Journal of Molecular Structure (Theochem) 632 (2003) 29–41

www.elsevier.com/locate/theochem

An approximate DFT method for QM/MM simulations

of biological structures and processes
Marcus Elstnera,b, Thomas Frauenheima, Sándor Suhaib,*
a
Theoretische Physik, Universität Paderborn, D-33098 Paderborn, Germany
b
Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
Accepted 3 January 2003

Abstract
In the last years, we have developed a computationally efficient approximation to density functional theory, the so called
self-consistent charge density functional tight-binding scheme (SCC-DFTB). To extend its applicability to biomolecular
structures, this method has been implemented into quantum mechanical/molecular mechanics (QM/MM) and linear scaling
schemes and augmented with an empirical treatment of the dispersion forces. We review here applications of the SCC-DFTB
QM/MM method to proton transfer (PT) reactions in enzymes like liver alcohol dehydrogenase and triosephosphate isomerase.
The computational speed of SCC-DFTB allows not only to compute minimum energy pathways for the PT but also the potential
of mean force. Further applications concern the dynamics of polypeptides in solution and of ligands in their biological
environment. The developments reviewed allowed for the first time realistic QM simulations of polypeptides, a protein and a
DNA dodecamer in the nanosecond time scale.
q 2003 Elsevier B.V. All rights reserved.
Keywords: Density functional theory; Quantum mechanical methods; Molecular mechanics methods; Combined quantum mechanical
molecular methods (QM/MM); SCC-DFTB; Density Functional Tight Binding

1. Introduction computational schemes became available which can

In the last decade, dramatic progress has been
made in the field of quantum chemical modeling of
biophysical processes. Since an appropriate treatment
of the effects of electron correlation is necessary to
achieve an accuracy which allows for a quantitative
description of biochemical reactions, only after their
inclusion within density functional theory (DFT) and
localized correlation methods [1] first principles
* Corresponding author. Tel.: þ 49-6221-422369; fax: þ 49-
6221-422333.
E-mail address: s.suhai@dkfz.de (S. Suhai).
0166-1280/03/$ - see front matter q 2003 Elsevier B.V. All rights reserved.
doi:10.1016/S0166-1280(03)00286-0
be applied to system sizes typical for biological
reaction centers. Quantum mechanical (QM) methods
have the advantage over molecular mechanics (MM)
methods that they include the effects of charge
transfer (CT), polarization, and bond breaking and
forming from the beginning. In addition, QM methods
compute the electronic structure of the molecular
system, which can be used for the derivation of
spectroscopic data (e.g. IR, Raman, NMR).
QM methods further may be of higher accuracy and
do not rely on a labour-intensive parameterization,
which is not always available for a particular system
of interest (e.g. biological ligands). However, all this
30 M. Elstner et al. / Journal of Molecular Structure (Theochem) 632 (2003) 29–41
is reached by an (sometimes extraordinary) increase
in computing time. With the introduction of linear
scaling methods [2 –4], QM treatment on the scale of
proteins and DNA fragments is in reach, but still at a
high cost.
A QM description of the whole system might be
important for the investigation of long range electron
transfer in proteins or DNA. Many other processes
appear, however, to be localized to a part of the
system, i.e. bond breaking and forming occur in
the limited region of the reaction center. Also the
electronic structure of biological molecules often
exhibits a local character, i.e. the density matrix
decays quickly in real space. This means that
spectroscopic properties of relevant parts can be
calculated from a localized region. For a realistic
description, the influence of the environment, whether
protein matrix or solvent, has to be taken into account.
To represent the electrostatic and steric effects of the
environment, MM methods have been coupled to QM
ones leading to combined QM/MM algorithms,
where the QM description of a localized region is
augmented with a MM description of its biological
environment.
Besides the details of this coupling, a shortcoming
in the commonly used algorithms can be seen in the
fact, that mostly MM methods with fixed point
charges are used. An improvement of these schemes
by including polarization may not be using a full QM
description of the system, but polarizable force fields
in the MM regime. In some applications, long range
cooperative effects (e.g. via H-bonded chains) can play
a role. A further computational upgrade may be given
by QM/QM/MM schemes (Section 2), where a
high-level quantum method is combined with a low
level one in a QM/MM algorithm, rather than a full
QM description.
Not only the computer time requirements lead to a
critical view on a full QM description but also the
accuracy of the QM methods. Although not perfect,
decades of development and refinement of empirical
force fields have led to methods, which describe the
static and dynamic properties of proteins and DNA
fragments with relatively good success. The same is
not necessarily true for popular QM methods for
different reasons. First, not all QM methods reproduce
the structures and energetics of the protein backbone
satisfactorily. The widely used semi-empirical AM1
and PM3 methods, for example, have been shown to
predict rather distorted protein secondary structural
elements, thus they cannot reliably describe the
protein backbone [5,6]. Additional problems with
H-bonding have led to the suggestion to use the AM1
method with a small QM region only [7]. A recent
study [8] compared linear scaling PM3 energy
profiles of an enzymatic reaction with those from
PM3 QM/MM calculations. Both methods agree, as
long as not much movement of the entire protein takes
place. They significantly disagree, however, when the
entire protein moves. Although the linear scaling PM3
calculation incorporates polarization of the whole
system, this full QM description may be worse than
the QM/MM, since MM methods can preserve
the protein structures, while this is not the case for
the PM3 method, which, e.g. untwists protein a
helices [5]. Ab initio Hartree Fock (HF) and DFT
methods (utilizing current gradient corrected
exchange correlation functionals) do not contain
long range Van der Waals forces, which are a critical
factor in the stability of protein and DNA structures.
Therefore, geometry optimizations or MD simulations
may not retain the experimentally determined
conformations (an indicative example will be
given below).
In this respect, QM (like DFT and HF) and MM
methods can be viewed as complementary, the former
being able to treat chemical reactions while the
latter can provide the biochemical environment for
these processes.
At first sight, the increase of the speed of
computers, which now allows an ab initio or DFT
treatment of biomolecular reaction centers,
reduces the usefulness of semi-empirical methods.
However, many biomolecular problems of interest
still represent a considerable challenge for the routine
application of DFT or HF due to computer time limits
(also in a QM/MM framework). Typical cases are:
† large systems, containing several hundreds of
atoms, or, in a linear scaling framework, several
thousands of atoms;
† computational problems where many different
molecular structures, sometimes hundreds or
thousands of them have to be investigated;
† extensive molecular dynamics (MD) or Monte
Carlo investigations of (thermo-) dynamical
 M. Elstner et al. / Journal of Molecular Structure (Theochem) 632 (2003) 29–41
properties, e.g. calculations of the potential of
mean force (PMF);
† investigations of the potential energy surface
(PES) with global transition state optimization
methods, which require thousands of energy and
gradient evaluations for a given system.
Here, semi-empirical methods can be of great
value (since they are several orders of magnitude
faster than ab initio and DFT) if they are carefully
tested (and eventually calibrated) before application.
They are described as the ‘middle ground’ in
molecular modeling [11] with respect to their
applicability to special molecular systems and with
respect to their computer time requirements. In this
sense, they are not in competition with ab initio or
DFT methods, but are complementary and will retain
their importance in molecular modeling [12]. They can
be applied to systems computationally too large for
DFT and ab initio, for which empirical force fields
either lack a parameterization (e.g. special ligands),
accuracy or are not designed for (e.g. bond breaking).
The two most popular approaches, AM1 [9] and
PM3 [10], are derived from HF theory by applying
various approximations to the Fock matrix elements
and a minimal, orthogonal valence basis set (partially
extended basis set are available as well, e.g. in the
MNDO/d method). The remaining matrix elements
are then parameterized with respect to empirical data.
In the last years, we have developed an
approximate DFT method, the so called
self-consistent density functional tight-binding
(SCC-DFTB) procedure, which is similar to the
semi-empirical methods in that it uses certain integral
approximations (to DFT instead of HF), applies a
minimal valence basis set (which is non-orthogonal)
and shows a similar computational speed.
However, no empirical data enter the parameteriza-
tion scheme in SCC-DFTB. While semi-empirical
methods go beyond HF by including correlation
through the parameterization, SCC-DFTB includes
them from the beginning by using a gradient corrected
exchange correlation functional. SCC-DFTB can be
seen as an alternative to semi-empirical methods in
the ‘middle ground’ of molecular modeling.
In this review, we first describe the combination of
SCC-DFTB with empirical force fields within
the QM/MM framework, its integration into a linear
31
scaling ðOðNÞÞ method, the augmentation of SCC-
DFTB with empirical dispersion terms and a first
QM/QM implementation. In the following, we review
different applications of the QM/MM SCC-DFTB
method. A first type of applications is proton transfer
reactions, a prototypical field for QM methods, since
bond breaking and forming is involved. As a second
type of chemical processes which requires a QM
description we mention a recent application of
SCC-DFTB to a redox reaction. The third type of
SCC-DFTB applications involves the conformational
dynamics of biological structures. This is the main
field of empirical force field methods and whether QM
methods can be applied successfully in this field,
as mentioned above, is not clear from the beginning.
The backbone and side chain PES have to be
represented with sufficient accuracy by the QM
method and the inclusion of VdW forces is necessary
for a realistic description of proteins and DNA
fragments. Using SCC-DFTB, MD simulations of a
ligand in aqueous solution and in the protein
environment have been realized. The bulk of
SCC-DFTB applications in this area concern,
however, the structure and dynamics of polypeptides
in gas phase and solution, which are discussed in some
detail. Using the methodological developments
described, the first time a QM simulation of a protein
and DNA fragment containing several 100
atoms in aqueous solution over nanosecond time
scales have been performed, which is reviewed as a
last example.
2. SCC-DFTB QM/MM schemes
2.1. DFTB: a short summary
The SCC-DFTB method has been introduced and
described in detail in Ref. [13]. It has been extended,
e.g. to the description of open-shell systems [14] or
excited state properties [15] (for comprehensive
reviews see Refs. [16,17]). SCC-DFTB is derived
from DFT and the underlying approximations can be
characterized as follows:
† The DFT total energy functional is expanded up
to second order in the charge density fluctuations
dn ¼ n 2 n0 around the reference density n0 ;
32 M. Elstner et al. / Journal of Molecular Structure (Theochem) 632 (2003) 29–41
which is constructed as a superposition of neutral
atomic densities na0 :
† The atomic contributions of the density
fluctuations, dna ; are approximated by charge
fluctuations on the atoms a; Dqa ¼ qa 2 q0a ; and
the second derivatives of the functional are
substituted by an analytical function gab :
† A minimal, ‘optimized LCAO’ basis set fm is
introduced to expand the Kohn – Sham orbitals
P Etot ¼ EQM þ EMM þ EQM2MM ;
Ci ¼ m cim fm : The Hamiltonian matrix elements
0
represented in this basis, Hmn ¼, fm lH½n0 lfn .;
are calculated in a two-center approximation.
† The ‘double counting’ terms and the nuclear –
nuclear repulsion contributions are joined into a
single energy contribution Erep ; which only
depends on n0 : Erep is also subjected to a
two-center approximation and then calculated
from DFT for suitable reference molecules.
The resulting energy expression consists of three
parts, as described above:
X
occ X
Etot ¼ cim cin Hmn ½r0  þ Erep ½r0 
i mn
1X
þ Dq Dq g :
2 ab a b ab
Applying the variational principle, one arrives at
approximate Kohn –Sham equations, which have to
be solved self-consistently with respect to the charges
qa : First energy derivatives with respect to nuclear
coordinates are calculated analytically, second
derivatives are calculated using finite differences.
All parameters of the SCC-DFTB method are
calculated from DFT. Due to the approximations
described above, SCC-DFTB is about 3 orders of
magnitude faster than DFT using a medium sized
basis set (i.e. 6-31Gp), but comparable in speed to the
semi-empirical methods (like MNDO, AM1 or PM3).
The parameterization for the atom types O, N, C
and H has been briefly described in Ref. [13] and also
test calculations for organic molecules have been
reported there. For reaction energies, a mean average
error of about 5 kcal/mole has been found,
experimental bond lengths are reproduced within
0.014 Å, bond angles within 28 and vibrational
frequencies between 5 and 7%. A similar accuracy
has been demonstrated for sulfur containing
molecules [18]. Parameters for zinc [19] and other
elements are under way.
2.2. Combination with a molecular mechanics
force fields
In the QM/MM approach [20,21,68], the total
energy is usually written as
ð2Þ
where EQM is the energy of the QM part of the
subsystem represented by the SCC-DFTB energy
(Eq. (1)), EMM is the energy of the MM subsystem
given by the energy function of the empirical force
field.
EQM2MM contains the interaction between the QM
and the MM region and consists of three distinct
contributions:
† Covalent bonding. In case the QM/MM boundary
intersects a covalent bond, the disrupted bond is
modeled by the empirical force field terms and the
QM region has to be saturated. This can be done by
introducing ‘link atoms’ [20,21], ‘pseudo-bonds’
[22] or frontier orbitals [23].
ð1Þ
† The VdW interaction can be modeled by the
interaction terms present in the empirical force
field method, i.e. the VdW parameters as derived
for the MM atoms are assigned to the atoms in the
QM region. This is also done in the SCC-DFTB
QM/MM scheme for the sake of simplicity,
however, it is of course not optimal, as has been
found in MD simulations of peptides in
aqueous solution (see below). Efforts for a
reparameterization are currently under way.
A special parameterization for QM/MM methods
has been accomplished before by various
other groups, e.g. for HF [24], DFT [25] and
semi-empirical methods [26 – 28].
† The Coulomb term is approximated by the
interactions of the point charges between
the subsystems, where the QM charges are given
by the Mulliken derived partial charges Dqa from
SCC-DFTB and the MM charges Qb are given by
the force field parameters. Within the QM region,
the interaction of the point charges Dqa is mediated
by the gab function, which instead of diverging
approaches a final value gaa ¼ Ua for small
 M. Elstner et al. / Journal of Molecular Structure (Theochem) 632 (2003) 29–41
interatomic distances Rab : In principle, gab could
also be utilized for the coulomb interaction of the
QM and MM charges, leading to:
X well known R26 behavior of two separate neutral
coul
EQM2MM ¼ Dqa Qb gab : ð3Þ
ab
While in SCC-DFTB a complicated analytical
form is used, semi-empirical methods often apply
the formula of Klopman and Ohno,
1 pairwise potential energy with a R26
gab ¼ qffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi ; ð4Þ
R2ab þ j £ 0:25ð1=Ua þ 1=Ub Þ2
which has a similar shape (with j ¼ 1:0). For the
QM/MM interaction in semi-empirical theory,
this formula was modified to improve
H-bonding, basically reducing the value of
j £ 0:25ð1=Ua þ 1=Ub Þ2 by either optimizing j to
roughly 0.1 [29], setting it to zero [28], or by
zeroing 1=Ub if b indicates a MM atom [21].
This reduction increases the coulomb interaction,
therefore leading to larger H-bonding energies.
The need for this procedure reflects the fact,
that atomic charges in semi-empirical methods are
usually smaller in magnitude compared to MM
charges or charges derived from ab initio methods.
The same holds for SCC-DFTB and therefore a
1=Rab scaling is used (i.e. j ¼ 0) for the interaction
of the partial charges between the QM and MM
regions. This is further motivated by the very good
description of H-bonded complexes [30].
The SCC-DFTB method has been integrated into
the AMBER [31] program [30], the CHARMM [32]
program [33], the TINKER [34] software [35] and the
Sigma program [36]. In the CHARMM version,
the link-atom approach is used, a pseudo-bond
approach is currently under development.
2.3. Augmentation of DFTB with a dispersion term
QM methods can also be combined with empirical
force field terms without defining distinct spatial
regions for the two methods, e.g. in early studies of
Van der Waals complexes, HF theory has been
augmented with an empirical dispersion interaction
term [37] to compensate for the neglect of correlation.
Although the exact exchange correlation energy in
DFT (Exc ) must also include dispersion, currently
33
available LDA and GGA functionals do not cover the
correlation between distant dipolar density
fluctuations, i.e. they do not reproduce the
(non-overlapping) fragments. Since SCC-DFTB is
derived from DFT, this shortcoming is inherited as
well. In order to apply SCC-DFTB to study DNA
oligomers, we augmented it with an empirical
dispersion term for the description of VdW com-
plexes, i.e. we added to the SCC-DFTB total energy a
ab dependence and
empirical C6ab coefficients, damped for small
distances with an appropriate damping function
f ðRab Þ; where the atomic fragments start to overlap
[38]. The total energy in the SCC-DFTB þ dispersion
(SCC-DFTB –D) method then reads:
X 1X
Etot ¼ cim cin Hmn
0
þ g Dq Dq þ Erep
imn
2 ab ab a b
X C6ab
2 f ðRab Þ : ð5Þ
ab R6ab
Including these additional energy contributions,
the interaction of DNA bases can be described in
good agreement with calculations at the MP2/
6-31G(0.25) level [38]. It has been recently shown
that this ab initio model reproduces the stacking
interaction energies very well, when compared to the
extrapolated basis set limit of MP2 and to CCSD(T)
calculations [39]. This method has been successfully
applied to the interaction of intercalators (ethidium,
ellipticine, daunomycin and DAPI) with DNA base
pairs [40]. SCC-DFTB – D gives stabilization energies
very close to the reference MP2 calculations.
This indicates that the extension for the dispersion
interaction is transferable also to other molecular
systems. As will be shown below, the additional
dispersion interaction is not only important for the
interaction of base pairs but also for the structure and
dynamics of peptides and proteins.
2.4. A linear scaling QM/MM implementation
Although DFTB is about 2 – 3 orders of magnitude
faster then DFT, the limits of modern computers are
met when considering long MD simulation times with
more than several 100 ps and/or large systems
34 M. Elstner et al. / Journal of Molecular Structure (Theochem) 632 (2003) 29–41
containing more than 500 atoms. In principle, there
are three strategies to go beyond these thresholds:
parallelization, linear scaling algorithms and
combination of different methods. All three
approaches have their merits and combinations are
also possible. Which one to choose depends on
the special problem of interest. The computational
cost of SCC-DFTB is determined by the diagonaliza-
tion of the Hamiltonian matrix, which exhibits N 3
(cubic) scaling with increasing system size N
(N stands for the number of atoms/electrons in the
system). Linear scaling ðOðNÞÞ can be achieved by
circumventing the matrix diagonalization in the
solution of the generalized eigenvalue problem.
In the last decade, there have been several proposals
for the realization of an OðNÞ scaling. For a more
detailed discussion of the different approaches see the
reviews of Goedecker [2], Galli [3] and Yang and
Perez-Jorda [4]. Recently, the SCC-DFTB method has
been implemented into one of these schemes,
the linear scaling ‘divide and conquer’ (DAC) method
[35], which has been introduced by Yang a decade ago
[41]. For small systems, DAC – SCC-DFTB is
computationally more expensive than the
conventional diagonalization, it becomes more effi-
cient only at a certain ‘cross-over’ point.
For biological systems like peptides and proteins,
which consist mainly of O, N, C and about 40% H
atoms, this cross-over point is reached for system
sizes of roughly 200 atoms (all atoms described in the
SCC-DFTB minimal basis). As a first benchmark,
we considered the protein crambin, which contains
639 atoms in total. Using conventional diagonaliza-
tion techniques, the evaluation of one step in energy
and gradients takes about 15 min on a DEC alpha EV6
machine, whereas the DAC method needs about 1 min
for the same task. Therefore, a complete geometry
optimization of this molecule can be performed within
several hours of wall clock time. In order to simulate
large molecules like crambin in aqueous solution over
a longer time scale, we combined the OðNÞ algorithm
with the QM/MM methodology, where the crambin
molecule can be treated within QM, and the solvent
water molecules within MM [35]. This allows to
center the protein into a cubic box, surrounded by
about 2400 water molecules. On a DEC alpha
machine, 1 ps of MD trajectory takes about one day
of CPU time. Therefore, a parallel version of
the DAC –QM/MM method was used, where about
10 ps dynamics per day could be achieved using 16
processors of an IBM-SP3 machine. In total,
a simulation for 350 ps has been performed.
2.5. Combination with DFT calculations: successive
refinement and QM/QM/MM methods
Most up to date QM/MM calculations use either
DFT, ab initio or semi-empirical methods for the QM
region, and empirical force fields with fixed point
charges. Refinement of the QM/MM models is
therefore possible on the one hand by introducing
polarizable force fields. On the other hand, QM/QM
combinations have been suggested [42 –44]. For large
reactive centers [43], for which a treatment with ab
initio or DFT is prohibitive, combinations of ab initio/
DFT with semi-empirical methods have been
suggested. Two QM methods can be combined with
and without allowing polarization and CT between the
QM subsystems. The first case has been called a
connection, the latter an extrapolation scheme [45].
Both methods allow for full geometry optimizations at
both QM levels.
For the molecular systems tested and applied to
so far, SCC-DFTB reproduces the structures,
compared to higher level calculations, very well.
This makes it possible to use SCC-DFTB as a
lower level method to calculate geometries,
reaction pathways, etc. and refine the energetics
using single energy evaluations at the determined
geometries with higher level methods, most likely
with DFT. This is a possible and desirable
procedure for QM/MM calculations [33] as well.
If geometries are to be refined at the higher level,
a QM/QM combination is the method of choice.
Extrapolation schemes like the ONIOM method [42]
have the advantage that they avoid the complicated
interaction of the QM subsystems by applying a
simple additive scheme but rely on the lower level
method to properly describe the effects of polarization
and CT. It has been shown that semi-empirical
methods are capable of this task, at least for the
particular molecular systems considered [44].
SCC-DFTB has also been integrated into an
ONIOM like DFT/semi-empirical scheme, showing
that the combination of SCC-DFTB with a DFT
method gives superior results compared to
 M. Elstner et al. / Journal of Molecular Structure (Theochem) 632 (2003) 29–41
the combination of AM1 with DFT [44]. A current
effort is to extend the SCC-DFTB into QM/QM/MM
algorithms.
3. Applications
3.1. Proton transfer reactions
The SCC-DFTB method has been benchmarked for
the description of H-bonded complexes by investi-
gating the structures and energetics of H-bonded
complexes an proton transfer reactions.
The H-bonded compounds considered so far were
chosen to represent typical structural motifes
occurring in biological molecules, starting from the
water and ammonia dimers, studying the interaction
of formic acid, formamide, N-methylamide and an
alanine dipeptide with several water molecules up to
DNA base pair interactions. We have further
investigated strongly H-bonded complexes as, e.g.
the protonated water dimer. For all compounds
investigated so far we found that [30,46,47]
† DFTB reproduces the structures very well, as
compared to ab initio and DFT data. The H-bond
lengths in weak H-bonded complexes are slightly
underestimated by about 0.1– 0.15 Å. This holds
for all H-bonded systems, from the water
dimer over H-bonded DNA base pairs up to the
H-bonding geometry in polypeptides [5].
† The binding energies of weakly bonded complexes
are systematically underestimated by about
1.5 kcal/mole. A typical example is the water
dimer, which has a binding energy of 3.3 kcal/mole
in SCC-DFTB, which underestimates converged
MP2 values by about 1.6 kcal/mole. A similar
deviation is found for all investigated weak
H-bonded complexes. The relative energies
between different conformers (and the respective
structures) are qualitatively correctly described.
Proton transfer barriers have been studied for
several small model systems like malonaldehyde,
protonated water and ammonia dimers, etc.
comparing different DFT functionals and ab initio
methods [48 – 54]. In general, HF overestimates PT
barriers, while DFT underestimates them with
35
respect to high-level CCSD data. Hybrid functionals
like B3LYP give reasonable values, still slightly
underestimating the barrier heights, a general trend
for the PT barriers predicted with different methods
is given by the order: B3LYP , MP2 , MP4 ,
CCSD.
Using SCC-DFTB, O2Hþ 5 has been investigated in
detail [46], finding good agreement of SCC-DFTB
with B3LYP concerning binding energy, geometry
and barrier heights. Meuwly and Karplus studied the
protonated ammonia dimer in great detail [55].
Here, B3LYP and MP2 (6-31G pp ) find an
asymmetric ground state structure, the central proton
being closer to one ammonia, while SCC-DFTB
describes a symmetric structure with the proton in the
center. This deficiency can be related to the use of a
non-hybrid density functional in SCC-DFTB,
for which symmetric structures of the protonated
ammonia dimer have been reported before [49].
Otherwise, the barrier height for the proton
transfer agrees nearly perfectly with the one from
B3LYP/6-31Gpp . However, the barriers in both
DFT methods are underestimated as compared to
MP2/6-31Gpp . Vibrational frequencies evaluated with
SCC-DFTB compare favorably with B3LYP/6-31Gpp
values, discrepancies can be explained by the
differences in the equilibrium structures. For larger
protonated ammonia clusters, the SCC-DFTB ener-
getics and geometries are in good agreement with the
corresponding B3LYP/6-31pp values as well. Cui et al.
performed a more comprehensive evaluation of SCC-
DFTB for Hþ transfer reactions, investigating various
proton transfer steps in triose phosphatase isomerase
(TIM) [33]. SCC-DFTB successfully describes the
energetics of the proton transfer, showing an rms error
of 2– 4 kcal/mole when compared to the B3LYP/6-
31 þ Gpp energies. Furthermore, the proton transfer
energetics in the protein environment with QM/MM
agrees very well where B3LYP energies are calcu-
lated for B3LYP and SCC-DFTB optimized geome-
tries. In summary, SCC-DFTB seems to predict
barrier heights comparable to those of B3LYP,
therefore still underestimating them compared to the
higher level calculations.
The energetics of PT reactions depend not only on
the barrier height, but also on a correct description of
the pKa values of the participating groups, especially
of the proton donor and acceptor. A simple way to
36 M. Elstner et al. / Journal of Molecular Structure (Theochem) 632 (2003) 29–41
evaluate methods in this respect is to compare proton
affinities (PAs) of proton donors and acceptors to
higher theoretical levels like MP2 and CCSD.
The differences in the PAs between the methods
will be retrieved in the potential energy profile of the
reaction, evaluated with the respective method. In the
case of TIM, the methods SCC-DFTB, B3LYP,
MP2 and CCSD (6-311 þ G pp ) agree within
5 kcal/mole as to the difference of the PA of the
proton donor and acceptor [33].
These successful tests encouraged further studies
of proton transfer reactions using QM/MM
schemes: Meuwly and Karplus [55] studied the proton
transfer along ammonia wires. To calculate proton
transfer rates as a function of temperature,
they performed MD simulations with both SCC-
DFTB and B3LYP methods. The solvation of the
proton wire in water was simulated with a QM/MM
method, treating water with MM and the protonated
ammonia cluster with SCC-DFTB. They found that
the presence of water impedes the proton transfer by
increasing the barrier for the proton hops.
Cui and coworkers [56] studied the hydride and
proton transfer in liver alcohol dehydrogenase.
The investigated pathway for the PT proceeds through
a hydrogen-bonded network, consisting of three
individual proton transfer steps. This PT was found
to occur in a concerted fashion, followed by the
hydride transfer. The reaction mechanism has been
studied by computing the adiabatic energy surface for
PT. A difference in the potential energy
profiles generated with SCC-DFTB and B3LYP/
DZP//HF/3-21 þ G has been found. This difference
can be traced back to the values for the PAs of the
proton donor and acceptor evaluated at the respective
theoretical level. While B3LYP/6-311 þ G(d,p)
underestimates the PA-difference by about 6 kcal/
mole with respect to the CCSD/6-311 þ G(d,p),
SCC-DFTB overestimates it by about 10 kcal/mole.
However, the description of the concerted PT is
expected to be qualitatively correct since the
energetics between the intermediates agree very well
between B3LYP and SCC-DFTB. Perturbation anal-
ysis has been used to study the influence of amino acid
residues close to the active site on the reaction and the
effect of mutations were investigated. Tunneling
calculations for the hydride transfer showed no
significant contribution to the transfer rate, but was
found to be important for the kinetic isotope effect.
Finally, the effect of the dynamics of the whole
protein on the hydride transfer was examined, finding
a very small and ‘local’ influence on the catalysis.
A forthcoming study using SCC-
DFTB/CHARMM examines the origin of functional
specificity between the two enzymes TIM and
methylglyoxal synthase (MGS), which have similar
active sites but catalyse different reactions [57].
While MGS eliminates a phosphate group from
DHAP, TIM catalyses the isomerization of dihydroxyl
acetone phosphate (DHAP). The functional specificity
are shown to arise mainly from the difference in
the electrostatic environments of the binding pocket
of DHAP.
Gu and coworkers [58] studied different
protonation states of the active site of B. Cereus
zinc-b-lacamase using SCC-DFTB QM/MM MD
simulations with TINKER. They discuss the
different reaction mechanisms related to the
different protonation states.
Applications to the description of the proton
transfer in bacteriorhodopsin [59] and the proton
uptake in the bacterial reaction center are under way.
3.2. Redox reactions
Formanek et al. [60] developed an approach for
computing redox potentials in enzymes, based on free
energy perturbation calculations in a QM/MM
scheme. The scheme was applied to calculate the
first reduction potential of FAD in cholesterol
oxidase. For these types of calculations, classical
models may not show sufficient accuracy, besides the
effort of parameterization for the special ligands.
DFT calculations, on the other hand, are not feasible
for the perturbation calculations aimed at. For this
application, a total of more than 3.5 ns of MD
trajectories were computed for a QM region
containing more than 30 atoms. Therefore, a fast
approximate or semi-empirical model is the method of
choice. Formanek and coworkers have tested
both AM1 and SCC-DFTB in comparison with
B3LYP/6-31 þ G(d,p) for the energetics of the
relevant redox process of flavin in gas phase, finding
a very good agreement of SCC-DFTB with B3LYP,
while AM1 showed large deviations. SCC-DFTB in
 M. Elstner et al. / Journal of Molecular Structure (Theochem) 632 (2003) 29–41
a QM/MM framework was then chosen to calculate
the first reduction potential of the system.
3.3. Conformational dynamics
3.3.1. Chorismate mutase
A first example of a QM/MM MD with
SCC-DFTB of conformational dynamics is the
study of the conformational transitions in the active
site of chorismate mutase within SCC-DFTB
QM/MM [61]. In a first step, SCC-DFTB was
tested for structures and relative energies for the
substrate in comparison with B3LYP/6-31Gp results.
In a second step, QM/MM MD simulations were
performed treating the chorismate substrate with
SCC-DFTB and the rest of the system (either
aqueous solvent or the enzyme active site) with
MM using the QM/MM implementation in
CHARMM. The QM/MM MD simulations show
that the active site rapidly converts inactive
chorismate conformers into active ones.
3.3.2. Structure and dynamics of polypeptides
and proteins in aqueous solution
3.3.2.1. Description of peptides within SCC-DFTB.
SCC-DFTB has been tested for relative energies,
structures [5,62] and vibrational frequencies [63] of
various secondary structure elements (a-helices,
b-sheets, turn-structures) of alanine and glycine
based polypeptides with up to 8 amino acid residues,
showing that
† SCC-DFTB can reliably describe the relative
energetics of the various conformations, predicting
the same trends as B3LYP/6-31Gp. Comparison
with B3LYP and MP2 (6-31Gp) energetics is,
however, somehow ‘complicated’, since at these
levels the relative energies are contaminated with
the basis set superposition error (BSSE), and DFT
might suffer from an insufficient treatment of
correlation, i.e. the dispersion interaction may be
important already for the energetics of small
peptides. This can be the reason for the deviations
in relative energies between B3LYP and MP2
results [5]. The smaller energy differences between
the conformations found with SCC-DFTB are in
better agreement with higher level treatment than
37
with B3LYP/6-31Gp, since BSSE seems to lead to
an overestimation of energy differences between
conformers. In total, SCC-DFTB provides a
reliable description of relative energies for the
typical conformations of amino acid residues.
Rotational barriers are expected to be somewhat
underestimated, since for small organic molecules
slightly too small barriers are found (unpublished
results).
† The structures agree very well with those evaluated
at the DFT and MP2 (6-31Gp) levels of theory.
All secondary structural motifes are reproduced
with SCC-DFTB and the backbone dihedral angles
are close to the values as predicted by the ab initio
and DFT methods.
† Vibrational frequencies are in satisfactory agree-
ment with B3LYP and MP2 results, showing
slightly larger deviations from the experimental
values (about 6%) than the ab initio and DFT
methods.
3.3.2.2. Influence of dispersion on the stability of
secondary structural motifes in DFT. Investigating
helical structures in polyalanine, aR helical structures
were found to be unstable with respect to geometry
optimization for polyalanines with less than
eight residues at the SCC-DFTB, HF/6-31Gp and
B3LYP/6-31Gp levels of theory [62]. For longer
chains, the aR helix becomes structurally metastable,
the 310 helix being still lower in energy. The latter
forms stable structures also for shorter peptides,
starting with four amino acid residues.
In order to compare relative energies, we have
optimized aR and 310 helical structures by keeping the
backbone dihedral angles fixed at their ideal values.
For all investigated peptide lengths, containing N
alanine residues with N ¼ 1 – 20; we found the 310
helical structure to be more stable than the aR
using B3LYP/6-31Gp and SCC-DFTB [62]. At the
MP2/6-31G p//B3LYP/6-31G p level, however,
the energy difference between 310 and aR in vacuo
stops increasing from N ¼ 3 to 5; and drops signifi-
cantly from N ¼ 5 to 8 (Table 1, see also Ref. [35]).
Only explicit inclusion of Van der Waals interactions
in the SCC-DFTB model reproduces the trend
predicted by MP2. Including dispersion interactions
at the B3LYP/6-31Gp level in the same way as done
with SCC-DFTB yields exactly the same result:
38 M. Elstner et al. / Journal of Molecular Structure (Theochem) 632 (2003) 29–41
Table 1
Energy difference (kcal/mole) between the aR and 310 helices of
Ace-AlaN-Nme for different peptide sizes, containing N alanine
residues
N MP2 HF B3LYP SCC-DFTB SCC-DFTB þ VdW
2 3.5 3.3 3.6 2.9 2.9
3 4.8 5.4 4.9 3.8 3.3
5 5.1 7.6 6.3 5.2 3.3
8 2.6 8.9 6.1 5.9 1.4
the energy difference between 310 and aR drops
significantly from N ¼ 5 to 8 [64].
Using SCC-DFTB – D instead of SCC-DFTB for
optimization of a helical structures yields stable
conformations beginning with peptide lengths of
N ¼ 4: Further, for the optimized structures aR
becomes energetically more stable for peptides with
9 alanine residues and more (unpublished results),
which is in agreement with their appearance in
structural databases for this size.
3.3.2.3. QM/MM simulations of peptides in water.
Aqueous solvation can completely change structures
and relative stabilities of polypeptides. For the
dipeptide model Ace-Ala-Nme we have shown this
in detail by optimizing six conformations with
B3LYP/6-31G p in the presence of four water
molecules, which represent the first solvation shell
[65]. Solvation stabilizes the helical and turn
structures with respect to the extended conformations,
which are more stable in gas phase.
In order to test SCC-DFTB and its QM/MM
implementation, we have taken these 6 solvated
dipeptide structures and reoptimized them with
SCC-DFTB and SCC-DFTB QM/MM, treating the
four water molecules with the empirical force field,
and the solute with the QM method [30].
The structures and the energetic ordering are well
reproduced, when solute and solvent are treated with
SCC-DFTB. However, in the QM/MM approach,
structures are much less accurate and qualitative
differences in the energetic ordering appear: the PII
conformer is no longer the global minimum, the a
helical conformation becomes more stable. This might
have two reasons: the empirical force field used
(TIP3P) might not be adequate to model the water
molecules at the solvent –protein interface (since the
water models are parameterized to reproduce
properties of bulk water), and/or the QM/MM
interactions are not adequately represented.
MD simulations over several nanoseconds have
been performed for Ace-Ala-Nme and Ace-Gly-Nme
in water (with explicit water molecules), using
different force fields and SCC-DFTB within a
QM/MM implementation, treating the peptides
with SCC-DFTB and the solvent with MM [36].
Comparing the distribution of the F and C angles
from the simulations with the distribution in high
resolution structures, QM/MM showed a good
agreement, while discrepancies among the different
force fields and with respect to the crystal data were
reported [36]. However, the QM/MM distribution
does not show the preference for the PII conformation
indicated by the experimental results. This might be
related to the QM/MM interaction, which is governed
by the parameters from the empirical force field.
As discussed above, while SCC-DFTB predicts the PII
conformer to be the one with the lowest energy, using
SCC-DFTB QM/MM it becomes a higher energy
state, which might be the main reason for its low
population in the QM/MM simulation and
a reparameterization of the QM/MM interaction may
improve this point.
Concerning the relative stabilities of aR vs 310
helices, the influence of aqueous solvent significantly
changes the structures and relative stabilities.
Geometry optimizations of the two helix types in
water solution, by treating the solute with SCC-DFTB
and the solvent with MM within a QM/MM scheme
have shown that the a helix is stabilized due to a more
favorable electrostatic interaction between the helix
dipole and the solvent [30] and becomes more stable
than the 310 helix. This has been confirmed by
performing a SCC-DFTB QM/MM MD simulation of
an octa-alanine 310 helix in aqueous solution.
Within 10 ps of a MD simulation, an a helical
conformation was adopted [33]. Here, explicit
inclusion of dispersion is not necessary for the
stability of the a helix, however, the situation in the
protein, where the dielectric constant has a lower
value than in water, is not clear. The MD simulation
of crambin in water discussed below shows how
sensitive the a helical structures are with respect to
 M. Elstner et al. / Journal of Molecular Structure (Theochem) 632 (2003) 29–41
the interplay of solvation effects and proper inclusion
of dispersion forces.
3.3.2.4. Linear scaling QM/MM simulations of
crambin in water. The linear scaling QM/MM
simulations on crambin in water, as described
above, showed the following [35]:
† Using the SCC-DFTB without empirical
dispersion as the QM method the protein structure
is not stable. Both a helices in crambin transform
into 310 helices within about 40 ps. A stable protein
structure, i.e. stable a helices in the protein, was
only retained by including dispersion forces,
i.e. using the SCC-DFTB – D approach. In
combination with the results for the helices in gas
phase discussed above, we conclude that, in
general, neither HF, nor DFT is able to reliably
describe polypeptide or protein structures,
unless weak VdW interactions are included.
† The geometrical details of the protein were better
reproduced with the QM/MM method than with
any of the MM force fields applied in this study.
† During the dynamics, the atomic charges show
significant instantaneous fluctuations.
† A significant CT between the N- and C-termini was
observed. While the charge fluctuations are not
included in the standard fixed point charge models,
the latter CT would not be included even in novel
polarizable force fields.
3.3.3. Linear scaling QM/MM simulations using SCC-
DFTB –D of a DNA dodecamer in water solution
The VdW contributions are essential for the
stacking interaction of DNA bases and they are
inadequately represented by the semi-empirical AM1
and PM3 methods, HF theory, current density
functionals [67] and SCC-DFTB. Hence, it is not
surprising that fragments of DNA are structurally
unstable at the AM1 and PM3 level or when computed
with SCC-DFTB (unpublished results). At the
SCC-DFTB –D level, the interaction of base pairs
can be described very well, and this led us to perform
a MD simulation of a DNA dodecamer in aqueous
solution with a similar setup to the one for crambin.
The DNA dodecamer was treated with linear scaling
SCC-DFTB –D and the water with MM. During the
350 ps MD, the double helical DNA structure was
39
well reproduced, showing a RMS deviation from the
crystal structure comparable to pure MM results [66].
This is the first large scale simulation of DNA using a
QM method and opens the way for further QM
studies, e.g. of the interaction of DNA with chemical
agents or intercalators.
4. Discussion and conclusion
We have presented methodological developments
of an approximate DFT method (SCC-DFTB) for the
treatment of biological structures and processes.
A conceptually simple QM/MM scheme based on
the interaction of partial charges between the QM and
MM region has been introduced. This scheme was
further extended for a linear scaling ðOðNÞÞ treatment
of the QM region and a mixed QM/QM algorithm
based on the ONIOM methodology.
SCC-DFTB has been augmented with an empirical
treatment of dispersion forces (SCC-DFTB – D),
which can be viewed as a QM – MM combination as
well. This extension is necessary to describe the
interaction of base pairs in DNA using DFT
(with current gradient corrected functionals) or
SCC-DFTB and it is therefore the basis for further
studies of DNA or DNA-intercalator interactions
within DFT.
The efficiency of SCC-DFTB allows applications,
which are computationally too demanding for DFT or
HF methods on the one hand and are, on the other
hand, beyond the applicability of empirical force field
methods, since they involve chemical processes like
bond breaking and forming.
SCC-DFTB has been applied to PT reactions in
various systems. Although HF and DFT methods
could cope with those QM regions containing less
than 100 atoms, the methods utilized in combination
with SCC-DFTB for finding transition states and
minimum energy pathways as well as the MD
simulations and PMF calculations are very time
consuming and imply a limit for the application of
HF and DFT. To assess the accuracy of DFT and
SCC-DFTB in this context, their PT barrier heights for
small model systems can be compared with those
from higher level methods like MP2, MP4 and CCSD.
These comparisons can be found in the literature and
indicate that barriers are slightly underestimated by
40 M. Elstner et al. / Journal of Molecular Structure (Theochem) 632 (2003) 29–41
B3LYP. SCC-DFTB finds PT barriers, which are
close to those from B3LYP, being therefore
underestimated with respect to more accurate methods
as well. A further test consists of comparing the gas
phase PAs of proton donor, acceptor and other
participating groups in the PT pathway from DFT
and SCC-DFTB with higher level calculations.
The deviations of gas phase values will be found
again in the QM/MM energetics for the reaction in the
protein environment.
Another area of application for SCC-DFTB is the
QM/MM MD simulation of ligands in their biological
environment, as discussed for two examples. Fast QM
methods are of interest here, since their application
circumvents the tedious parameterization for the
molecules of interest and may show a better accuracy
while only slightly increasing the computational cost.
The QM/MM calculations using SCC-DFTB for a
QM region with around 30 atoms and a MM region
with several 1000 atoms slows down the calculations
by a factor of 2 – 5, when compared to a MM
simulation of the entire system.
The energetics, structures and dynamics of alanine
based peptides in gas phase and solution have been
investigated using SCC-DFTB with and without the
QM/MM framework. While structures are reproduced
with good accuracy, relative stabilities of the compact
vs the more extended structures differ between the
DFT and MP2 methods. This is a first hint that static
correlation as included at the MP2 level is important
for theses systems. The qualitatively wrong
description of relative stabilities within DFT becomes
crucial, when only small barriers separate two
conformations, as in the case of 310 and aR.
Here, the inclusion of dispersion changes the relative
stabilities significantly and QM/MM MD simulations
of crambin using SCC-DFTB and SCC-DFTB –D
showed drastic consequences. The neglect of
dispersion leads to a transition of the two helices in
crambin from a into 310 conformations, i.e. a
significant quantitative and qualitative deviation
from the crystal structure. Gas phase calculations on
the relative stabilities of the two helix types indicate
that using HF or DFT instead of SCC-DFTB would
lead to the same problem. Therefore, QM simulations
of polypeptides and proteins using DFT (or HF)
methods should be performed with some care, unless a
proper inclusion of dispersion forces is assured, either
empirically or by developing density functionals
which take them explicitly into account.
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