program, and are from refs. [5] and [93]. But, the coefficient of partition is a hydrophobic
measure of the whole molecule based on an empirical physicochemical model. It is not a
structural parameter. Using only the partition coefficient in QSAR studies of toxicity, it is not
possible to point out molecular structural features or subclasses of structural influences on the
toxicity [99].
In Table 7 are listed the toxic activities of the alcohols used in correlations for testing the
molecular topological descriptors presented in this section [92].
The toxicity data are collected from literature [5, 62, 99]. They include the narcotic
concentration (pC) against Arenicola Larvae, frog tadpoles and Barnacle Larvae [62] and
relative toxicity for the static 48-h Tetrahymena pyriformis 50% population growth
impairment and the flow-through 96-h Pimephales promelas 50% mortality endpoints
[99]. The data set in Table 7 is chemically homogeneous, including only aliphatic
alcohols [100].
We used the MLR method for analyzing the usefulness of GTRDIs for QSAR study of
narcotic effects of the alcohols. Previous studies have analyzed the ability of these topological
molecular descriptors to correlate the boiling points of alkanes, and their informational
content in terms of molecular van der Waals space [24, 73]. The obtained results are
summarized in Table 8 and 9. Table 8 contains only the correlation coefficients of the
regressions with all data of each series of alcohols acting to a specific biological organism.
The results of correlation analysis [100] are very good for the majority of biological
activities in Table 7 and for topological molecular descriptors developed on the basis of
reciprocal distance matrix. Topological molecular descriptors k, k=1,2,3,4, =0,1,2,3 (with
exception of k3, k=1,2,3,4) correlate very well with the narcotic effect generated by the 15
tested alcohols on Tetrahymena pyriformis and Pimephales promelas; the correlation
coefficients are r 0.950.
Table 8. Correlation coefficients (r) of linear regressions between GTDIs and

toxicological activities Ai, i=1,5 (see Table 7) and partition coefficient (log Kow)
GTDI A1 A2 A3 A4 A5 Log Kow

1
0.993 0.949 0.973 0.994 0.979 0.986
2
0.997 0.932 0.968 0.997 0.988 0.988
3
0.997 0.935 0.970 0.997 0.989 0.989
4
0.997 0.941 0.974 0.997 0.990 0.990
1
1 0.999 0.969 0.987 0.998 0.992 0.995
2
1 0.998 0.962 0.985 0.998 0.991 0.994
3
1 0.998 0.947 0.978 0.997 0.989 0.991
4
1 0.997 0.934 0.970 0.997 0.989 0.989
1
2 0.997 0.993 0.985 0.997 0.995 0.997
2
2 0.998 0.995 0.988 0.997 0.992 0.997
3
2 0.998 0.993 0.989 0.997 0.992 0.997
4
2 0.998 0.990 0.991 0.998 0.992 0.997
1
3 0.748 0.471 0.532 0.822 0.818 0.627
2
3 0.892 0.635 0.715 0.958 0.947 0.864
3
3 0.917 0.650 0.729 0.971 0.959 0.883
4
3 0.919 0.632 0.708 0.972 0.959 0.875
The correlation coefficients obtained for all 5 series of alcohols with narcotic action are
generally greater than 0.980, when descriptors k, where k=1,2,3,4 and =0,1,2, are used in
deriving fitting equations of structure toxicity. Weaker results were obtained for the k3
indices. These are based on paths of length two from the molecular graph describing the
topological structure of the alcohols under study. One can assume that this descriptor does not
adequately describe the toxic effect of this series of alcohols. This fact is not surprising, since
the contribution of the vertices situated at a greater distance is smaller. Furthermore, the
considered path length in the graph for this index is greater than for the other GTDIs. These
two topological structural elements act in the same direction, relieving the strain between the
nodes under consideration. Globally, the effect leads to a diminution of the scale of k
values, reducing also the discriminative capacity of these molecular topological descriptors.
The values of the k index in Table 5 show that this level effect increases together with the
values of k and .
As we have seen from Table 8, these indices are linearly related to the partition
coefficient log Kow. However, indices k3 fail as in the previous case. We can suppose that the
topologies of molecular graphs, as described by these successful indices obtained from the
reciprocal distance matrix, have a contribution to this experimental physicochemical
parameter.
We report in this chapter a more complete analysis using only the 10 molecular structural
descriptors. Statistical results are given in Table 9. The best results are obtained by the QSTR
analysis of the toxicity of aliphatic alcohols on Tetrahymena pyriformis (A4) see the values
of the statistical indicators in Table 9; for example, the explained variance is greater than 98%
and the QSTR model has a very good predictive ability, as measured by the cross-validation
2
coefficient, qLOO =0.981. Obviously, the number of compounds in this studied series is small,
but the work is in progress for very large series of chemicals. The poorest results were
obtained for QSTR study of the narcosis of frog tadpole; it is the series from the first reported
QSAR study of Overton [62].
Table 9. Statistical results for fitting equations with GTRDS 10 as structural variables*
Ai = a ( a ) + b ( b) 10
2
a a b b s EV F rCV
A1 -0.511 0.094 0.111 0.006 0.150 0.983 349.075 0.920
A2 -0.014 0.174 0.094 0.011 0.287 0.889 72.952 0.766
A3 -0.299 0.139 0.117 0.008 0.242 0.943 215.809 0.936
A4 -2.708 0.082 0.090 0.003 0.184 0.986 990.383 0.981
A5 -2.761 0.167 0.102 0.006 0.375 0.957 308.520 0.938
*
x (x=a, b) are the 95% confidence limits; s is the standard error of the estimates; EV represents explained
2 2
variance ( radj ); F is the Fisher test; rCV is the cross validation coefficient.
The topological indices developed on the basis of reciprocal distance matrix of the
molecular graphs are good molecular descriptors for quantitative treatment of toxicological
effects of alcohols. The best results are obtained for the toxicity of alcohols on the ciliate
Tetrahymena pyriformis. The QSTR models explain more than 80% of the variance of
experimental data.
6. GTDIS versus VDW MDS

The statistical quality of the QSTRs obtained with the aid of the vdW molecular
descriptors, CiD and iD , and the topological descriptors, k, is as good as for all linear
models presented above. One can see above that the obtained results are similar for all
compressibility, ovality and topological descriptors GTRDIs.
In this section we analyze the extent to which the molecular descriptors formerly
presented are linearly interrelated. In this way we can establish to what extent these MDs are
orthogonal. If the MDs used in MLR analysis of experimental toxicity of various chemicals
are orthogonal, the reliability in QSTR models is high and they may be easily interpreted in
terms of the structural factors quantified by the used MDs. On the other hand, the non-
orthogonal MDs may express the same type of structural information, and the correlations and
predictions of QSTR models may be artificially improved.
We have investigated the linear relationship between the pairs of molecular descriptors
presented here, MDa and MDb, by means of the following linear relation
MDa = + MDb (48)
where MDa are the GTRDIs and the topological distance indices W-Wiener [81], P-polarity
[77], F-Platt [78], and J-Balaban [80], and MDb are the compressibility and ovality (size and
shape) MDs; the equations (48) are characterized only by the correlation coefficient, r.
The correlation coefficient, r, is a measure of the linear relationship (48). If r = 0 no
linear relationship exists between MDa and MDb. If r = 1, there is a direct linear relationship,
and if r = -1, there is an inverse linear relationship between MDa and MDb. The correlation
coefficient r 0.900 was proposed as the criterion for the intercorrelated pairs of molecular
descriptors [73]. Strongly intercorrelated pairs of the molecular descriptors are those with
r 0.980. The results of the correlation analysis are displayed in Table 10.
The vdW volume (VW) and surface (SW) and the compressibility and ovality descriptors
are linearly related not only to GTDRI descriptors k (=0,1,2; k=1,2,3,4) but also to the
Wiener (W) topological distance index. There is no correlation against J and the other MDs
related to the molecular vdW space of aliphatic alcohols. The intrinsic density of these
molecules is not related to the topological indices in Table 10.
The steric component of the most topological indices is poorly explained by the
characteristics of the vdW space. Weak correlations were also obtained for P, F and J.
The results suggest the impossibility of testing the vector nature of steric effects by
means of the topological distance indices, which is rather important for modeling
biological interactions. This is a possible explanation for the lesser utility of topological
indices for QSAR studies.
Table 10. Coefficients of correlation (r) corresponding to the linear relation (48)
vdW MD
SW VW C1D C2D C3D 1D 2D 3D ID
GTRDI
1
0.985 0.993 0.967 0.971 0.962 0.946 0.949 0.950 -0.697
2
0.985 0.995 0.967 0.964 0.950 0.951 0.952 0.951 -0.719
3
0.990 0.998 0.974 0.970 0.955 0.961 0.962 0.960 -0.740
4
0.994 0.999 0.980 0.975 0.960 0.968 0.969 0.967 -0.752
1
1 0.999 0.998 0.994 0.989 0.974 0.984 0.986 0.986 -0.781
2
1 0.999 0.999 0.990 0.986 0.972 0.979 0.980 0.980 -0.769
3
1 0.995 0.999 0.983 0.978 0.963 0.971 0.972 0.971 -0.756
4
1 0.991 0.998 0.977 0.971 0.956 0.964 0.965 0.963 -0.748
1
2 0.985 0.972 0.994 0.989 0.972 0.989 0.991 0.994 -0.815
2
2 0.991 0.980 0.995 0.994 0.980 0.986 0.990 0.992 -0.794
3
2 0.995 0.988 0.996 0.995 0.980 0.985 0.988 0.990 -0.785
4
2 0.996 0.992 0.995 0.994 0.979 0.984 0.987 0.989 -0.780
1
3 0.707 0.727 0.680 0.646 0.615 0.700 0.690 0.673 -0.681
2
3 0.907 0.921 0.885 0.868 0.847 0.884 0.881 0.872 -0.740
3
3 0.912 0.929 0.886 0.874 0.856 0.880 0.878 0.870 -0.705
4
3 0.897 0.917 0.867 0.856 0.839 0.860 0.857 0.849 -0.674
W 0.927 0.913 0.928 0.958 0.976 0.891 0.904 0.914 -0.634
F 0.869 0.900 0.828 0.819 0.804 0.812 0.809 0.801 -0.579
P 0.866 0.899 0.824 0.822 0.809 0.799 0.798 0.795 -0.521
J 0.491 0.542 0.432 0.392 0.359 0.445 0.430 0.409 -0.382
7. Conclusion
Molecular structure is one of the basic concepts of chemistry, since properties and
chemical and biological behaviors of molecules are determined by it. The quantification of
various aspects of the molecular structure is one of the formidable tasks of the actual research
studies in toxicology. The purpose is to develop molecular descriptors (MDs) for quantitative
structure toxicity relationships (QSTRs) with good explicative and predictive capabilities.
The potential utility of these MDs must be established on the series of chemical compounds
with well determined toxic activity. From this point of view, saturated aliphatic alcohols are
among the best studied classes of industrial organic chemicals. Therefore, we used various
series of aliphatic alcohols, which are neutral narcosis-acting compounds, to validate the
MDs.
Three molecular size (CiD, i=1,2,3) and three molecular shape ( iD , i=1,2,3) descriptors
developed on the basis of molecular vdW space supposedly isotropic, homogeneous, and
compressible in some extent, and sixteen generalized topological descriptors based on the
reciprocal distance matrix, GTRDIs ( ) were presented here. GTRDIs are non-empirical
k
descriptors based on chemical topology. They are derived from the application of chemical
graph theory. The advantage of topological properties is that they are a direct, simple
description of molecular structure; the disadvantage is those that chemical topologies have no
direct mechanistic meaning to toxicology. On the contrary, the molecular descriptors
developed on the basis of the vdW molecular space may have clear physical meaning when
the analysis is performed on the toxicity of various series of chemicals, especially when using
series of congeners in QSTR studies.
The vdW molecular descriptors CiD (i=1,2,3) measure the i-dimensional relation between
the packed and the extended vdW size of a molecule within its specific environment, during
physical and chemical interaction. Consequently, the vdW compressibility measures were
used to model the biological activity of chemical compounds, including their toxicity. This
was done with good results in the present QSTR analysis of the toxicity of aliphatic alcohols
to Tetrahymena pyriformis. The structural molecular descriptors CiD can be also used in such
studies of toxicity in place of logP. The aliphatic alcohols act toward the cellular membranes
and the packing degree of the molecules, as measured by CiD, influences their capacity to
accumulate, thus their toxicity. The iD , i=1,2,3 vdW descriptors are measures of the
molecular shape. They indicate the degree of deviation of a molecule from the round
(globular) shape.
The development of the GTRDIs was base on the following hypothesis: each vertex i
supports a topological distance strain (TDS) from all other vertices of the molecular graph.
This TDS is a function of the distance between the vertex i and j, j=1,N, ji. Naturally, there
is an inverse relationship between the topological strain and the topological distance.
Consequently, we defined as a local vertex invariant (LOVI) the local topological distance
strain (LTDS) of order k,
k
i , as the sum of the reciprocal distances of all vertices (atoms) of
the chemical graph to the given vertex, i. The i value represents the contribution of the
vertex (atom), i, to the total topological strain of a given molecule represented by its
molecular graph . Therefore, the sum of
k
i over all atoms in represents the total
topological strain of order k, k
0 , that characterizes a molecule described by . We consider
that k
0 may be viewed as an internal topological distance strain (ITDS) of order k, due to
the reciprocal influences of molecular graph vertices. ITDS is a topological distance
contribution to the total topological energy of a molecule represented by . These interactions
decrease as the topological distances between vertices in increase. In this way, ITDS offers
an a priori physical meaning of the GTDIs. Introducing various metrics on the molecular
topological graphs one can differentiate the (hetero)atoms, and thus can obtain reliable
molecular descriptors for QSPR and QSAR studies.
These molecular descriptors, CiD, iD , and GTRDIs were calculated for a set of 33
alcohols, which all exhibit toxic action on Tetrahymena pyriformis, and, in variable
proportion, they present toxic action on Arenicola larvae, Barnacle larvae, frog tadpole, and
Pimephales promelas. We conclude that the obtained results prove that these indices are
valuable molecular descriptors in modeling the toxic activity of aliphatic alcohol, In order to
arrive to more definite conclusions, we deem it is necessary to extend the calculations to quite
different molecular sets and other biological activities and physicochemical properties. The
relations among vdW descriptors and GTRDIs suggest a same physical meaning for these
topological indices based on the reciprocal distance matrix.
It has been also shown in this chapter that accurately describing the toxicity of aliphatic
alcohols with a single correlation is quite feasible if the molecular descriptors have clear
physical meaning, and they are related to the physical and chemical interacting forces
between molecules, and particularly between biological receptors and the toxin molecules.
The reason is that the mode of action is the same, a reversible accumulation of the alcohol
within the cell membrane that results in distortion and disruption of function.
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INDEX
300, 301, 302, 303, 304, 308, 311, 313, 315, 317,
A 318, 321, 331, 332, 349, 351, 390, 391, 397, 398,
400, 401, 402, 403, 404, 407, 408, 409, 414, 415,
absolute electronegativity, 254, 255, 257, 259 416, 504
absolute hardness, 255, 274 Cauchy-Schwartz inequality, 543, 547
achiral, 458, 459, 518 chamfering, 452, 461, 477
Adaptive Fuzzy Partition, 613, 623 charge conservation, 266
ADF, 63, 65, 66, 84 chemical action, 1, 2, 6, 9, 256, 269, 270
Alchemy, x chemical binding, x, 6, 7, 8, 14, 15, 16, 313, 321,
algebraic correlation, 569, 570, 571, 574, 579 541
all-ring, 461, 464, 466, 470, 472 chemical binding functions, 6
Amino acid map, 529 chemical bond, x, xi, 1, 2, 5, 9, 12, 19, 84, 113, 251,
amplification, 141, 142, 148, 154 252, 256, 261, 270, 271, 272, 273, 315, 320, 335,
anionic-cationic interaction, 572 347, 356, 363, 480
annihilation, 161, 261 chemical electronegativity, 253, 257, 258, 261
Anthocyanidins, 357 chemical graph, 479, 480, 482, 484, 487, 489, 494,
anti-bonding, 2, 5, 6, 7, 8, 9, 12, 13, 16, 17, 18 496, 500, 503, 629, 644, 651, 662
architecture, 404, 615, 616, 620, 626 chemical hardness, 253, 255, 271, 272, 273, 274, 275
Arrhenius, 93 chemical reactions, 93, 94, 108, 109, 217, 218, 271,
Artificial Neural Networks, 609, 613, 623 272, 334, 425, 447, 485, 635
ATMOL, 65, 84 chemical reactivity, 18, 191, 252, 255, 261, 265, 267,
Azoles, 353 268, 269, 270, 271, 273, 500, 634
chemical structure, 92, 274, 437, 461, 480, 481, 482,
483, 484, 493, 500, 539, 579, 601, 629, 630, 631,
B 632, 634, 651
chemoinformatics, 482
binding spinor, 9
chemometrics, 480, 482, 493, 497
Biot-Savart law, 267
chiral, 214, 409, 410, 411, 412, 430, 432, 454, 456,
bonding, x, xi, 1, 2, 3, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15,
458, 459, 460
16, 17, 18, 19, 66, 157, 158, 183, 186, 253, 266,
Cluj, 426, 429, 473, 474, 476, 478, 507, 519
270, 271, 273, 326, 327, 328, 336, 361, 363, 389,
Cluster Analysis, 612, 623
391, 397, 398, 408, 417
coalescence, 440
Born-Oppenheimer, 81, 93, 134, 213
coherent states, 146, 288
Bose operators, 144, 149
common factors, 541
Boys, 63, 64, 83, 85, 159, 164, 184, 186, 340
complete set of commutative operators, 573
complexity, x, 192, 218, 305, 427, 431, 480, 482,
C 485, 494, 495, 496, 525, 561, 612, 613, 614
conditioned probability, 554, 555
CADPAC, 65, 84 Configuration Interaction (CI), 61, 62
cage, 298, 347, 441, 442, 443, 456, 462, 464, 465, correlation coefficient, 546, 551, 552, 634, 648, 652,
472, 477 654, 655, 656, 658, 659, 660
capra, 427, 461, 477 Coulomb integral, 64, 69, 75, 77, 85, 86
carbon atom, 277, 281, 282, 283, 284, 285, 286, 288, Coulomb resolution, 63, 73, 74, 75, 77, 78, 80
289, 290, 292, 293, 294, 295, 296, 297, 298, 299, Coulomb Sturmian, 72, 85
670 Index
covariance index, 546 508, 509, 510, 511, 512, 513, 514, 515, 517, 518,
covering, 194, 425, 426, 427, 428, 429, 430, 431, 645
436, 437, 438, 440, 441, 443, 444, 445, 447, 456, eigen-value, 5
457, 461, 470, 472, 473, 474, 579 Electric El, 573
Coxeter, 406, 423, 458, 467, 474 electric field, 91, 98, 100, 114, 268, 269
creation operator, 261 electric susceptibility, 269
critical electronegativity, 16 electrodynamics, 266
crystals, 141, 143, 189, 192, 234, 251, 277, 278, 279, electromagnetic theory, 217, 247
286, 288, 293, 294, 296, 297, 300, 301, 303, 304, electron, ix, x, 18, 48, 64, 65, 66, 69, 70, 73, 86, 91,
306, 308, 315, 391, 392, 393, 405, 462 92, 95, 98, 105, 111, 112, 113, 142, 143, 144, 148,
cube, 299, 300, 389, 460, 462, 477 149, 158, 159, 163, 164, 167, 176, 182, 195, 196,
CVNET, 427, 447, 462, 474 198, 200, 202, 203, 204, 205, 206, 207, 208, 212,
213, 214, 218, 219, 220, 221, 222, 223, 224, 225,
226, 227, 228, 229, 230, 231, 232, 235, 236, 237,
D 238, 241, 247, 248, 255, 256, 270, 271, 273, 274,
278, 294, 297, 319, 320, 321, 326, 335, 336, 337,
Daphnia magna, 573, 585 343, 344, 345, 346, 347, 348, 349, 350, 351, 352,
Database, 473, 580, 581, 593, 604, 623, 625 353, 354, 355, 356, 358, 359, 360, 361, 362, 363,
de Broglie, 5, 28, 39, 52, 54, 59, 195, 196, 199, 203, 364, 365, 373, 375, 376, 379, 390, 391, 392, 393,
206, 207, 608 394, 396, 397, 406, 413, 439, 440, 475, 476, 520,
Debye model, 94 635, 639
degree of membership, 610, 613, 614, 617, 623 electronegativity, 1, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18,
degree-degree association, 479, 480, 489, 490 191, 192, 212, 251, 253, 254, 255, 256, 257, 258,
delocalization, 13, 344, 348, 349, 350, 354, 355, 356, 259, 261, 262, 263, 265, 266, 267, 268, 270, 271,
362, 363, 364, 365 272, 273, 274, 275, 352, 358, 373, 608
density functionals, 184, 189, 252, 253, 259, 261, electronic affinity, 254, 256
270, 370 endohedral, 439
DERIC, 65, 84 endpoint, 541, 573, 574
descriptor, 256, 482, 488, 501, 563, 613, 614, 623, endpoint paths, 573
625, 641, 642, 643, 656, 659 energy gap, 92, 141
design, 50, 327, 461, 473, 482, 497, 506, 540, 571, Enrichment, 594, 595, 596, 604
578, 579, 583, 596, 598, 601, 605, 611, 630, 631 entropy, 480, 481, 483, 484, 487, 488, 489, 490, 491,
difference equations, 149 493, 494, 535, 616, 626
differential electronegativity, 255 Esaki, 92, 108
Difficulty, 593, 596 Euler, 76, 405, 447, 449, 461, 466, 467, 475, 504,
Dirac, 1, 2, 3, 5, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 647
18, 19, 323, 391, 393, 561, 586 exchange, 64, 68, 69, 70, 75, 76, 77, 78, 79, 83, 113,
Dirac binding functions, 12, 17 142, 143, 144, 145, 146, 159, 178, 200, 206, 213,
Dirac equation, 2, 3, 5, 9, 10, 13, 17, 18, 393 278, 279, 292, 293, 307, 308, 313, 314, 315, 316,
Discriminant, 612, 624 317, 318, 319, 321, 328, 472
dispersion, 173, 182, 415, 545, 546 Exchange integral, 63
distribution, 22, 62, 64, 69, 105, 106, 191, 192, 193, excitons, 141, 142, 143, 145, 149, 151, 153, 154, 155
200, 201, 210, 246, 272, 280, 285, 308, 335, 356, Expert System, 608, 609, 623
358, 359, 360, 362, 389, 398, 400, 401, 402, 403, expert systems, 541
408, 409, 414, 415, 416, 417, 421, 473, 480, 481, external potential, 255, 259, 272, 292, 293, 306
482, 484, 489, 490, 491, 552, 553, 554, 574, 587, Eyring, 73, 93, 109
589, 590, 594, 598, 599, 601, 602, 605, 612, 614,
621, 635
dodecahedron, 460, 462 F
Drug, 583, 584, 596, 624, 625, 665, 666
dual, 328, 427, 448, 449, 450, 451, 458, 465, 470 factionary occupancy, 265, 271
factor indeterminacy, 578, 587
Faraday-Lenz law, 268
E Fermi Golden rule, 94
Fermi operator, 143
ECG, 81, 82 Fock electronic space, 261
edge, x, 13, 295, 395, 405, 426, 427, 428, 430, 436, Fourier transform, 61, 63, 68, 71, 75, 76, 86, 145,
439, 441, 444, 447, 448, 449, 452, 453, 454, 458, 149, 208
461, 466, 472, 485, 500, 501, 502, 504, 506, 507, Fourier transformation, 145, 149
Index 671
FuGeNeSys, 611, 612, 624 ICI, 81, 82

Fukui index, 255 icosahedron, 404, 450, 462
fullerene, 271, 387, 390, 403, 404, 405, 406, 407, Imidazole, 354
408, 409, 413, 415, 417, 418, 420, 421, 439, 440, in silico, 540, 578
441, 456, 461, 472, 477, 504, 507, 508, 519 Independent action Model, 617, 623
Fuzzy ARTMAP Neural Networks, 615 Indoles, 348
Fuzzy Clustering Method, 612 information functional, 480, 483, 484, 487, 489, 490,
Fuzzy Least Squares Regression, 621, 623 493, 494
Fuzzy Logic Theory, 607, 608, 609, 611, 613, 615, information index, 485, 486
617, 619, 621, 622, 623, 625, 627 inter-endpoint molecular activity difference
Fuzzy set, 611 (IEMAD), 575
inter-endpoint norm difference (IEND), 575
ionic liquid internal angle, 572
G ionic liquids, 571, 572, 573, 585, 586
ionization potential, 114, 218, 219, 220, 221, 225,
Gamow, 92, 108 240, 244, 245, 248, 255, 256
gauge equilibrium, 253 ionization potentials, 218, 219, 220, 225, 240, 244,
Gauss law, 268 245, 248, 255
GAUSSIAN, 62, 65, 84 isomerization, 271, 328, 376, 426, 439, 441, 442,
Gaussian transform, 71 443, 445, 446, 447
genus, 447, 466, 467
global softness, 257, 258
Goldberg, 452, 453, 457, 476, 663 J
Gram-Schmidt, 563, 565
Graph, 426, 447, 476, 480, 483, 494, 495, 497, 499, Jaccard similarity coefficient, 482
506, 510, 511, 517, 521, 522, 605, 666, 667 Josephson, 91, 92, 108
graph entropy, 479, 480, 483, 484, 491, 493, 494
green chemistry, 571, 579
Gurney, 92, 108 K
Kim, 93, 109, 189, 422, 423
H Kozhushner, 94, 109
K-paths, 575
Hamiltonian, 2, 17, 63, 69, 95, 109, 113, 114, 143, Kramers, 93, 109
144, 145, 146, 148, 149, 159, 160, 161, 163, 184,
185, 199, 265
Hansch, 496, 533, 541, 562, 572, 583, 619, 627, 634, L
664
hardness principles, 265 Lattice Representation of DNA, 522
Hartree orbitals, 63 leapfrog, 427, 438, 450, 451, 453, 461, 464, 470,
Hartree-Fock (HF), 62, 158 474, 476, 477
H-depleted, 480, 481 lipophylicity, 571, 572
heat of molecule formation, 217 local response function, 258
Heisenberg, 22, 23, 24, 545 local softness, 257, 258
hidden variable, 265, 270 localization, 6, 13, 16, 18, 164, 186, 252, 270, 271,
Hilbert space, 2, 539, 542, 561, 563, 570 274, 307, 346, 364, 373
Hybrid integrals, 69, 70 localization functions, 252, 270, 271
hydrogen atom, 69, 77, 78, 91, 117, 200, 201, 204, Lofti A. Zadeh, 608
208, 286, 313, 319, 320, 328, 331, 332, 336, 344, luminescence, 143, 387
374, 481, 500
hydrogen molecule, 81, 85, 88, 288, 319
hydrophobicity, 541, 571, 641, 654, 656 M
Hylleraas, 63, 65, 67, 81, 82, 88, 161, 185
Hynes, 93, 109 magnetic field, 205, 214, 266, 268
map, 112, 193, 245, 246, 425, 426, 427, 428, 430,
447, 448, 449, 450, 451, 452, 454, 455, 457, 459,
I 461, 466, 467, 468, 470, 472, 473, 478, 534, 535,
562, 574, 613, 614, 616, 619
IBMOL, 64, 84 Maxwell theory, 247
672 Index
medial, 427, 448, 449, 450, 461, 462, 463, 464, 465, pi-bonding, 7, 8
466, 470 PLS regression, 482
metabolization power, 577 Poisson integral, 580
methane molecule, 301, 302 polarizability, 114, 356, 541, 561, 572
molecules, ix, x, xi, 1, 19, 61, 62, 64, 65, 68, 70, 73, polarization, 111, 112, 116, 168, 169, 176, 182, 229,
74, 77, 78, 80, 81, 82, 83, 84, 85, 86, 87, 92, 94, 231, 232, 269
110, 111, 112, 113, 141, 148, 149, 157, 158, 159, POLYATOM, 64, 83
163, 174, 180, 182, 188, 192, 195, 203, 217, 218, polyethylene chain, 141, 142, 143, 151
224, 225, 226, 229, 230, 231, 232, 234, 239, 251, polyethylene foil, 141, 142, 154
275, 279, 286, 288, 296, 297, 298, 301, 303, 308, polyhedron, 404, 449
310, 311, 313, 315, 319, 320, 321, 325, 328, 331, potential energy surface, 80, 87, 93, 98, 113, 158,
334, 335, 344, 353, 354, 357, 360, 361, 362, 363, 160
364, 367, 382, 387, 393, 405, 413, 425, 439, 440, Probability, 322, 593, 596, 608, 609, 623
480, 486, 494, 504, 521, 562, 574, 575, 576, 578, probability density function, 544
579, 583, 589, 590, 593, 594, 595, 596, 597, 598, propagator, 576
599, 600, 601, 603, 613, 614, 617, 631, 632, 635, Protein Distance Matrix, 528
636, 639, 641, 643, 649, 651, 654, 656, 660, 661, Protonation, 362, 364, 365
662, 663
Moore-Penrose, 558, 560
Morse oscillator, 91, 97, 99, 100, 102, 107 Q
MPFUN, 82
Mulliken electronegativity, 254, 274 QSAR, 482, 484, 494, 495, 496, 521, 533, 534, 535,
multi-shell, 462, 463, 466, 467 537, 540, 541, 542, 561, 564, 567, 569, 571, 572,
573, 574, 578, 579, 581, 582, 583, 584, 589, 590,
591, 593, 595, 597, 598, 599, 601, 603, 604, 605,
N 612, 613, 614, 618, 619, 621, 624, 625, 626, 627,
628, 629, 630, 631, 632, 633, 634, 635, 643, 644,
nanotube, 387, 399, 409, 410, 411, 412, 413, 415, 652, 657, 658, 659, 660, 662, 663, 664, 665, 666,
417, 419, 420, 421, 440, 512, 513, 517, 518, 519 667, 668
norm, 542, 569, 575, 577 QSPR/QSAR, 482, 494, 517, 537, 585, 664, 666,
normal distribution, 389, 551, 553, 633 667
QSPR-QSAR Theory, 623
QTAIM, 343, 344, 345, 346, 347, 348, 349, 352,
O 353, 359, 360, 362, 364
quadrupling, 427, 452, 477
Omega, 428, 434, 461, 472, 474, 475, 478 quantum chemistry, 1, 74, 192, 270, 327, 328, 333,
operation, 44, 427, 438, 444, 448, 449, 450, 451, 427
452, 453, 454, 455, 457, 458, 459, 460, 461, 462, quantum mechanics, 32, 42, 56, 86, 92, 192, 205,
463, 464, 466, 470, 472, 474, 542, 558, 611 217, 294, 499, 540, 546, 576
operator, 3, 19, 61, 63, 66, 67, 68, 70, 74, 75, 77, 80, quantum phase space diagram, 100
87, 114, 162, 201, 261, 262, 443, 614 quantum rules, 264
orthogonal descriptors, 533, 563, 585 quantum-SAR factor, 576, 577, 578
orthogonality, 542, 548, 561, 579 quantum-SAR transformation, 577
oscillations, 102, 141, 143, 147, 281, 316
oxygen molecule, 309, 310
R
P R12-wave function, 81
Randic M., 82
pair-localization, 6 Ranking, 593
Pauli, 2, 3, 5, 144, 191, 210, 363 reactive biological activity, 253
Pauli matrices, 5 Regression towards the mean effect, 590
Pauli operators, 144 ring, 180, 283, 286, 305, 306, 347, 350, 351, 352,
peapod, 441 354, 355, 356, 357, 358, 359, 362, 375, 398, 400,
Pearson coefficient, 548, 551, 552, 554 401, 404, 405, 418, 433, 437, 438, 440, 442, 461,
Pearson correlation, 547, 548, 552, 556 467, 480, 482, 502, 503, 636
periodic table, 208, 209, 210, 285, 286, 289, 365 Runge-Kutta method, 96
perturbation factor, 263, 264
phonon, 141, 146
Index 673
567, 569, 571, 573, 575, 577, 579, 581, 583, 585,
S 586, 587, 629, 664, 665, 666, 667, 668
Timisoara Theorem, 569
scalar product, 263, 542, 543, 547, 548, 562, 568, topological descriptor, 480, 481, 483, 488, 652, 658,
569 659, 660, 661, 668
Schlfli, 425, 470, 478 topological distance, 481, 629, 644, 647, 648, 651,
Schrdinger, 1, 2, 5, 115, 277, 294, 362, 388, 393 660, 662
second quantization, 149, 265, 266 topology, x, 194, 427, 449, 481, 484, 494, 496, 613,
self-transformation, 577 616, 619, 630, 631, 662
Sensitivity, 495, 599, 600 torus, 427, 428, 429, 430, 431, 432, 433, 438, 439,
septupling, 453, 454, 477 466, 478
sigma-bonding, 7, 8, 13 toxicity, 540, 541, 571, 572, 580, 582, 583, 584, 586,
similarity, 28, 50, 86, 158, 170, 183, 245, 300, 482, 617, 618, 626, 629, 630, 631, 632, 643, 651, 652,
495, 526, 533, 536, 609, 617, 635 653, 654, 655, 656, 657, 658, 659, 660, 661, 662,
skeletons, 480, 483 663
SMILES, 63, 65, 71, 73, 84 truncation, 427, 451, 452, 453, 461, 470
snub, 450 tubercular, 442, 443
solitons, 141, 142, 143, 148, 154
special relativity theory, 217, 246
Specificity, 340, 341, 599, 600 U
spectral mechanistic map, 572
spectral norm, 574 uniform probability, 545, 547, 549, 556
spectral path, 574, 575, 576, 579 Utility, 593, 596
spectral path principle, 575
Spectral Representation of DNA, 524
Spectral-SAR, 539, 541, 542, 543, 545, 547, 549, V
551, 553, 555, 557, 559, 561, 562, 563, 564, 565,
566, 567, 569, 571, 573, 574, 575, 577, 579, 581, vectorial length, 541, 548
583, 585, 587 vectorial space, 542
Spectral-SAR determinant, 564, 574 vertex, 294, 295, 425, 428, 436, 447, 448, 449, 450,
Spin, 19, 198, 201, 375, 381 451, 452, 454, 455, 458, 465, 468, 481, 483, 484,
spin waves, 141 485, 486, 487, 488, 489, 492, 493, 494, 500, 501,
spongy, 469, 473 507, 508, 509, 518, 629, 646, 647, 650, 651, 662,
standard deviation, 546, 550, 551, 553, 617 667
steric effects, 541, 562, 634, 636, 660 vertices, 297, 298, 299, 425, 426, 428, 442, 447, 448,
Stone-Walls, 441 449, 451, 452, 453, 454, 459, 464, 465, 466, 467,
STOP, 63, 65, 74, 77, 78, 79, 80, 84 480, 481, 483, 484, 485, 488, 489, 491, 492, 499,
structural complexity, 479, 480, 493 500, 501, 507, 508, 509, 511, 512, 513, 629, 644,
structure-activity, 495, 521, 533, 539, 540, 541, 556, 645, 646, 647, 650, 651, 659, 662
572, 581, 582, 583, 584, 585, 586, 587, 616, 627, Vibrio fischeri, 573, 585
628
sum of residues, 555
superposition principle, 540, 562 W
symmetry, 2, 77, 78, 79, 98, 99, 102, 114, 165, 173,
194, 200, 201, 214, 273, 277, 288, 290, 298, 349, water molecule, 229, 307, 308, 371, 373
399, 411, 412, 458, 467, 470, 481, 483, 501, 609 wavelength, 52, 192, 195, 196, 197, 199, 203, 206,
207, 246
Wiener index, 494, 499, 500, 517, 518, 519, 644,
T 645
Tanimoto index, 482

tessellation, 427, 430, 433, 436, 439, 451, 452, 461,
472
tetrahedron, 460
Theorem, 35, 38, 39, 451, 452, 454, 491, 586
tiling, 322, 426, 430, 431, 443, 445, 454, 461, 467,
470, 473
Timisoara, xi, 1, 141, 155, 251, 539, 541, 543, 545,
547, 549, 551, 553, 555, 557, 559, 561, 563, 565,

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CHEMISTRY RESEARCH AND APPLICATIONS

QUANTUM FRONTIERS OF ATOMS

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QUANTUM FRONTIERS OF ATOMS

Nova Science Publishers, Inc.

NOTICE TO THE READER

LIBRARY OF CONGRESS CATALOGING-IN-PUBLICATION DATA

Quantum frontiers of atoms and molecules / editor, Mihai V. Putz.

Published by Nova Science Publishers, Inc. New York

Chapter 9 Emergent Properties in Bohmian Chemistry 191

Chapter 10 The Algebraic Chemistry of Molecules and Reactions 217

Chapter 23 Application of the Fuzzy Logic Theory to QSPR-QSAR Studies 607

ATOMS AND MOLECULES AS THE QUANTUM FRONTIERS OF LIFE

FULFILLING DIRACS PROMISE ON QUANTUM

with the free particle and applied potential components:

in terms of bi-dimensional Pauli and unitary matrices (operators)

and employing it to the stationary operatorial equation:

which reduce the above stationary condition (6) to the form

the last form (9) further rearranges as

leaving with the system:

and substituting into the second one, there is obtained:

while the Pauli matrices basic property

3. Quantum Chemical Bond

Employing the dimensional quantum-relativity relationship

< energy > < distance >~ Joule meter ~ = c (16)

recently, there were introduced the chemical binding functions [19]:

covalent binding is characterized by a symmetric higher and thinner well of

3.2. Chemical Bond by Dirac Equation

providing the yield:

the free + potential term:

it is then replaced in the first equation (25a) to obtain:

whose solutions expresses the energy conservation

and the Dirac adapted bonding equation

providing the second accompanied solution

(II) : f B (RAB II , B ) = f Dir

(III) : f A (III , A ) = f Dir

which give the information of precisely localization of pairing of anti-parallel electronic

I = IV = 0.445571 [ RAB ] , (34a)

II = III = 0.554429 [ RAB ] (34b)

bonding function anti bonding function

DUALITY WITHIN THE STRUCTURE

1. Why a Reappraisal Is Necessary

2. The Relevance of the Classical Framework

P: An object occupies a state at some time, if at all (energy states included).

3. On the Two Kinds of Incompatibility

Complementarity is a term suited to embrace the features of individuality of quantum

4. Wholeness and the Proper Logic for Complementarity

5. The Reduction of Duality

AXIOM: If an indivisible thing is successfully predicated, the predication will

It would then follow that alternative predications of an indivisible thing, in being

[28] Mackay, D.M. Complementarity. Proceedings of the Aristotelian Society,

COMPLEMENTARITY OUT OF CONTEXT:

2. Complementarity: A Stumbling Block on the Way to Context

3. The Duality Route to Context

produce information in one frame that is not logically, conceptually, theoretically, or

4. Incommensurability: Last Resortand Last Exit

5. The Concept of Action Quantization

6. Tying Loose Ends

[21] Karakostas V. Nonseparability, Potentiality and the Context-Dependence of Quantum

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