DFT Studies of Small Organic Molecules

A Thesis
submitted to the University of Lucknow
For the Degree of

Doctor of Philosophy
in Physics
by

Hriday Narayan Mishra

Under the Supervision
of

Prof. Onkar Prasad

Department of Physics
University of Lucknow
Lucknow – 226007, (U.P.)
INDIA
(2013)
 Dedicated
to
MOM, DAD
&
BADI AMMA
 CERTIFICATE

This is to certify that all the regulations necessary for the submission of

Ph.D. thesis “DFT Studies Of Small Organic Molecules” by Hriday

Narayan Mishra have been fully observed.

(Prof. Onkar Prasad) (Prof. K. Sinha)

Professor Professor & Head
Department of Physics Department of Physics
University of Lucknow University of Lucknow
Lucknow – 226007 Lucknow- 226007
 CERTIFICATE

This is to certify that the work contained in this thesis entiled “DFT

STUDIES OF SMALL ORGANIC MOLECULES” by Hriday Narayan

Mishra has been carried out under my supervision and the contents of this

thesis are original and have not been presented anywhere else for the

award of a Ph.D. degree.

(Prof Onkar Prasad)

Professor
Department of Physics
University of Lucknow
Lucknow - 226007
 Words of Gratitude

At the very outset I find it difficult to appositely express my deepest sense of

gratitude to Almighty God for His immense grace to enable me to complete my Ph. D
thesis work within time. It is a dream come true on my part.
With a profound reverence, it gives me immense pleasure to express my deep
sense of gratitude and high regard to my honoured supervisor Prof. Onkar Prasad, for
his considerate guidance and constructive criticism. Without his guidance, sound
counseling and sympathetic attitude towards all my shortcomings, this work would
not have seen the light of day.
I am indebted beyond words to acknowledge my heartfelt gratification at the
completion of this momentous task to Dr. Leena Sinha, Associate Professor
Department of Physics University of Lucknow, for her invaluable guidance, precious
ideas, suggestions and continuous support during my present research activities.
My gratitude is also expressed to Prof. Kirti Sinha, Head of Department,
Department of Physics, University of Lucknow for her kind support.
I would like to convey my special thanks to my lab mates Dr. Jitendra Pathak, Mr.
Amrendra Kumar, Mr. Naveen Saxena and Mr. Rajesh Shrivastava, for their
constant help during aforesaid work. I find myself unable to thank them for their
helping hand and for the wonderful and cheerful times spent together. I am
extremely grateful to them. I also express my profound thanks to all my other lab
colleagues; Mr. Satish Chand, Mr. Alok Kumar Sachan, Mr. Vikas Shukla, Mr. S. K.
Pathak, for their help and co-operation throughout the course of study.
I am also thankful to my friends Dr. Anoop Kumar Pandey, Dr. Raj Kumar Singh
Yadav, Mr. Ranjani Ranjan, Mr. V. Anmol and Mr. Avaneesh Mishra for their
lovely and joyful company and cooperation throughout my research work.
I would never have managed to withstand odd circumstances without the support of
my family and my good friends. I would like to show my gratitude to my wonderful
parents, elder brother and bhabhi ji; Shri. R. N. Mishra & Smt. Anjali Mishra who
always encouraged me to go on with my studies and showed to me how to become a
better person. Also, personal thanks to my sister and jija ji; Smt. Kumud Mishra &
Dr. Susheel Mishra and my Younger brother Mr. V. N. Mishra, without his help and
support I couldn’t have complete my work. Finally I would express my gratitude to
my wife Mrs. Nisha Mishra and my lovely children Sanjivani & Shivansh for their
incessant support.

(Hriday Narayan Mishra)

 LIST OF PUBLISHED / COMMUNICATED PAPERS

1. Structural and spectroscopic characterization of Novel potential

chemotherapeutic agent 3-(1-adamentyl)-1-{[4-(2-methoxy phenyl)
piperazin-1-yl] methyl}-4-methyl-1H-1,2,4-Triazole-5(4H)-thione by
first principal calculations, Journal of Molecular Structure
(Elsevier), Vol. 1022, 49-60, (2012).

2. Electronic structure, electric moments and vibrational analysis of 5-

nitro 2- furaldehyde semicarbazone: A D.F.T. study. Computational
and Theoretical Chemistry (Elsevier). Vol. 973, 20-27, 2011.

3. Study of electrostatic potential surface and molecular orbitals of O4

Nano-Cluster by first principles, Der Pharma Chemica, Vol. 1(2),
79-85, 2009.

4. Quantum Chemical study of Molecular structure, Non Linear Optical

and Vibrational Properties of ortho and meta - Fluorobenzaldehyde.
Journal of Chemical and Pharmaceutical Research, Vol.3, Issue 5,
2011.

5. Electronic structure, non-linear properties and vibrational analysis of

ortho, meta and para -Hydroxybenzaldehyde by density functional
theory. Research Journal of Recent Sciences Vol 2 (ISC-2012) 150-
157 (2013).

6. Quantum-chemical (DFT, MP2) and spectroscopic studies of

monomeric and dimeric structures of 2(3H)-Benzothiazolone –
Communicated to Spectrochimica Acta Part A: Molecular and
Biomolecular Spectroscopy
 TABLE OF CONTENTS

Page Number
Chapter 1: Introduction 1-25
1.1 Introduction
1.2 Prime Methods of study of Electronic Structure
1.3 Vibrational Analysis
1.3.1 Infrared-Spectroscopy
1.3.2 Raman Spectroscopy
References

Chapter 2: Theory 26-64

2.1 The Schrodinger equation and its solutions

2.2 Alternative approach to solve Schrodinger equation
2.3 The Hohenburg Kohn Theorems
2.3.1 The Energy Functional
2.3.2 The Local Density Approximation for Exc[ρ]
2.3.3 Generlized gradient Approximation
2.3.4 Hybrid model
2.3.5 Advantages
2.3.6 Disadvantages
2.4 Application of Quantum Chemical Methods
2.4.1 Geometry Optimization
2.4.2 Frequency Calculations
2.4.3 Calculation of dipole moment and Polarizability
2.5 Calculation of UV Spectra
2.6 Graphical user interface for Gaussion09-Gauss View
References

Chapter 3: Electronic structure, electric moments 65-93

and vibrational analysis of 5-nitro 2- furaldehyde
semicarbazone: A DFT STUDY

3.1 Introduction
3.2 Experimental: Structure and Spectra
3.3 Results and Discussion
3.3.1 Molecular Geometry
3.3.2 Electronic Properties
3.3.2.1 Electric Moments
3.3.3 Vibrational Analysis
3.3.3.1 Nitro group vibration
3.3.3.2 Furan group vibration
3.3.3.3 Amide group vibrations
3.3.3.4 C-N and C=N vibrations
3.3.3.5 N-N and C-C vibrations
3.3.3.6 NH2 vibrations
3.3.3.7 UV-VIS spectra
3.4 Conclusions
References

Chapter 4: Electronic structure, Non-linear properties 94-110

and Vibrational analysis of ortho, meta
and para –Hydroxybenzaldehyde
by Density Functional Theory

4.1 Introduction
4.2 Structure and Spectra
4.3 Results and Discussion
4.3.1 Molecular Geometry Optimization and energies
4.3.2 Electronic Properties
4.3.3 Eletric Moments
4.3.4 Vibrational Assignement
4.3.4.1 C-O and C=O vibrations
4.3.4.2 OH vibrations
4.3.4.3 Ring Modes
4.4 Conclusions
References

Chapter 5: Quantum-chemical (DFT, MP2) and 111-133

spectroscopic studies of monomeric and
dimeric structures of 2(3H)-Benzothiazolone

5.1 Introduction
5.2 Experimental
5.3 Result and Discussion
5.3.1 Molecular Geometry
5.3.2 UV-VIS Studies and Electronic Properties
5.3.3 Electric Moments
5.3.4 Vibrational Analysis
5.3.4.1 Phenyl Ring Vibration
5.3.4.2 N-H group Vibration
5.3.4.3 C=O group Vibration
5.3.4.4 C-S Streching Vibration
5.3.5 Atomic Charge
5.4 Conclusions
References

Chapter 6: Conclusions 134-140

1.1 Introduction
Quantum chemistry is a branch of chemistry whose principal effort is to use

the quantum mechanics in physical models and experiments of chemical

systems. Quantum Chemical methods propose powerful implements for the

computation of countless properties of molecules such as ground state

geometry, reaction mechanism, thermodynamics, infrared, raman, UV and

NMR spectra [Fig. 1.1(a)-1.1(e)][1-10]. Quantum chemists normally use

mathematical methods executed by computer programs to determine the

energies and structures of molecules. These programs employ a wide variety

of methods to approximate wave functions, which are the solutions to

complex wave equations. The molecular wave function, contains

information about all the electrons, spatial as well as spin coordinates. The

wave function is calculated by solving the wave equations central to

quantum chemistry—the non-relativistic Schrödinger equation. Nearly all of

these methods start from effective one-electron models in which electrons

move independently (Hartree Fock method) [11], experiencing only an

average potential due to the influence of other electrons, nuclei, and external

fields. These one-electron wave functions are termed atomic orbitals, and

since molecules are comprised of atoms, a very effective technique has been

to expand the molecular orbitals in terms of atom-centered atomic orbitals.

1
Undeniably, this linear combination of atomic orbitals (LCAO) method [12]

has been responsible for many of the achievements of the first fifty years of

quantum chemistry. The ab initio methods for approaching electronic

structure can be classified into two classes. The first class includes

wavefunction-based methods, namely post-Hartree Fock schemes in the

framework of Configuration Interaction or Coupled Cluster schemes which

can be used for molecules containing up to a few ten atoms (for single

geometry calculations) and are likely to provide precise results whenever

applicable. The second class of methods is that of density-based methods

(DFT) which cover systems between a few tens up to a few hundreds of

atoms. It is often of wide-ranging applicability and reasonably accurate in

many cases. The 1998 noble prize in chemistry recognized the convergence

of traditional quantum chemical methodology and DFT. The recipient were

John Pople, a pioneer in the development of quantum chemical techniques

embodies in the Gaussian electronic structure codes, and Walter Kohn, one

of the founders of DFT.

1.2 Prime Methods for the Study of Electronic Structure

There are three main approaches to calculate molecular properties - ab

initio methods [13-14], Semi empirical method [15], and molecular

mechanics method [16-17]. Schrödinger equation is the equation at the root

2
Fig. 1.1(a). Application of Quantum chemistry : Unit cell structure along

with optimized molecular structure of C25H35N5OS from density

functionaltheory[7].

3
Fig. 1.1(b). Application of Quantum chemistry : Transition state

structure along with reactants and Products

4
Fig. 1.1(c ) Application of Quantum chemistry : Experimental FTIR and

theoretical IR spectra of Acenaphthenequinone [8].

5
Fig. 1.1 (d). Application of Quantum chemistry : Experimental and

simulated UV absorption spectra of 4-chloro-3,5- dinitrobenzoic acid

(CDNBA) [9].

6
 Most negative potential

Most positive potential

Fig. 1.1 (e). Application of Quantum chemistry : Plots of HOMO, LOMO

and MESP of 3-Benzoyl-5-chlorouracil [10]

7
of all Quantum chemical models. It treats molecules as collections of nuclei

and electrons, without any reference whatsoever to chemical bonds. The

solution to the Schrödinger equation is in terms of the motions of electrons,

which in turn leads directly to molecular structure and energy among other

observables, as well as to information about bonding. However, the

Schrödinger equation cannot actually be solved for any but a one-electron

system (the hydrogen atom), and approximations need to be made. Quantum

chemical models differ in the nature of these approximations, and span a

wide range, both in terms of their ability, consistency and their ―cost‖. The

first approximation made in treating the quantum mechanics of a set of

electrons interacting with a set of nuclei is to ―separate‖ the electronic

motion from the nuclear motion. This was a very good approximation

because the electrons are much lighter than the nuclei and nearly ―instantly‖

adjust their motion to a change in the position of the nuclei. We can then

write an expression for the electronic energy of the electrons in the fixed

electrostatic field of the nuclei:

Ee(R) = Ekin + Eelec–nuc + Eelec–elec . (1.1)

The energy Ee(R) is written as a function of the fixed nuclear coordinates R,

8
where R = (R1, R2, …, RN) represents the coordinates of all the nuclei in the

molecule. The succeeding terms in Eq. (1.1) represent the kinetic energy of

the electrons, the attractive interaction between the electrons and the nuclei,

and the electron-electron repulsion energy. It is interesting to note that the

decoupling of the electronic motion from the nuclear motion is known as the

Born-Oppenheimer approximation. It was first introduced by J. Robert

Oppenheimer and Max Born, the German physicist and Oppenheimer’s

postdoctoral advisor. A further obstacle was due the last term of eq. (1.1)

electron-electron repulsion. Without this term it would be possible to use the

method of separation of variables to solve the Schrödinger equation

independently for each electron, but this is not possible when the term is

taken into consideration. The standard approximation, developed by Hartree

and Fock, to avoid this problem is to assume that each electron moves in the

average field due to the nuclei and the other electrons. The original Hartree

method expresses the total wavefunction of the system as a product of one-

electron orbitals. In the Hartree-Fock method, the wavefunction is an

antisymmetrized determinantal product of one-electron orbitals (the "Slater"

determinant). Schrodinger's equation is transformed into a set of Hartree-

Fock equations. The Hartree-Fock approximation is also known at the self-

consistent field (SCF) method which begins with a set of approximate

9
orbitals for all the electrons in the system. One electron is selected, and the

potential in which it moves is calculated by freezing the distribution of all

the other electrons and treating their averaged distribution as the

centrosymmetric source of potential. The Schrodinger equation is solved for

this potential, which gives a new orbital for it. This procedure is repeated for

all the other electrons in the system, using the electrons in the frozen orbitals

as the source of the potential. At the end of one cycle, there are new orbitals

from the original set. The process is repeated until there is little or no change

in the orbitals. The square of the AO gives the probability density. The

orbital is a mathematical expression, describing the probability of finding an

electron at some point near the nucleus. Generally, MOs are expressed as

linear combinations of atomic orbitals (LCAO), the sum of atomic orbitals

centered on each nucleus. Because of the central field approximation, the

energies from HF calculations are always greater than the exact energy and

tend to a limiting value called the Hartree-Fock limit as the basis set is

improved. Within HF theory the probability of finding an electron at some

location around an atom is determined by the distance from the nucleus but

not the distance to the other electrons. This is not physically true, but it is the

consequence of the central field approximation, which defines the HF

method. A number of types of calculations begin with a HF calculation and

10
then correct for correlation. Some of these methods are Moller-Plesset

perturbation theory (MPn, where n is the order of correction), the

generalized valence bond (GVB) method, multi-configurational self-

consistent field (MCSCF), configuration interaction (CI), and coupled

cluster theory (CC) and Density Functional theory (DFT). As a group, these

methods are referred to as correlated calculations. Correlation is important

for many different reasons. Including correlation generally improves the

accuracy of computed energies and molecular geometries.

Density functional theory (DFT) has become very popular in recent years.

This is justified based on the pragmatic observation that it is less

computationally intensive than other methods with similar accuracy. The

premise behind DFT is that the energy of a molecule can be determined from

the electron density instead of a wave function. This theory originated with a

theorem by Hoenberg and Kohn that stated this was possible. The original

theorem applied only to finding the ground-state electronic energy of a

molecule. A practical application of this theory was developed by Kohn and

Sham who formulated a method similar in structure to the Hartree-Fock

method. In general, ab initio calculations give very good qualitative results

and can yield increasingly accurate quantitative results as the molecules in

question become smaller. The advantage of ab initio methods is that they

11
eventually converge to the exact solution once all the approximations are

made sufficiently small in magnitude.

Semiempirical calculations are set up with the same general structure as a

HF calculation in that they have a Hamiltonian and a wave function. Within

this framework, certain pieces of information are approximated or

completely omitted. Usually, the core electrons are not included in the

calculation and only a minimal basis set is used. Also, some of the two-

electron integrals are omitted. In order to correct for the errors introduced by

omitting part of the calculation, the method is parameterized. Parameters to

estimate the omitted values are obtained by getting the results to

experimental data or ab initio calculations. Often, these parameters replace

some of the integrals that are excluded. The advantage of semiempirical

calculations is that they are much faster than ab initio calculations. The

disadvantage of semiempirical calculations is that the results can be erratic

and fewer properties can be predicted reliably.

1.3 Vibrational analysis:

The vibrational states of a molecule are observed experimentally via infrared

and Raman spectroscopy. These techniques can help to determine molecular

structure and environment, intra molecular and inter molecular forces,

computation of degree of association in condensed phases, elucidation of

12
 Prime Quantum Chemical Methods

Wavefunction based Density based methods

methods

HF Method
 simplest ab-initio calculation Density Functional Theory
 electron correlation is not taken (DFT)
into consideration  System is described via its
density and not via its many-
body wavefunction
Moller-Plesset Perturbation Theory
 Improves on the Hartree-Fock method
 Electron correlation effects added
 Use of Rayleigh-Schrodinger perturbation
theory

Configuration Interaction (CI)

 Uses a variational wavewunction that
is a linear combination of
configuration state functions built
from spin orbitals

Figure 1.2: Different types of ab-initio methods and their basic

characteristics

13
molecular symmetries, identification and characterization of new molecules,

deducing thermo dynamical properties of molecular system, etc. [18-21]. A

brief description of these two experimental techniques is presented below -

1.3.1 Infrared- spectroscopy

Infrared (IR) spectroscopy is one of the most common spectroscopic

techniques used by organic and inorganic chemists. It is basically the

absorption measurement of different IR frequencies by a sample positioned

in the path of an IR beam. The main goal of IR spectroscopic analysis is to

determine the chemical functional groups in the sample. Different functional

groups absorb characteristic frequencies of IR radiation. Using various

sampling accessories, IR spectrometers can accept a wide range of sample

types such as gases, liquids, and solids. Thus, IR spectroscopy is an

important and popular tool for structural elucidation and compound

identification. Infrared spectroscopy directly measures the natural

vibrational frequencies of the atomic bonds in molecules. These frequencies

depend on all the parameters that constitute the structure of the molecule

such as the masses of the atoms involved in the vibrational motion (i.e. on

their elemental and isotopic density), the strengths of the bonds, and the

resting bond lengths and angles . For this reason, infrared spectroscopy is

a powerful technique for the identification, quantification and structural

14
analysis of small molecules, and has been established for many decades as

an indispensible tool in organic chemistry, polymer chemistry,

pharmaceuticals, forensic science, and many other areas. IR spectroscopy is

a measurement of the wavelength and intensity of the absorption of mid

infrared light by a sample. Mid-infrared light (2.5 - 50 cm-1, 4000 - 200 cm-
1
) is energetic enough to excite molecular vibrations to higher energy levels.

Each atom has three degrees of freedom, corresponding to motions along

any of the three cartesian coordinate axes (x, y, z). A polyatomic molecule

having n atoms, has 3n total degrees of freedom. However, 3 degrees of

freedom are required to describe translation, the motion of the entire

molecule through space. Additionally, 3 degrees of freedom correspond to

rotation of the entire molecule. Therefore, the remaining 3n – 6 degrees of

freedom are true, fundamental vibrations for nonlinear molecules. Linear

molecules possess 3n – 5 fundamental vibrational modes because only 2

degrees of freedom are sufficient to describe rotation. Among the 3n – 6 or

3n – 5 fundamental vibrations (also known as normal modes of vibration),

those that produce a net change in the dipole moment may result in an IR

activity and those that give polarizability changes may give rise to Raman

activity. Naturally, some vibrations can be both IR- and Raman-active. The

total number of observed absorption bands is generally different from the

15
 Figure 1.2: A Typical FT-IR spectrometer

(Courtesy: Ernest Orlando Lawrence Berkeley National Laboratory)

16
total number of fundamental vibrations. It is reduced because some modes

are not IR active and a single frequency can cause more than one mode of

motion to occur. Conversely, additional bands are generated by the

appearance of overtones (integral multiples of the fundamental absorption

frequencies), combinations of fundamental frequencies, differences of

fundamental frequencies, coupling interactions of two fundamental

absorption frequencies, and coupling interactions between fundamental

vibrations and overtones or combination bands (Fermi resonance). The

intensities of overtone, combination, and difference bands are less than those

of the fundamental bands [20]. The combination and blending of all the

factors thus create a unique IR spectrum for each compound. The major

types of molecular vibrations are stretching and bending. Infrared radiation

is absorbed and the associated energy is converted into motions like bond

stretching, bending, torsion, wagging etc.. The absorption involves discrete,

quantized energy levels. However, the individual vibrational motion is

usually accompanied by other rotational motions. These combinations lead

to the absorption bands, not the discrete lines, commonly observed in the

mid IR region. IR radiation does not have enough energy to induce

electronic transitions as seen with UV and visible light. Absorption of IR is

restricted to excite vibrational and rotational states of a molecule. Even

17
though the total charge on a molecule is zero, the nature of chemical bonds

is such that the positive and negative charges do not necessarily overlap in

this case. Such molecules are said to be polar because they possess a

permanent dipole moment. For a molecule to absorb IR, the vibrations or

rotations within a molecule must cause a net change in the dipole moment of

the molecule. The alternating electrical field of the radiation interacts with

fluctuations in the dipole moment of the molecule. If the frequency of the

radiation matches the vibrational frequency of the molecule then radiation

will be absorbed, causing a change in the amplitude of molecular vibration.

The result of IR absorption is heating of the matter since it increases

molecular vibrational energy. Molecular vibrations give rise to absorption

bands throughout most of the IR region of the spectrum.

Fourier Transform Infrared (FT-IR) spectrometry was developed in order to

overcome the limitations encountered with dispersive instruments. The main

difficulty was the slow scanning process. A method for measuring all of the

infrared frequencies simultaneously, rather than individually, was needed.

The solution resulted in the development of FT-IR spectrometer. It produces

a unique type of signal which has all of the infrared frequencies ―encoded‖

into it. The signal can be measured very quickly, usually of the order of one

second or so. Thus, the time element per sample is reduced to a matter of a

18
few seconds rather than several minutes. Fourier-transform infrared (FTIR)

spectroscopy is based on the idea of the interference of radiation between

two beams to yield an interferogram. The latter is a signal produced as a

function of the change of path length between the two beams. The two

domains of distance and frequency are inter-convertible by The

mathematical method of Fourier-transformation [22-23]. The basic

components of an FTIR spectrometer are shown schematically in Fig 1.3.

The radiation emerging from the source is passed through an interferometer

to the sample before reaching a detector. Upon amplification of the signal,

in which high-frequency contributions have been eliminated by a filter, the

data are converted to digital form by an analog-to-digital converter and

transferred to the computer for Fourier-transformation .

1.3.2 Raman spectroscopy

Raman spectroscopy is a spectroscopic technique rooted in the inelastic

scattering of monochromatic light, generally from a laser source (Fig 1.4).

In 1928 C V Raman discovered Raman Scattering (or the Raman effect) and

won the Nobel prize for his work. If the substance being studied is

illuminated by monochromatic light, for example from a laser, the spectrum

of the scattered light consists of a strong line (the exciting line) of the same

frequency as the incident illumination together with weaker lines on either

19
side shifted from the strong line by wavenumbers ranging from a few to

about 3500 cm-1. The lines of frequency less than the exciting lines are

called Stokes lines, the others anti-Stokes lines. Inelastic scattering implies

that the frequency of photons in monochromatic light changes upon

interaction with a sample. Photons of the laser light are absorbed by the

sample and then reemitted. Frequency of the reemitted photons is either

shifted up or down in comparison with original monochromatic frequency,

which is called the Raman effect. The difference in frequency/energy is

made up by change in the rotational and vibrational energy of the molecule

and gives information on its energy levels. The Raman effect is based on

molecular deformations in electric field E determined by molecular

polarizabilities α. Raman spectroscopy can be used to study solid, liquid and

gaseous samples. By combination of Raman and IR a lot of information

about symmetry and asymmetry of molecule nature of bond can be found.

Raman spectroscopy is very important practical tool for quickly identifying

molecules and minerals [24]. The mechanism of Raman scattering is

different from that of infrared absorption, and Raman and IR spectra provide

complementary information. Typical applications are in structure

determination, multicomponent qualitative analysis, and quantitative

analysis. Raman spectroscopy can also provide exquisite structural insights

20
Figure 1.3 – The Raman spectrometer, which is linked by a dual fiber optic

cable to the sample holder (bottom right), and the sample bottles (left).

[Courtesy Choon Kiat Sim (Fall, 2005) for the picture]

21
into small molecule because it involves an intimate interplay between atomic

positions, electron distribution and intermolecular forces. The FT-Raman

spectroscopy has made possible the study of materials that was previously

impossible because of fluorescence [24].

The work presented in the thesis deals with the investigation of molecular,

structural, vibrational and energetic data analysis of 5-nitro-2-furaldehyde-

semicarbazone (NFZ), ortho, Para and meta- Hydroxybenzaldehyde and

2(3H)-Benzothiazolone which are biologically and pharmaceutically

important molecules, using Quantum Chemical methods. The structure and

the ground state properties of the molecules under investigation has been

analyzed employing Density functional theory (DFT). In order to obtain a

complete description of molecular dynamics, vibrational frequency

calculations have been carried out at the DFT level. The vibrational analysis

also yields the detailed information about the intramolecular vibrations in

the molecular fingerprint region. The reported geometries, molecular

properties such as equilibrium energy, dipole moment and vibrational

frequencies along with the electrostatic potential maps, have also been used

to understand the activity of the molecules.

22
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19. A.J. Misquitta , K. Szalewicz J. Chem. Phys. Vol. 122,(21) 2005.

20. F. A. Gianturco, F. Paesani, M. F. Laranjeira, V. Vassilenko, M. A.

Cunha vol. 110(16)1999.

21. S.L.Garrison, S.I.Sandler J Chem Phys. Vol. 123(5 ) 2005.

22. Introduction to Fourier Transform Infrared Spectrometry- Thermo

Nicolet, 2001, Thermo Nicolet corporation.

23. M. Ibrahim, M. Alaam,, H. El-Haes, A. F. Jalbout,, A. de Leon

ECLETICA Quimica vol.31(3) 2006.

24. K.Wong , L.M. Song , N. E. Marcon Gastrointest Endosc Clin N

Am. Vol.13(2) 279-296 ,2003.

25
The thesis is based on the calculation of ground state properties and the vibrational

analysis of small organic molecules. The work reported is based on the calculation

of molecular properties and the vibrational analysis of small molecules after the full

geometry optimization using the Density functional B3LYP method. Density-

functional theory is one of the most fashionable and successful quantum mechanical

approaches to matter. The basic premise is that there is a one-to-one mapping from

the ground state electron density to the ground state electronic wavefunction. This

gives us another method for solving the electronic Schrödinger equation. The

theoretical details of density functional theory method are discussed below. The

theoretical framework presented here is mainly based on the article “An Introduction

to Density Functional Theory” by N. M. Harrison [1].

2.1 The Schrödinger Equation and its solution

The ground state energy of a collection of atoms may be computed by solving the

time independent, non-relativistic Schrödinger equation using Born-Oppenheimer

approximation [2] it can be written as:

Hˆ (r1 , r2 ,.......rN )  E (r1 , r2 ,.......rN ) ……….. [2.1]


The Hamiltonian operator, H is a sum of three terms; the kinetic Energy, the

interaction with the external potential ( Vext ) and the electron-electron interaction


( Vee ), that is

26
 N N
ˆ   1   2  Vˆ   1
H ……….. [2.2]
i ext
2 i ij ri  rj

In materials simulation the external potential is simply the interaction of the

electrons with the atomic nuclei;

N at
Z
Vˆext   ……….. [2.3]
 ri  R

Here, ri is the coordinate of electron i and the charge on the nucleus at Rα is Zα. For

simplicity of notation, the spin coordinate has been omitted. Eq. 2.1 is solved for a

set of ψ subject to the constraint that the ψ are anti-symmetric. The sign is changed if

the coordinates of any two electrons are interchanged. The lowest energy eigenvalue,

E0, is the ground state energy and the probability density of finding an electron with

any particular set of coordinates {ri} is |ψ0|2.

The average total energy for a state specified by a particular ψ, is the expectation

value of H , that is;

E[ ]    Hˆ dr   Hˆ  ……….. [2.4]

The notation [ψ] emphasizes the fact that the energy is a functional of the Wave

function. The energy is higher than that of the ground state unless ψ corresponds to

ψ0 – which is the variational theorem;

E[ ]  E0 ……….. [2.5]

27
The ground state wave function and energy may be found by searching all possible

wave functions for the one that minimizes the total energy. Hartree-Fock theory

consists of an ansatz for the structure of ψ - it is assumed to be an anti symmetric

product of functions (  i ) each of which depends in the coordinates of a single

electron, that is;

1
 HF  det[123 .....n ] ……….. [2.6]
N!

Where, dot indicates a matrix determinant [3]. Substitution of this ansatz for ψ into

the Schrödinger equation results in an expression for the Hartree-Fock energy;

1 N i (r1 )i (r1 ) j (r2 ) j (r2 ) 1 N i (r1 ) j (r1 )i (r2 ) j (r2 )
   
 1 N 2 ˆ 
EHF    (r )    i  Vext  r dr   
i

dr1dr2    dr1dr2
 2 i  2 i, j ri  rj 2 i, j ri  rj
……….. [2.7]

The second term is simply the classical Coulomb energy written in terms of the

orbitals and the third term is the exchange energy. The ground state orbitals are

determined by applying the variation theorem to this energy expression under the

constraint that the orbitals are orthonormal. This leads to the Hartree-Fock (or SCF)

equations;

1  (r ' ) '
[  2  vext (r )   dr ]i (r )   X (r , r ' )i (r ' )dr ' i i (r ) ……….. [2.8]
2 r r '

Where the non-local exchange potential, υX is such that:

28
 N  j (r ) j (r ' )
  X (r, r )i (r )dr  j  r  r ' i (r )dr ……….. [2.9]
' ' ' ' '

The Hartree-Fock equations describe non-interacting electrons under the influence of

a mean field potential consisting of the classical Coulomb potential and a non-local

exchange potential. From this starting point better approximations (correlated

methods) for ψ and E0 are readily achieved but the computational cost of such

improvements is very high and scales prohibitively quickly with the number of

electrons treated. In addition, accurate solutions require a very flexible description of

the wave function’s spatial variation, i.e. a large and basis set is required which also

adds to the expense for practical calculations. Many correlated methods have been

developed for molecular calculations [3]. The cost of the most commonly used

methods, MP2, MP3, MP4, CISD, CCSD, CCSD (T) formally scales with the

number of electrons raised to the power of 5, 6, 7, 6, 6, 7 respectively. In most cases

CCSD (T) calculations are of sufficient accuracy to determine the chemical

properties of systems to sufficient accuracy to predict chemical properties (stability,

reaction rates etc.) however, due to the computational expense the routine

application of such methods to realistic models of systems of interest is not practical.

As the direct solution of the Schrödinger equation is not currently feasible for

systems of interest in condensed matter science – this is a major motivation for the

development and use of density functional theory.

29
2.2 Alternative approach to solve Schrödinger Equation:

The Hamiltonian operator (Eq. 2.1) consists of single electron and bi-electronic

interactions – i.e. operators that involve on the coordinates of one or two electrons

only. In order to compute the total energy we do not need to know the 3N

dimensional wave function. Knowledge of the two-particle probability density – that

is, the probability of finding an electron at r1 and an electron at r2 is sufficient. A

quantity of great use in analyzing the energy expression is the second order density

matrix, which is defined as:

N ( N  1) 
P2 (r1 , r2 ; r1 , r2 ) 
2  (r1 , r2 ,........, rN ) (r1 , r2 ,........, rN )dr3 dr4 ......drN ……….. [2.10]

The diagonal elements of P2, often referred to as the two-particle density matrix or

pair density, are;

P2 (r1 , r2 )  P2 (r1 , r2 ; r1 , r2 )

This is the required two electron probability function and completely determines all

two particle operators. The first order density matrix is defined in a similar manner

and may be written in terms of P2 as;

2
N 1 
P1 (r1 ; r2 )  P2 (r1 , r2 ; r1 , r2 )dr2 ……….. [2.11]

Given P1 and P2 the total energy is determined exactly;

30
  1 N at
Z 
E  tr ( Hˆ Pˆ )   [   i2   P (r ' , r )] ' dr  P2 (r1 , r2' )dr1 dr2 ………..
1
 2  ri  R
 1 1 1 r1  r1 1  r1  r2
[2.12]
 

It is concluded that the diagonal elements of the first and second order density

matrices completely determine the total energy. This simplifies the task vastly. The

solution of the full Schrödinger equation for ψ is not required – it is sufficient to

determine P1 and P2 and the problem in a space of 3N coordinates has been reduced

to a problem in a 6 dimensional space.

Approaches based on the direct minimization of E(P1, P2) suffer from the specific

problem of ensuring that the density matrices are legal – that is, they must be

constructible from an anti symmetric ψ . Imposing this constraint is non trivial and is

currently an unsolved problem [4,5]. It implies that Eq. 2.12, does not lead

immediately to a reliable method for computing the total energy without calculating

the many body wave function.

The observation which strengthens density functional theory is that we do not even

require P2 to find E – the ground state energy is completely determined by the

diagonal elements of the first order density matrix – the charge density.

31
2.3 The Hohenburg-Kohn Theorems

In 1964 Hohenburg and Kohn proved the two theorems [6]. The first theorem may

be stated as follows:

“For any system of interacting particles in an external potential, the density is

uniquely determined (in other words, the external potential is a unique functional of

the density)”

If this statement is true then it immediately follows that the electron density uniquely

determines the Hamiltonian operator (Eq. 2.2). This follows as the Hamiltonian is

specified by the external potential and the total number of electrons, N, which can be

computed from the density simply by integration over all space. Thus, in principle,

given the charge density, the Hamiltonian operator could be uniquely determined

and this the wave functions ψ (of all states) and all material properties computed.

Hohenburg and Kohn gave a straightforward proof of this theorem, which was

generalized to include systems with degenerate states in proof given by Levy in

1979 [7]. It is believed that E. B. Wilson put forward a very straightforward proof

of this theorem in 1965. Wilson’s observation is that the electron density uniquely

determines the Positions and charges of the nuclei and thus trivially determines the

32
Hamiltonian. This proof is both transparent and elegant – it is based on the fact that

the electron density has a cusp at the nucleus, such that;

1    (r ) 
Z    
2  (0)  r  r 0


where ρ (r) is the spherical average of ρ and so a sufficiently careful examination of

the charge density uniquely determines the external potential and thus the

Hamiltonian. Although less general than the Levy proof this observation establishes

the theorem for the case of interest – electrons interacting with nuclei. The first

theorem may be summarized by saying that the energy is a functional of the density

– E[ρ].

The second theorem establishes a variational principle; For any positive definite

trial density, ρt such that

  (r )dr  N then
t E[  t ]  E0

The proof of this theorem is straightforward. From the first theorem we know that

the trial density determines a unique trial Hamiltonian (Ht) and thus wave function

(t ); E[  ]  t H t  E0 follows immediately from the variational theorem of the

Schrödinger equation (Eq. 2.5), this theorem restricts density functional theory to

studies of the ground state. A slight extension allows variation to excited states that

33
can be guaranteed orthogonal to the ground state but in order to achieve this

knowledge of the exact ground state wave function is required.

The two theorems lead to the fundamental statement of density functional theory;

  
 E      r dr  N  0 ……….. [2.13]

The ground state energy and density correspond to the minimum of some functional

E[ρ] subject to the constraint that the density contains the correct number of

electrons. The Lagrange multiplier of this constraint is the electronic chemical

potential μ.

The remarkable fact that has been established, is that a universal functional E[ρ] (i.e.

it does not depend on the external potential which represents the particular system of

interest) which, if we knew its form, could be inserted into the above equation and

minimized to obtain the exact ground state density and energy.

2.3.1 The Energy Functional

From the form of the Schrödinger equation (Eq. 2.1) we can see that the energy

functional contains three terms – the kinetic energy, the interaction with the external

potential and the electron-electron interaction and so we may write the functional as;

E[  ]  T [  ]  Vext [  ]  Vee [  ]

The interaction with the external potential is trivial;

34
 Vext [  ]   Vˆext  (r )dr

The kinetic and electron-electron functionals are unknown. If good Approximations

to these functionals could be found direct minimization of the energy would be

possible; this possibility is the subject of much current research [8]. Kohn and Sham

proposed the following approach to approximating the kinetic and electron-electron

functionals [9]. They introduced a fictitious system of N non-interacting electrons to

be described by a single determinant wave function in N “orbitals”  i . In this system

the kinetic energy and electron density are known exactly from the orbitals;

1 N1
Ts [  ]    i  2 i
2 i

Here the suffix emphasizes that this is not the true kinetic energy but is that of a

system of non-interacting electrons, which reproduce the true ground state density;
N
 (r )    i ………..
2
[2.14]
i

The construction of the density explicitly from a set of orbitals ensures that it is valid

as it can be constructed from an asymmetric wave function. If we also note that a

significant component of the electron-electron interaction will be the classical

Coulomb interaction – or Hartree energy (this is simply the second term of Eq. 2.7

written in terms of the density);

1  (r1 )  (r2 )
2  r1  r2
VH [  ]  dr1 dr2

35
the energy functional can be rearranged as;

E[  ]  Ts [  ]  Vext [  ]  VH [  ]  E XC [  ] ……….. [2.15]

Where we have introduced the exchange-correlation functional;

E xc [  ]  T [  ]  Ts [  ]  Vee [  ]  VH [  ]

Exc is simply the sum of the error made in using a non-interacting kinetic energy and

the error made in treating the electron-electron interaction classically. Writing the

functional (Eq. 2.15) explicitly in terms of the density built from non-interacting

orbitals (Eq. 2.14) and applying the variational theorem (Eq. 2.13) we find that the

orbitals, which minimize the energy, satisfy the following set of equations;

1 2  (r ' ) '
[   Vext (r )   dr  Vxc (r )]i (r ) i i (r ) ……….. [2.16]
2 r  r'

In which a local multiplicative potential which is the functional derivative of the

exchange correlation energy with respect to the density has been introduced.

E xc [  ]
V xc  ……….. [2.17]


This set of non-linear equations (the Kohn-Sham equations) describes the behaviour

of non-interacting “electrons” in an effective local potential. For the exact

functional, and thus exact local potential, the “orbitals” yield the exact ground state

density via Eq. 2.14 and exact ground state energy via Eq. 2.15.

These Kohn-Sham equations have the same structure as the Hartree-Fock equations

(Eq. 2.8) with the non-local exchange potential replaced by the local exchange-
36
 
correlation potential V xc . Here Exc contains an element of the kinetic energy and is

not the sum of the exchange and correlation energies as they are understood in

Hartree-Fock and correlated wave function theories.

The Kohn-Sham approach achieves an exact correspondence of the density and

ground state energy of a system consisting of non-interacting Fermions and the

“real” many body system described by the Schrödinger equation.

The correspondence of the charge density and energy of the many-body and the non-

interacting system is only exact if the exact functional is known. In this sense Kohn-

Sham density functional theory is an empirical methodology. The form of exact

functional is not known. However, the functional is universal – it does not depend on

the materials being studied. For any particular system we could, in principle, solve

the Schrödinger equation exactly and determine the energy functional and its

associated potential. This, of course, involves a greater effort than a direct solution

for the energy. Nevertheless, the ability to determine exact properties of the

universal functional in a number of systems allows excellent approximations to the

functional to be developed and used in unbiased and thus predictive studies of a

wide range of materials – a property usually associated with an ab initio theory. For

this reason the approximations to density functional theory are often referred to as

ab initio or first principles methods.

37
The computational cost of solving the Kohn Sham equations (Eq. 2.16) scales

formally as N3 (due to the need to maintain the orthogonality of N orbitals) but in

current practice is dropping towards N1 through the exploitation of the locality of the

orbitals.

For calculations in which the energy surface is the quantity of primary interest DFT

offers a practical and potential highly accurate alternative to the wave function

methods. In practice, the utility of the theory rests on the approximation used for

Exc[ρ].

2.3.2 The Local Density Approximation for Exc[ρ]

The generation of approximations for Exc has lead to a large and still rapidly

expanding field of research. There are now many different flavors of functional

available which are more or less appropriate for any particular study. Ultimately

such judgments must be made in terms of results (i.e.: the direct comparison with

more accurate theory or experimental data) but knowledge of the derivation and

structure of functionals is very valuable when selecting which to use in any

particular study.

The early thinking that lead to practical implementations of density functional theory

was dominated by one particular system for which near exact results could be

obtained – the homogeneous electron gas. In this system the electrons are subject to

38
a constant external potential and thus the charge density is constant. The system is

thus specified by a single number - the value of the constant electron density ρ=N/V.

Thomas and Fermi studied the homogeneous electron gas in the early 1920’s [10].

The orbitals of the system are, by symmetry, plane waves. If the electron-electron

interaction is approximated by the classical Hartree potential (that is exchange and

correlation effects are neglected) then the total energy functional can be readily

computed [10]. Under these conditions the dependence of the kinetic and exchange

energy (Eq. 2.7) on the density of the electron gas can be extracted [11,2,12] and

expressed in terms of a local functions of the density. This suggests that in the

inhomogeneous system we might approximate the functional as an integral over a

local function of the charge density. Using the kinetic and exchange energy

densities of the non-interacting homogeneous electron gas this leads to;

5
T [  ]  2.87  3 (r )dr

and,

4
E x [  ]  0.74  5 (r )dr ……….. [2.18]

These results are highly suggestive of a representation for Exc in an inhomogeneous

system. The local exchange correlation energy per electron might be approximated

as a simple function of the local charge density (say, εxc(ρ)). That is, an

approximation of the form;

39
 E xc [  ]    (r ) xc  r dr ……….. [2.19]

An obvious choice is then to take εxc(ρ) to be the exchange and correlation energy

density of the uniform electron gas of density ρ -this is the local density

approximation (LDA). Within the LDA εxc(ρ) is a function of only the local value of

the density. It can be separated into exchange and correlation contributions;

 xc (  )   x (  )   c (  ) ……….. [2.20]

The Dirac form can be used for εx (Eq. 2.18);

 x (  )  C 13 ……….. [2.21]

Where for generality a free constant, C, has been introduced rather than that

determined for the homogeneous electron gas. This functional form is much more

widely applicable than is implied from its derivation and can be established from

scaling arguments [2]. The functional form for the correlation energy density, εc, is

unknown and has been simulated for the homogeneous electron gas in numerical

quantum Monte Carlo calculations which yield essentially exact results [13]. The

resultant exchange correlation energy has been fitted by a number of analytic forms

[14, 15, 16] all of which yield similar results in practice and are collectively referred

to as LDA functionals.

The LDA has proven to be a remarkably fruitful approximation. Properties such as

structure, vibrational frequencies, elastic moduli and phase stability (of similar

40
structures) are described reliably for many systems. However, in computing energy

differences between rather different structures the LDA can have significant errors.

For instance, the binding energy of many systems is overestimated (typically by 20-

30 %) and energy barriers in diffusion or chemical reactions may be too small or

absent. Nevertheless, the remarkable fact is that the LDA works as well as it does

given the reduction of the energy functional to a simple local function of the density.

The accuracy of LDA is often considered satisfactory in condensed-matter systems,

but it is much less so in atomic and molecular physics, for which highly accurate

experimental data are available. However it is surprisingly successful and even

works reasonably well in systems where the electron density is rapidly varying.

Even for dynamical processes like the phonon dispersion, it has been shown to yield

good results [17,18]. In the meantime, it tends to underestimate atomic ground state

energies and ionization energies, while overestimating binding energies. It makes

large errors in predicting the energy gaps of some semiconductors. An obvious

approach to improving the LDA is to include gradient correction.

2.3.3 Generalized Gradient Approximation

The LDA neglects the in-homogeneities of the real charge density which could be

very different from the HEG. The exchange-correlation energy of inhomogeneous

charge density can be significantly different from the HEG result. This leads to the

development of generalized-gradient approximations (GGA’s) [19] which include

41
density gradient corrections and higher spatial derivatives of the electron density and

give better results than LDA in many cases. The idea is that to improve on the LSD

approximation, we allow the exchange-correlation energy per particle to depend not

only on the (spin) density at the point r, but also on the (spin) density gradients. This

generalizes Eq. (2.19) to the form

E xcGGA n =  f nr , nr  dr …. [2.22]

Where, the function f is chosen by some set of criteria.

In past years several generalized correlation functional were introduced and

their properties were studied. The most popular ones are those of Lee, Yang and Parr

[20], Perdew 1986 [21], and Perdew and Wang 1991 [22,23]. All these have been

widely used in studies of atoms, molecules and large systems such as bulk solids and

surfaces [24]. In particular, the description of the hydrogen bond is well achieved

using the exchange functional of Becke [25] and the correlation functional of Lee,

Yang and Parr [20] (BLYP).

On the other hand, the results of many applications as well as formal analysis

suggest [26] that GGA functional are still too limited to yield a fully consistent

improvement over the LDA. Finally, the hybrid methods, which were developed in

1990s, show in many applications the most satisfactory performance. The most

prominent example of this class is B3LYP.

42
2.3.4 Hybrid Method

In 1993, Becke [27] noticed that a linear combination of exact Hartree-Fock

exchange energy and GGA exchange energy

Exc  Exexact  1   ExcGGA ….. [2.23]

fitted atomic and molecular data better than either exact exchange or pure GGA

calculations. His three-parameter hybrid functional takes the following form,

Exc  1  AExSlater  AE xHF  BE xBecke  EcLSD  CEcPW 91 …. [2.24]

where E xHF is the Hartree-Fock exchange, E xSlater is the local exchange functional taken

from Slater, E xBecke is the gradient correction for exchange taken from Becke [25],

EcLSD is the LSD local correlation functional and CEcPW 91 is the 1991 gradient

functional of Perdew and Wang [23,28].Functional of this sort, where a certain

amount of exact exchange is incorporated are frequently called DFT/HF hybrid

functional, because they represent a hybrid between pure density functional for

exchange and exact Hartree-Fock exchange.

2.3.5 Advantages

One important advantage of DFT is that DFT scales three dimensionally, or as N3,

(N = number of basis functions). Ab-initio methods, on the other hand, scale as N4.

As a result DFT calculations are slightly faster with better accuracy. DFT includes

some component of electron correlation for much the same computational cost as HF

methods. This means that it is a highly efficient way of performing a more advanced
43
calculation on the system. DFT can also perform calculations on some molecules

that are not possible with ab-initio methods, most notably transition metals.

2.3.6 Disadvantages

Not unlike other methods, the computational chemist must make decisions about

which DFT method to use for a particular application. For example, the BLYP

method is considered by some to be appropriate for transition metal applications, but

not for organic compounds. B3LYP, on the other hand, has the opposite

characteristics.

2.4 Application of Quantum Chemical Methods

2.4.1 Geometry Optimization

Geometry Optimization is the name for the process that attempts to find the

configuration of minimum energy of the molecule. A sensible starting point for

geometry optimization is to use experimental data i.e. the X-Ray diffraction data of

the molecules whenever possible. The energy and wave functions are computed for

the initial guess of the geometry, which is then modified iteratively until (I) an

energy minimum has been identified and (II) forces within the molecules are zero.

This can often be difficult for non-rigid molecules, where there may be several

energy minima, and some effort may be required to find the global minimum. But in

those cases where molecules have unknown or unconfirmed structures, geometry

optimization can also be used to locate minima on a potential energy surface (PES)

44
Fig.2.3 A three-dimensional potential energy curve that shows global minima,
transition state and local minima

45
An input geometry is provided for geometry optimization and the calculation

proceeds to move across the PES. At each point the energy and the gradient are

calculated and the distance and direction of the next step are determined. The force

constants are usually estimated at each point and these constants specify the

curvature of the surface at that point; this provides additional information useful to

determining the next step. Convergence criteria about the forces at a given point and

the displacement of the next step determine whether a stationary point has been

found. To determine whether the geometry optimization has found a minimum or a

transition state (TS), it is necessary to perform frequency calculations. A TS is a

point that links two minima on the PES, and is characterized by one imaginary

frequency. The eigenvector from the Hessian force constant matrix determines the

nature of the imaginary frequency and indicates a possible reaction coordinate. A

minimum structure will have no imaginary frequencies.

2.4.2 Frequency Calculations

IR and Raman spectra of molecules can be predicted for any optimized molecular

structure. The position and relative intensity of vibrational bands can be gathered

from the output of a frequency calculation. This information is independent of

experiment and can therefore be used as a tool to confirm peak positions in

experimental spectra or to predict peak positions and intensities when experimental

data is not available. Calculated frequencies are based on the harmonic model, while

46
real vibrational frequencies are anharmonic. This partially explains discrepancies

between calculated and experimental frequencies.

The total energy of a molecule comprising N atoms near its equilibrium structure

may be written as

3 3  
1 3 2  2V
    V   qi  Veq     qi q j …. [2.25]
2 i 1 
i 1 j 1  qi q j

 eq

Here the mass-weighted cartesian displacements, qi, are defined in terms of the

locations Xi of the nuclei relative to their equilibrium positions Xi’eq and their masses

Mi,

qi  1i 2  i   ieq  …. [2.26]

Veq is the potential energy at the equilibrium nuclear configuration, and the

expansion of a power series is truncated at second order [29]. For such a system, the

classical-mechanical equation of motion takes the form

3
Qi   f ij qi , j = 1, 2, 3 …3N. …. [2.27]
i 1

The fij term quadratic force constants are the second derivatives of the potential

energy with respect to mass-weighted Cartesian displacement, evaluated at the

equilibrium nuclear configuration, that is,

  2V 
f ij    …. [2.28]
 q q 
 i j  eq

47
The fij may be evaluated by numerical second differentiation,

 2V V 
 ….. [2.29]
qi q j qi Vq j

By numerical first differentiation of analytical first derivatives,

 2V V q j 
 ….. [2.30]
qi q j qi

or by direct analytical second differentiation, Eq. (2.29). The choice of procedure

depends on the quantum mechanical model employed, that is, single-determinant or

post-Hartree-fock, and practical matters such as the size of the system.

Equation (2.27) may be solved by standard methods [30] to yield a set of 3N normal-

mode vibrational frequencies. Six of these (Five for linear molecules) will be zero as

they correspond to translational and rotational (rather than vibrational) degrees of

freedom. Normal modes of vibration are simple harmonic oscillations about a local

energy minimum, characteristic of a system's structure and its energy function for a

purely harmonic potential any motion can be exactly expressed as a superposition of

normal modes. In the present work the computed vibrational wavenumbers, their IR

and Raman intensities and the detailed description of each normal mode of vibration

are carried out in terms of the potential energy distribution. The DFT calculated

wavenumbers, for the majority of the normal modes, are typically slightly higher

48
than that of their experimental counterpart and thus proper scaling factors [31,32] are

employed to have better agreement with the experimental wavenumbers.

The Raman intensities were calculated from the Raman activities (Si) obtained with

the Gaussian 09 program, using the following relationship derived from the intensity

theory of Raman scattering [33,34]

Ii = [f(ν0 – ν i)4 Si] / [ν i{1- exp(-hc ν i/kT)}] ….[2.31]

Where ν0 being the exciting wavenumber in cm-1, νi the vibrational wave number of

ith normal mode, h, c and k universal constants and f is a suitably chosen common

normalization factor for all peak intensities.

2.4.3 Calculation of dipole moment and polarizability

The Gaussian 09 program was used to calculate the dipole moment (µ) and

polarizability (α) of the molecules, based on the finite field approach. Following

Buckingham’s definitions [35], the total dipole moment and the mean polarizability

in a Cartesian frame is defined by

µ = (µx2 + µy2 +µz2)1/2 ...…[2.32]

<α> = 1/3 [αxx + αyy + αzz ] ….. [2.33]

2.5 Calculation of UV spectra:

The absorption of radiation in the UV-VIS region of the spectrum is dependent on

the electronic structure of the absorbing species like, atoms, molecules, ions or

49
complexes. In molecules, the electronic, vibration as well as rotational energies are

quantized. A given electronic energies level has number of vibration energy levels

in it and each of the vibrational energy level has a number of rotational energy levels

in it. When a photon of a given wavelength interacts with the molecule it may cause

a transition amongst the electronic energy levels if its energy matches with

difference in the region of these levels. UV-VIS spectroscopy studies the electronic

transitions of molecules as they absorb light in the UV and visible regions of

electromagnetic spectrum. The data is used to produce absorbance spectra. The

visible region of the spectrum comprises photon energies of 36 to 72 Kcal/mol, and

the near ultraviolet region, out of 200 nm, extends this energy range to 143

Kcal/mole, this energy is enough to promotes the outer electron to higher energy

levels .As a rule the energetically favored electron promotion will be form of highest

occupied molecular orbital (HOMO) to lowest un occupied molecular orbital

(LUMO). The resulting species is said to be in excited statistical. An optical

spectrometer records, the wavelength at which absorption occurs together with

degree of absorption at each wave length to produce spectrum. The absorption of

UV or visible radiation corresponds to three types of electronic transition. (Fig-2.1)

1. Transition involving π, σ and n electrons

2. Transition involving charge- transfer electron

50
Fig 2.1 electronic transistion of π, σ and n electrons.

51
 3. Transition involving d and f electron

Possible electronic transition of π, σ and n electrons are;

In the course of such transitions, for the sample in gaseous or vapour phase, the

spectrum consists of a number of closely space lines (Fig 2.2) constituting what is

called band spectrum. However in the solution phase, the absorbing species are

surrounded by solvent molecules and undergo constant collision with them. These

collision and the interaction among the absorbing species and the solvent molecules

cause the energies of quantum states to spread out .As a consequence , the sample

absorb photons spread over a range of wavelength. Thereby the spectrum acquires

the shape of smooth and continuous absorption peak in the solution phase. A typical

UV-VIS spectrum in the solution phase is depicted in the fig 2.2.

The UV spectra of substance are characterized by two major parameters namely, the

position of maximum of the absorption band called λmax, and the intensity of the

bands. The λmax refers to the wavelength of most absorbed radiation and is a measure

of difference in the electronic energy levels involved in the transition. The intensity

on the other hand is indicative of the probability of transition i.e. whether the

transition are allowed or not. It is also measure of concentration of the absorbing

species. UV spectroscopy obeys the Beer- Lambert law, which states that: when a

52
Fig. 2.2 Representative UV spectrum: a) in vapour phase b) in solution phase.

53
beam of monochromatic light is passed through a solution of an absorbing

substance, the rate of decrease of intensity of radiation with thickness and absorbing

solution is proportional to the incident radiation as well as concentration of solution.

The expression of Beer- Lambert Law is-

A= log (I0/I) = Ecl ...…[2.34]

Where A= absorbance

I0 = intensity of light incident upon sample cell

I = Intensity of light leaving sample cell

C = molar concentration of solute

L = length of sample cell ( cm.)

E = molar absorptivity

From the Beer- Lambert law it is clear that greater the number of molecules capable

of absorbing light of a given wavelength, the greater the extent of light absorption.

This is basic principle of UV spectroscopy. UV-VIS spectroscopy forms the basis of

analysis of different substance such as, inorganic, organic and biochemical. It finds

applications in research, industries, clinical laboratories and in the chemical analysis

of environmental samples. [36].

54
2.6 Basis Set Superposition Error and Counterpoise Correction:

In quantum chemistry, calculations of molecular properties are susceptible to basis

set superposition error (BSSE) if they use finite basis sets. As the atoms of

interacting molecules (or of different parts of the same molecule) approach one

another, their basis functions overlap. Each monomer “borrows” function from other

nearby components, effectively increasing its basis set and improving the calculation

of derived properties such as energy. If the total energy is minimized as a function of

the system geometry, the short range energies of the mixed basis sets must be

compared with the long - range energies from the unmixed basis sets, and this

mismatch introduces an error [37].

Other than using infinite basis sets, two methods exist to eliminate the BSSE. In the

Chemical Hamiltonian approach (CHA) [38], basis set mixing is prevented a priori,

by replacing the conventional Hamiltonian with one in which all the projector-

containing terms that would allow mixing have been removed. In the counterpoise

method (CP), [39-41] the BSSE is calculated by re- performing all the calculations

using the mixed basis sets and the error is then subtracted a posteriori from the

uncorrected energy. (The mixed basis sets are realized by introducing “ghost

orbitals”; basis set functions which have no electrons or protons) [42]. Though

conceptually very different, the two methods tend to give similar result [43]. The

55
theoretical details presented below has been obtained from an article by C. David

Sherril, School of Chemistry and Biochemistry, Georgia Institute of Technology.

In the Boys and Bernardi counterpoise correction (CP) [44] for removing BSSE, the

typical uncorrected interaction energy between monomers A and B would be

computed as:

……… [2.35]

Where superscript denote the basis used, the subscript denote the geometry, and the

symbol in parentheses the chemical system considered. Thus, represent the

energy of the bimolecular complex AB evaluated in dimer basis (the union of the

basis sets on A and B), computed at the geometry of the dimer. Likewise, monomers

A and B are each evaluated at their own geometries in their own basis sets. This can

be performed as three separate, standard computations: one on the dimer, one on

monomer a, and one on the monomer B. alternatively, one could obtain the energy

of the dissociation limit by a computation of the A+B supermolecule at some very

large intermolecular separation (where the distance between A and B would be so

large that the basis function of one monomer would not overlap with those of the

other); this might be necessary for theoretical methods which are not size-extensive,

such as truncated configuration interaction, for which the energy of A+B at infinite

separation is not equal to the sum of the energies from separate computation on A

and B.

56
The eq. [2.35] can be corrected by estimating the amount by which monomer A is

artificially stabilized by the extra basis functions from monomer B (and vice versa).

This may be estimated as:

………… [2.36]

…………. [2.37]

Where the energy of monomer A in its monomer basis is subtracted from the energy

of monomer A in the dimer basis (and likewise for monomer B). For the moment, it

has been assumed that the geometries of the monomers A and B do not change as

they approach each other and form the bimolecular complex. This is often a very

good approximation and simplifies the procedure. Now considering the possibility

that the monomer geometries are deformed as they join in the bimolecular complex;

the energy of monomer A in dimer basis must necessarily be lower (more stable)

than the energy of monomer A in the monomer basis, so and thus

as defined above (the error is stabilizing). If this error is subtracted

from the interaction energy defined in eq. [2.35], the terms and cancel,

yielding:

……….. [2.38]

Practically speaking, to evaluate the energy of monomer A in the dimer basis, one

places all the basis functions of monomer B on the atomic centers of monomer B

while neglecting the electrons and the nuclear charges of monomer B. The functions

57
of monomer B are thus referred to as “ghost functions” or the atoms of B are

referred as “ghost atoms” in such a computation. It has been argued that such a

procedure should “overcorrect” the BSSE, because some of the basis functions in

monomer B are occupied and hence unavailable to monomer A because of the

Pauli’s exclusion principle. Indeed there do appear to be situations in which the

counterpoise correction overcorrects, particularly for smaller basis sets [45,46].This

appears to happen in particular for hydrogen bonded complexes (although the

counterpoise corrected interaction energies approach the complete basis set more

smoothly and more suitable for extrapolation.) [47] on the other hand, for dispersion

dominated systems it appears that the counterpoise corrected values are superior

[48].

2.6 Graphical user interface for Gaussian 09 - Gauss View:

Gaussview is an affordable, full-featured graphical user interface for Gaussian 09

[49]. With the help of Gaussview [50], one can prepare input for submission to

Gaussian and to examine graphically the output that Gaussian produces. The first

step in producing a Gaussian input file is to build the desired molecule. The bond

lengths, bond angles, and dihedral angles for the molecule will be used by

Gaussview to write a molecular structure for the calculation. Gaussview incorporates

an excellent Molecule Builder. One can use it to rapidly sketch in molecules and

examine them in three dimensions. Molecules can be built by atom, ring, group,

58
amino acid and nucleoside. Gaussview is not integrated with the computational

module of Gaussian, but rather is a front-end/back-end processor to aid in the use of

Gaussian. Gaussview can graphically display a variety of Gaussian calculation

results, including the following:

 Molecular orbitals

 Atomic charges

 Surfaces from the electron density, electrostatic potential, NMR shielding

density, and other properties. Surfaces may be displayed in solid, translucent

and wire mesh modes.

 Surfaces can be colored by a separate property.

 Animation of the normal modes corresponding to vibrational frequencies.

 Animation of the steps in geometry optimizations, potential energy surface

scans, intrinsic reaction coordinate (IRC) paths.

59
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25. A. Becke, Phys. Rev. A 38 (1988) 3098.

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35. A. D. Buckingham, Adv. Chem. Phys., 12 (1967) 107.

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37.[22] Wikipedia encyclopedia

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C. M., van Lenthe, Joop H., Chem. Rev. 94 (7), (1994) 1873.

40.[25] Rosch, N. (2003). “Counterpoise correction”. Technical University of

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41.[26] Sedano, Pedro Salvador (2000). “Counterpoise Corrected Potential

Energy Surfaces”. University of Girona. Retrieved 14 May 2010.

42.[27] Hobza, Pavel; Muller Dethlefs, Klaus, Royal society of chemistry.

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49. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R.

Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H.

Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G.

Zheng, J.L. Sonnenberg,M. Hada, M. Ehara, K. Toyota, R. Fukuda, J.

Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven,

J.A. Montgomery Jr., J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E.

Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K.

Raghavachari, A.Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M.

Cossi, N. Rega, J.M.Millam,M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C.

Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin,

R. Cammi, C.Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G.

Zakrzewski, G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A.D.

Daniels, Ö. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, D.J. Fox,

Gaussian 09, Revision A.1, Gaussian, Inc., Wallingford CT (2009).

50. Æ. Frisch, H.P. Hratchian, R.D. Dennington, II, T.A. Keith, John Millam

with, B. Nielsen, A.J. Holder, and J. Hiscocks, GaussView Version 5.0.8,

Gaussian, Inc., Wallingford, CT, USA, 2009.

64
3.1 Introduction

Chagas a tropical disease also referred to as American trypanosomiasis, is caused

by the etiologic parasite agent Trypanosomacruzi, which is transmitted to people

and animals by insect vectors mainly, in rural areas, where poverty is widespread.

Chagas' disease is endemic in almost all Latin American countries, including

Mexico and the Central American nations.It is estimated that around 16- 18

million people are infected by the parasite and 50,000 people die annually as a

consequence of the illness [1]. Brener [2,3] unequivocally demonstrated

that therapeutic application of 5-nitro-2-furaldehyde-semicarbazone (5N2FSC),

used in a long term scheme (53 days in average) healed more than 95% of

chronically infected mice, and a new era in Chagas disease therapeutics began.

Reports of novel trypanocidal5-nitro-2-furaldehyde-semicarbazone (nitrofurazone)

and its derivatives continue to appear [4-6], which emphasizes the fact that

trypanosomes are fairly sensitive to this class of compound.5-nitro-2-furaldehyde-

semicarbazone is a broad-spectrum bactericidal drug and was earlier used for the

treatment of wounds, burns, ulcers and skin infections [7,8].

The present chapter deals with investigation of molecular structural properties,

vibrational and energetic data of 5N2FSC, in gas phase, due to its pharmaceutical

importance. The ground state and the excited state properties of the title molecule

65
have been calculated employing HF and DFT/ B3LYPlevel of theories. As

vibrational and electronic spectroscopic study provides very useful information

about the structure and conformation of the molecules if used in synergy with

quantum chemical calculations, therefore in order to obtain a complete description

of molecular dynamics, vibrational wavenumber calculation along with the normal

mode analysis has been carried out at the HF and DFT level of theories. The

comprehensive investigation of geometrical and electronic structure in ground and

the first excited electronic states, dipole moment, polarizability, first static

hyperpolarizability, along with the molecular electrostatic potential surface and

contour map may lead to better understanding of the structural, spectral

characteristics of the compound under study.

3.2 Experimental: Structure and Spectra

The optimized molecular structure of 5N2FSC is given in Figure 3.1 The

calculated IR and Raman spectra have been shown in Figure 3.2 and is found to

match well with the spectra reported at Sigma Aldrich website [9]. The theoretical

UV-vis spectra has been compared with the experimental spectra reported at NIST

web data [10].

66
 Figure 3.1 : Optimize geometry of 5N2FSC

Figure 3.2 : Raman and IR spectra of 5N2FSC

67
Figure 3.3 Graph between bond angle and bond length Vs their magnitude

68
 Table 3.1 Theoretically computed ground state optimized parameters

Nitrofurazone HF/ Nitrofurazone B3LYP/

Parameters
6-311++G(d,p) 6-311++G(d,p)

Energy (in Hartree) -747.96822 a.u. 752.22750a.u.

Frontier orbital energy gap

0.30577 0.13448
(in Hartree)
Dipole moment
10.50 10.55
(in Debye)

Polarizabilitya / a.u. 115.891 145.706

a
In atomic units. Conversion factor to the SI units-
1e2a02Eh-1= 1.648 778 × 10-41C2 m2 J-1
Table 3.2 First static hyperpolarizability and its components
Hyperpolarizabilityb/DFT/6-311++G(d,p)

βXXX 2113.9665
βXXY -780.1934
βXYY 332.3267
βYYY -48.1968
βXXZ -13.8285
βXYZ -20.5715
βYYZ 6.4759
βXZZ -32.2027
βYZZ 77.3383
βZZZ 11.0817
βTOTAL 2528.2
βµ -1133.67

b
In atomic units. Conversion factor to the SI units-
1e3a03Eh-2= 3.206 361 × 10-53C3 m3 J-2

69
3.3 Result and Discussion

3.3.1 Molecular Geometry

The optimized structure along with the numbering scheme of 5N2FSC at

DFT/B3LYP level using the 6-311++G (d, p) basis is shown in Figure.3.1The X-

ray diffraction data of 5N2FSC reported by Tomasz et.al [11] has been used as the

starting point for the optimization of structure. The crystallographic data of

5N2FSC shows that the three dimensional network of molecule linked through

bifurcated hydrogen bonds. The crystal lattice is monoclinic with P21symmetry.

The optimized geometry of the molecule is found to be nearly planer except for

O7, N8 and hydrogen atoms as reported in the crystal structure [11]. The optimized

structure of 5N2FSC and the experimental crystal structure shows good coherence

showing that geometry optimization at proper basis set almost exactly reproduces

the experimental conformation. As evident from Figure.3.3, all the bond lengths

and bond angles of the optimized structure calculated at DFT/B3LYP are very

close to the x-ray data with a maximum deviation of 0.063 A0 and 2.90 in bond

lengths and bond angles respectively with the exception the angle N5-C6-O7

which deviation by 3.80 to the reported values, whereas at HF level the deviation

slightly increases (0.069 A0 for bond lengths, 3.20 for bond angles and maximum

angle deviation 4.20) The deviation of O7 atom with the molecular plane, 40 higher
70
than the value reported in X-ray data may be due to the fact that oxygen atoms are

involved in inter-molecular hydrogen bonding and that the molecular conformation

in the gas phase is different from that in the solid state, where inter molecular

interactions play an important role in stabilizing the crystal structure. The C-C

bond in furan ring is found to vary from 1.365 to 1.416 A0. The C-N bond length in

5N2FSC lies in the range 1.386-1.431 A0. The C3=N4 bond length w.r.t. which the

molecule has a trans conformation is calculated to be 1.282 A0.

3.3.2 Electronic Properties

HOMO-LUMO orbitals are also called frontier orbitals as they lie at the outermost

boundaries of the electrons of the molecules. The frontier orbital gap helps

characterize the chemical reactivity and kinetic stability of the molecule. A

molecule with a small frontier orbital gap is generally associated with a high

chemical reactivity, low kinetic stability and is also termed as soft molecule [12].

The 3D plots of the frontier orbitals HOMO, LUMO and the Molecular

electrostatic potential map (MESP) figures for the 5N2FSC are shown in

Figure3.4. It can be seen from the Figure.3.4, that HOMO is spread over the entire

molecule and shows appreciable amount of π bonding character. The LUMO is

also found to be uniformly distributed over the molecule and reflects a lot of anti

bonding π character.
71
Figure 3.4 : MESP and HOMO-LUMO plot of 5N2FSC

72
The basis set 6-311G++(d,p) which also includes asymptotically correct functions

with diffuse electron distribution and polarization functions, has been suitably

chosen to describe the HOMO and LUMO orbitals adequately. The frontier orbital

energy gap in case of 5N2FSC is found to be 0.13448hartree.

The MESP which is a plot of electrostatic potential mapped onto the constant

electron density surface which simultaneously displays molecular size and shape

and electrostatic potential value in terms of colour grading. The MESP may be

employed to distinguish regions on the surface which are electron rich (subject to

electrophilic attack) from those which are electron poor (subject to nucleophilic

attack)and has been found to be avery useful tool in investigation of correlation

between molecular structure and the physiochemical property relationship of

molecules including biomolecules and drugs [13-19].The MESP map in case of

5N2FSC clearly suggests that the potential swings wildly between oxygen atoms

(dark red) on one side and five-membered furan ring (blue)and the semi carbazone

region(dark blue) on the opposite side. The oxygen atoms of nitro and carbonyl

groups (reflect the most electronegative region) and may show high nucleophilic

activity due to excess negative charge, and the hydrogen atoms attached to the

semicarbazone bear most the brunt of positive charge (blue region) may be center

for electrophilic activity. The sliced 2D MESP contour map of the title molecule

has also been plotted in Figure. 3.5. Such a representation provides more detailed
73
information regarding molecular electrostatic potential distribution, by showing the

values in a manifold of spatial location around the molecule. The MESP 2D

contour map is drawn in the plane 1.5 Å above the molecular plane. As evident

from the MESP 2D contour maps the extent of the electron rich red region is

mainly over all oxygen and nitrogen atoms and all the hydrogen atoms along with

almost the entire furan ring (except the oxygen atom attached to furan ring) is the

electron deficient region. The map in the plane 1.5 Å above the molecular plane

clearly shows that the maximum values of positive potential and negative potential

corresponding to the electrophilic and nucleophilic region are 0.08 a.u. and 0.04

a.u. respectively.

3.3.2.1 Electric Moments

The dipole moment in a molecule is an important property that is mainly used to

study the intermolecular interactions involving the non bonded type dipole-dipole

interactions, because higher the dipole moment, stronger will be the intermolecular

interactions. The higher value of dipole moment in case of 5N2FSC molecule

(10.55Debye) is mainly attributed to an overall imbalance in charge from one side

of a molecule to the other side is also evident from the MESP plot. The high dipole

moment of5N2FSC, along with the typical variation in electrostatic potential

(almost one half part is highly electron rich as compared to the other half which is

74
Figure 3.5 : Contour plotting of 5N2FSC

75
electron deficient) may be considered largely responsible for its broad activity for

target/ receptor binding sites.

The extensive and important studies on electric polarizability and

hyperpolarizability, by Maroulis and others [20-24], have laid down the relative

importance of electron correlation, choice of basis set and the different methods

employed for the calculation of these quantities. Consequently the electric

polarizability and hyperpolarizability have been calculated at different basis sets

employing different level of theories to arrive at the better understanding/

description of the title molecule under investigation in absence of experimental

data. The mean polarizability, total intrinsic hyperpolarizability (β TOTAL) and the

component of the hyperpolarizability along the direction of the dipolemoment βµ

are presented in Table 3.1 and Table 3.2 The variation in polarizability and

hyperpolarizability with the addition of the basis functions at HF and DFT/B3LYP

and DFT/B3PW91 are plotted in Figure. 3.6 &. 3.7 respectively. The β

components and total hyperpolarizability (βTOTAL) at DFT/B3LYP/6-311G++(d,p)

are given in Table 3.2 The molecule under investigation is found to have a large

value of hyperpolarizability (βTOTAL / e3a03Eh-2 = 2528.2 or in e.s.u. 1 a.u. = 8.3693

x 10-33 ; βTOTAL = 21.2X10-31e.s.u.).

76
Figure 3.6 : Graphical Studies between polarizability and basis set.

Figure 3.7 : Graphical Studies between Hyperpolarizability and basis set

77
Figure 3.8: Graph between modes of vibration and wavenumber

78
Table 3.3 Theoretical and Experimental* wavenumbers of 5N2FSC

Experimental* Theoretical (B3LYP/6-311++G(d,p) )

FTIR RAMAN Unsc. scaled IR Raman
(cm-1) (cm-1) (cm-1) (cm-1) Intensity Intensity Assignment with PEDa

3464 - 3683 3564 46 2.50 νas(N8-H2)(99)

3349 - 3572 3457 68 9.51 νs(N8- H2)(99)

3240 - 3475 3363 2 15.18 ν(N5-H16)(100)

3157 - 3279 3174 5 5.25 ν(C-H)FR(95)

3138 - 3249 3145 1 4.33 ν(C-H)FR (96)

2957 - 3043 2945 46 5.48 ν(C3-H15)(100)

1728 1685 1822 1764 375 12.32 ν(C6-O7)(80)

- 1600 1668 1614 47 684.94 ν(C3-N4)(52)+ β(H16-N5-C6)(22)

1587 1580 1630 1578 130 10.91 sc( N8-H2)(80)

1561 1535 1602 1551 44 14.68 FR quarter ring stretching(49)+ νas (N12- O2)(14)+ ν(C3-N4)(12)

1536 - 1580 1529 436 11.79 νas (N12- O2)(54)+ ν(C3-C2)(14)+ ν(C3-N4)(13)+β(H16-N5-C6)(12)

1505 1490 1557 1507 19 21.63 β(H16-N5-C6)(43)+ νas (N12- O2)(32)

1472 1475 1502 1454 359 389.83 FR quarter ring stretching(63)+ β(H16-N5-C6)(31)

1396 1358 1423 1377 27 105.64 FR half ring stretching(54)+β(H15-C3-N4)(20)

1345 1344 1374 1330 332 81.69 νs(N12-O2)(42)+FR half ring st.(25)+β(H16-N5-C6)(16)+β(H15-C3-N4)(13)

1319 1330 1355 1312 135 132.20 β(H15-C3-N4)(47)+νs(N12-O2)(20)

1255 1265 1296 1254 239 8.79 r(N8-H2)(36)+ν(C6-N8)(26)+β(H16-N5-N4)(15)+β(H15-C3-N4)(14)

- - 1285 1244 570 144.99 FR half ring st.(23)+ νs(N12-O2)(21)+ β(H16-N5-N4)(17)+ β(H15-C3-

C2)(14)+r(N8-H2)(11)

1204 1205 1257 1217 15 6.27 FR half ring st. (37)+β(H20-C10-C11)(20)+β(H19-C9-C2)(20)

- - 1204 1165 254 5.94 ν(N4-N5)(30)+ ν(C11-N12)(17)+ FR whole ring st.(14)+

β(H20-C10-C11)(13)+β(H19-C9-C10)(12)

1153 - 1178 1140 266 139.67 ν(N4-N5)(40)+β(H20-C10-C11)(10)+β(H19-C9-C10)(10)+β(H16-N5-N4)(10)

1026 1030 1093 1058 85 8.28 r(N8-H2)(48)+ ν(C6-N8)(36)

- - 1039 1006 50 96.39 β(H20-C10-C9)(36)+β(H19-C9-C10)(36)+ ν(C10-C9)(10)

971 - 1015 982 10 4.64 β(N5-N4-C3)(35)+ ν(C2-O1)(30)+ r(N8-H2)(16)

- 965 986 954 12 20.45 FR Ring deformation (67)

79
Table 3.3 Continued…..

- 930 972 941 32 3.30 FR Ring deformation(38)+ν(N5-C6)(25)+r(N8--H2)(19)

905 - 929 899 18 4.70 Wag(C3-H15)(46)+ Wag (C-H)FR(28)

- - 905 876 6 0.61 Wag (C-H)FR(61)+ Wag(C3-H15)(11)

813 815 832 805 31 18.67 sc(N12-O2)(44)+FR deformation(30)

784 785 810 784 41 0.72 Wag (C-H)FR(87)

765 756 799 773 6 19.07 β(N4-C3-C2)(37)+FR Ring Deformation(25)

741 - 757 733 25 0.79 βout (H16-N5-C6)(81)

724 - 738 714 12 0.82 wag (N12-O2)(45)+βout(O1-C11-N12)(36)

665 676 697 676 22 8.01 β(O7-C6-N5)(40)+ β (N4-N5-C6)(27)

656 - 687 665 1 1.82 FR ring torsion(71)

595 586 594 575 1 0.00 FR ring torsion(74)+ τ(C11-N12)(21)

561 - 553 535 5 3.74 r(N12-O2)(46)+β(C3-C2-C9)(30)+ wag (N8-H2)(12)

- - 543 526 56 6.39 r(H18-N8-H17)(30)+β(H16-N5-N4)(30)

- - 535 518 203 5.23 wag (N8-H2)(63)

473 485 482 467 64 27.39 wag (N5-H16)(80)

- 440 452 437 6 5.04 β(C3-C4–N5)(42)+ β(O13–N12–C11)(28) +β(O7–C6–N5)(13)

- - 419 406 18 5.62 β(N8–C6–N5)(47)+ β(O14–N12–C11)(26)

- 385 380 368 38 6.52 twisting(N8-H2)(56)+ τ(C2-C3)(16)+ τ(C3-N4)(15)

- - 369 357 34 9.11 twisting(N8-H2)(61)+ τ(C3-N4)(21)+τ(C2-C3)(11)

- 280 302 292 2 9.34 β(C3-C2–C9)(34)+ β(C3-N4-N5)(27)+ β(N4–N5–C6)(17)

- 268 249 241 1 4.24 β(O14–N12–C11)(34)+β(O1-C2-C3)(20)+β(N8-C6-N5)(13)

- - 239 231 20 4.55 τ(C3-N4)(21)+τ(N5-N4)(19)+ τ(C6-N5)(17)+FR ring torsion(15)

- 182 177 171 6 15.08 τ(C-N)(29)+ τ(C-C)(27)+ FR ring torsional mode(20)

- 165 159 154 9 27.11 β(N4–N5–C6)(47)+ β(C10-C11–N12)(30)

- - 132 128 1 12.51 τ(C-C)(30)+ τ(C-N)(28)+ FR ring torsional mode(22)

- - 419 406 18 5.62 β(N8–C6–N5)(47)+ β(O14–N12–C11)(26)

- 385 380 368 38 6.52 twisting(N8-H2)(56)+ τ(C2-C3)(16)+ τ(C3-N4)(15)

*
Note : Experimental FTIR and Raman data as reported in www.sigmaaldrich.com/united-states.html
website. Abbreviations used here have following meaning :: stretching; s: symmetric stretching;
as: asymmetric stretching; β: in plane bending; βout: out of plane bending; sc: scissoring; τ: torsion; FR :
Furan Ring
80
3.3.3 Vibrational analysis

The experimental and computed vibrational wave numbers, their IR and Raman

intensities and the detailed description of normal modes of vibration of the

5N2FSC, carried out in terms of their contribution to the total potential energy are

given in Table 3.3. Comparison of calculated wavenumbers at HF/6-311++G (d, p)

and B3LYP/6-311++G (d,p) level with experimental values (Figure. 3.8) reveals an

overestimation of the vibrational wavenumbers due to neglect of the anharmonicity

present in the actual system. Moreover, it is interesting to note that although the

optimized parameters at HF and DFT are not much different but the deviation of

theoretical wavenumbers from experimental ones at HF clearly indicates that DFT

approach is far superior to HF theory in the calculation of vibrational spectra. For

complete vibrational analysis the vibrational modes are discussed under the

following heads:

3.3.3.1 Nitro group Vibration

The NO2 stretching vibrations are very useful group vibrations because of their

spectral position and strong intensity. The NO2asymmetrical stretching vibrations

in nitro-alkanes occur in the range 1560-1530 cm-1 and the symmetric vibration

lie in the range 1390-1370 cm-1,the asymmetrical stretching being the stronger

than the symmetrical stretching. In aromatic compounds, the NO2 stretching bands

81
shift to down to slightly lower wavenumbers in the range 1540-1500 cm-1 and

1370-1330 cm-1[25]. For 5N2FSCthe strong absorption at 1536 cm-1 in FTIR

corresponds well the B3LYP wavenumber at 1529 cm-1with 54% contribution from

asymmetric NO2 stretching. The mode calculated at 1330 cm-1 has major

contribution from NO2 symmetric stretching mode and is assigned with the peaks

at 1345/1344 cm-1 in FTIR/Raman spectra. While the hydrogen bonding has very

insignificant effect on asymmetric stretching it shows appreciable effect on the

symmetric NO2 vibration [26], hence the deviation in this wavenumber from the

experimental values is justified. Near and below 800 cm-1 there are three bending

modes of NO2 namely- wagging, twisting and rocking. The peak at 805 cm-1is

assigned to scissoring mode of the nitro group; the corresponding experimental

values in FTIR and Raman are at 813 and 815 cm-1, which is in accordance with

the other investigators. [27]. The band calculated at 518 cm-1 and 714 cm-1are the

rocking and wagging modes of NO2 group.

3.3.3.2 Furan Ring Vibration

Five membered ring heteroaromatic compounds with two double bond in the ring,

generally shows three ring stretching bands near 1590, 1490 and 1400 cm-1[28].

Furan quarter ring, half ring and whole ring stretching [29] are calculated in the

range 1551 – 1165 cm-1 and modes with major contribution from stretching

vibrations are assigned well with the peaks at 1153, 1396/1358, 1472/1475 and
82
1561/1535 cm-1 in the FTIR/Raman spectra. The mode with major contribution

from furan ring deformation is calculated at 954 cm-1 and corresponds well with

the peak at 965 cm-1 in Raman Spectra. The peaks observed at 656 cm-1 and

595/586 cm-1 in FTIR/Raman spectra are assigned to the furan ring torsional

modes, the calculated values are at 665 and 575 cm-1.

3.3.3.3 Amide group vibrations

The intermolecular amide hydrogen bonding is clearly reflected in the deviation of

theoretical wavenumbers of N-H stretching modes. The peak at 3246 cm-1 in the

FTIR is assigned to the N-H stretching of amide group. The calculated mode is at

3366 cm-1 indicating strong N-H…O interaction. The N5-H16 in-plane and out of

plane bending vibrations are calculated at 1507 cm-1and 733cm-1, in good

agreement with a strong peak at 1505 cm-1 and a medium intensity peak at 741 cm-
1
in the reported experimental FTIR spectra [9] and in line with the assignments

made by R. A. Yadav et. al. for 2-Thiocytosine [30].

V.M. Kolb et. al. [31] have reported abnormally high infrared (IR) C==O

wavenumbers (> 1700 cm-1) in a study of several semicarbazones and concluded

that the abnormally high IR C==O wavenumbers are caused, at least in part, by the

vibrational coupling of the C==O in the solid-state H-bonded structure. Inspection

of Raman spectra of a series of amides reveals that the Raman C=O band is indeed

of a very low intensity in the cases where vibrational coupling is indicated [32];
83
otherwise it is of a medium intensity [3348].The strong peak in the FT-IR spectra

at 1726cm−1 and very weak peak in the Raman spectra at 1680 cm−1 corresponds

to C=O stretching vibration. The theoretical wavenumber has a positive deviation

of 36 cm-1/79 cm-1 with the experimental FTIR/Raman wavenumber which may be

due to the intermolecular hydrogen bonding in the molecular packing structure.

3.3.3.4 C-N and C=N vibrations

In the vibrational analysis of benzimidazole, Sundaraganesan et al. assigned the

band at 1689 cm−1 and 1302 cm−1 to C=N and C–N stretching vibrations,

respectively [34]. Krishna Kumar and Ramasamy have assigned C-N stretching

mode at 303 and 1256 cm−1 in the vibrational analysis of 4,5-dichloro-3-

hydroxypyridazine [35]. Referring to the above workers, we have assigned the

C=N stretching mode at 1614 cm-1 and C-N stretching at 1254 cm-1. The observed

peak agrees well with the theoretically calculated values.

3.3.3.5 N-N and C-C vibrations

Both N-N and C-C stretching vibrations for 5N2FSC are found to be as mixed

modes. The N-N stretching appears at wavenumber 1165 and 1140 cm-1 while the

C-C vibration is assigned at 1529 cm-1; these wavenumbers are in full agreement

with the experimental wavenumbers for the corresponding modes.

84
3.3.3.6 NH2 vibrations

Primary amines have two sharp N-H stretching bands near 3335 cm-1, a broad NH2

scissoring band at 1615 cm-1, and NH2 wagging and twisting bands in 850-750

cm-1 range [25]. The scaled NH2symmetric and asymmetric stretching modes are

at 3457 and 3564 cm-1 and the corresponding experimental values are 3365 and

3474 cm-1 in the FTIR spectrum. A large deviation in N-H stretching

wavenumbers from the corresponding experimental ones is due to the fact that the

three dimensional network of molecule is linked through bifurcated hydrogen

bonds [11] and the calculations are being done for an isolated molecule in gas

phase. The N-H stretching vibrations are pure modes contributing almost 100% to

P.E.D. The NH2 scissoring wavenumber at 1578 cm-1 match with the 1587/1580

cm-1 medium intensity band in FTIR/RAMAN spectra. The rocking modes

calculated at 1254 and 1058 cm-1 has potential contribution from C-N stretching

modes. NH2 wagging mode is calculated at 518 cm-1 and match well with

experimental values. NH2 twisting modes are assigned in the RAMAN spectrum as

weak band at 385 cm-1, the calculated values are at 368 and 357 cm-1.These

85
Figure 3.9: UV-VIS spectra of 5N2FSC

86
Table 3.4. TD-B3LYP singlet excitation energies and their molecular orbital contributions
for 5N2FSC.

TD-B3LYP/6-311++G(d,p)

State Energy (cm-1) Oscillator Strength Contribution

Singlet-A 27957.78928 0.4916 0.99 (H→L)
Singlet-A 33587.57808 0.0013 0.42 (H-6→L)
Singlet-A 33998.92368 0.0038 0.72 (H-1→L)
Singlet-A 34037.63856 0.2191 0.75 (H→L+1)

87
assignments are well in range with the assignments of NH2 group as reported in

literature [25].

3.3.3.7 UV-Vis Spectra

Time dependent density functional theory has been carried out on 5N2FSC to

understand the electronic spectra/ transition in terms of transition energies and their

respective oscillator strengths. We have characterized the electronic transitions

localized under the two broad absorption spectral bands in the spectral region

between 250-290 nm and 350-390 nm [10]. The theoretically calculated UV

spectrum of 5N2FSC is plotted in Figure.3.9which matches well with the

experimental spectra [10].The calculated results involving the vertical excitation

energies their molecular orbital contribution, oscillator strength (f) and wavelength

are reported in Table 3.4 The HOMO lying at -6.77 e. V. is delocalized π orbital

and includes mixing of lone pairs of electrons on all the oxygen as well as nitrogen

atoms. The H-1, 1.16 e.V. below the HOMO is localized over amino group through

the amide bond. The H-6 is 1.03 e.V. below the HOMO and has mainly of π

bonding character along with some sigma bond character, whereas the LUMO

lying at -3.12 eV, is a π* orbital, delocalized over the entire molecule with large

anti-bonding character. From the Table 3.4, it is evident that the absorption band

centered around 290-310 nm arises mainly due to the three electronic transitions

given by H(HOMO)→L(LUMO)+1, H-1→L and H-6→L are assigned as π→

88
π*type, whereas the more intense band around 340-360 nm, having maximum

oscillator strength (0.4916), corresponds to H→L transition and is mainly

characterized as n→ π* type. The higher intensity of band corresponding to the

n→ π* type transition is attributed to the presence of large no of free lone pairs of

electrons available on four oxygen and four nitrogen atoms.

3.4 Conclusion

The equilibrium geometry and harmonic wavenumbers of the molecule under

investigation was determined and analyzed at HF and DFT levels employing the 6-

311++G(d,p) basis set. In general, a good agreement between experimental and

calculated normal modes of vibrations has been observed. Furthermore, it is

interesting to note that although the optimized parameters at HF and DFT are not

much different but the divergence of theoretical wavenumbers from experimental

ones at HF clearly indicates that DFT approach is far superior than HF theory in

the calculation of vibrational spectra. Both the dipole moment (10.55 Debye) and

hyperpolarizabilty (21.2x 10-30e.s.u.) of 5N2FSC is found to be very high. The

polarizabilty of 5N2FSC is calculated to be 145.706/a.u.. The molecular orbitals,

MESP contour/surface drawn and the electronic transitions identified for UV-vis

spectra may lead to the understanding of properties and activity of 5N2FSC and

89
may also help in synthesizing its derivatives with lesser side effects in the

treatment of Chagas disease.

90
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http://www.who.int/tdr/diseases/chagas/ in Dec. 2007.

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1025-1030.

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12. I. Fleming, Frontier Orbitals and Organic Chemical Reactions, John Wiley
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13. J. S. Murray and K. Sen, Molecular Electrostatic Potentials, Concepts and
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154316-5.

22. G. Maroulis, J. Chem. Phys. 129 (2008) 044314-7.

23. J. M. Stout and C. E. Dykstra, J. Am. Chem. Soc. 117 (1995) 5127-5132.

24. M. A. Spackman, J. Chem. Phys. 93 (1989) 7594-7603.

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27. V. Krishnakumar, N. Jayamani, R. Mathammal and K. Parasuraman,
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(1961)600-606.

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and Raman Spectroscopy, Academic Press, New York, London 1964.

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(1988) 1201-1206.

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2526-2532.

93
4.1 Introduction

Benzaldehyde, the simplest representative of the aromatic aldehydes is a key

intermediate for the processing of perfume and flavouring compounds and in the

preparation of certain aniline dyes. Benzaldehyde can have carcinostatic or

antitumor properties [1-3]. Hydroxybenzaldehyde, derivative of benzaldehyde, are

used primarily as chemical intermediates for a variety of products. Out of the

three isomers ortho, para and meta-Hydroxybenzaldehyde, otho-

Hydroxybenzaldehyde (or salicylaldehyde) is used in the manufacture of

coumarin. Coumarin is an important commercial chemical used in soaps,

flavors and fragrances, and electroplating. Recently it has been shown that

the incorporation of the benzaldehyde increases the activity of the benzaldehyde-

thiosemicarbazone which exhibits high anti-trypanosomal potential [4]. Although

much work has been done on benzaldehyde and its derivatives [5-9], however a

comprehensive comparative study of ortho, para and meta- Hydroxybenzaldehyde

on electronic structure, non-linear properties along with the detailed potential

energy distribution of normal modes of vibrations has not been reported so far.

The present chapter is aimed at comparing the molecular structural properties,

vibrational and energetic data of ‘o’-Hydroxybenzaldehyde, ‘p’-

Hydroxybenzaldehyde and ‘m’-Hydroxy-benzaldehyde, in gas phase, due to their

commercial importance. The structure and the ground state energy of the

molecules under investigation has been analyzed employing DFT / B3LYP level.

The optimized geometry and their properties such as equilibrium energy, frontier
94
orbital energy gap, dipole moment and vibrational frequencies along with the

electrostatic potential maps have also been used to understand the activity of the

isomers of Hydroxybenzaldehyde.

4.2 Structure and Spectra:

The optimized molecular structures of ‘o’- Hydroxybenzaldehyde, ‘p’-

Hydroxybenzaldehyde and ‘m’-Hydroxybenzaldehyde are given in fig 4.1. The

theoretically calculated IR spectra have been given in fig 4.2. The calculated IR

spectra of the molecules agree well with the experimental spectral data reported

by the NIST web book [10].

4.3 RESULTS AND DISCUSSION

4.3.1 Molecular geometry optimization and energies:

The structures of ‘o’- Hydroxybenzaldehyde, ‘p’-Hydroxybenzaldehyde and ‘m’-

Hydroxybenzaldehyde have been optimized to compare the variation in electronic

and non-linear properties on substitution of hydroxyl (OH) group at ortho, para

and meta positions. The equilibrium geometry optimization for three isomers has

been achieved by energy minimization, using DFT at the B3LYP level, employing

the split valence basis set 6-311++G(d,p). The optimized molecular structures

with numbering scheme of three molecules are shown in fig.4.1. The ground state

optimized parameters are reported in table 4.1. As the calculated vibrational

spectra have no imaginary frequency, the optimized geometry is confirmed to be

located at the local minima on potential energy surface.

95
Figure-4.1 Optimized structures of (a) ‘o’-Hydroxybenzaldehyde

(b) ‘m’-Hydroxybenzaldehyde (c) ‘p’-Hydroxybenzaldehyde

96
Figure-4.2 Theoretical IR spectra of ortho, meta and para Hydroxybenzaldehyde

97
The C-H/C-C bond lengths vary in the range 1.083 Å-1.086 Å/1.386 Å-1.481 Å,

1.083 Å-1.086 Å/1.391 Å-1.400 Å and 1.083 Å-1.086 Å/1.385 Å-1.402 Å

(standard value 1.10 Å/1.40 Å) in ortho, meta and para Hydroxybenzaldehyde

respectively. The C-O/C=O bond lengths for three molecules are calculated to be

1.365 Å/1.214 Å, 1.366 Å/1.210 Å and 1.360 Å/1.213 Å which are close to

standard value 1.359 Å /1.208 Å [11].

4.3.2 Electronic properties:

The most important orbitals in a molecule are the frontier molecular orbitals,

called highest occupied molecular orbital (HOMO) and lowest unoccupied

molecular orbital (LUMO).These orbitals determine the way the molecule

interacts with other species. The frontier orbital gap helps characterize the

chemical reactivity and kinetic stability of the molecule. A molecule with a small

frontier orbital gap is more polarizable and is generally associated with a high

chemical reactivity, low kinetic stability and is also termed as soft molecule [12].

The frontier orbital gaps of ‘o’-Hydroxybenzaldehyde/ ‘m’-

hydroxybenzaldehyde/‘p’-Hydroxybenzaldehyde are to be 0.17723/0.17229

/0.18304 a.u. which clearly shows that ‘m’-hydroxybenzzaldehyde is most

reactive among the three isomers. The 3D plot of HOMO, LUMO and MESP are

shown in figure 4.3 and fig4.4 respectively. The HOMO in three molecules is

distributed over entire molecule except the carbon and hydrogen atom of aldehyde

group. The LUMO’s show more anti-bonding character than the HOMO’s. The

98
Table 4.1: Parameters corresponding to optimized geometry of Ortho- meta- and para-

Hydroxybenzaldehyde at B3LYP/6-311++G(d,p) level of theory.

Parameter Ortho meta Para

Ground state energy -420.915 -420.916 -420.919

(in Hartree)

Dipole moment 5.0201 4.9101 3.4655

(in Debye)

Frontier orbital energy gap 0.1772 0.1723 0.1830

(in Hartree)

Polarizability/a.u. 88.4153 89.357 90.933

99
oxygen atom of the hydroxyl group contribute to the LUMO, only in case of ‘o’-

Hydroxybenzaldehyde .The importance of MESP is that it shows the size, shape

as well as positive, negative and neutral electrostatic potential in terms of colour

grading. It is also very useful to correlate the molecular structure with its

physiochemical property relationship [13-17]. The MESP in case of ‘o’-

Hydroxybenzaldehyde shows three distinct electron rich sites including the

aromatic ring, the MESP of meta and para show two strong electronegative,

whereas a small negative potential at the aromatic ring site.

4.3.3 Electric Moments :

The dipole moment in a molecule is another important electronic property that

results from non-uniform distribution of charges on the various atoms in a

molecule. It is mainly used to study the intermolecular interactions involving the

van der Waal type dipole-dipole forces, etc., because higher the dipole moment,

stronger will be the intermolecular interactions. The calculated dipole moment for

three molecules is given in table 4.1. Table 4.1 show that the calculated value of

dipole moment in case of ‘o’-Hydroxybenzaldehyde and ‘m’ are nearly equal and

quite higher than ‘p’-Hydroxybenzaldehyde. The determination of electric

polarizability and hyperpolarizability is of basic importance to study the

phenomenon induced by intermolecular interactions, simulation studies and

nonlinear optical effects. The values of polarizability and hyperpolarizability

calculated at the same level of theory and the same basis set for the title

100
Figure-4.3 Homo Lumo orbitals and energy gap of ‘o’, m’ and ‘p’

Hydroxybenzaldehyde

Figure-4.4 MESP map of ‘o’, m’ and ‘p’ Hydroxybenzaldehyde

101
Table 4.2 All β components and βTotal of Hydroxybenzaldehyde at

B3LYP/6-311++G(d,p)

β components Ortho Meta Para

βXXX -149.5 340.2 100.2

βXXY -36.1 -33.4 -31.2

βXYY 90.5 129.6 -98.2

βYYY 216.5 -179.8 864.3

βXXZ 0 0 0

βXYZ 0 0 0

βYYZ 0 0 0

βXZZ -47.7 -14.5 15.8

βYZZ -58.5 -63.1 -4.8

βZZZ 0 0 0

βTOTAL 162.0 532.6 828.5

102
molecules, can provide a reasonable comparison of these quantities, in the absence
of experimental data. Although the mean polarizability of ‘o’, ‘m’- and ‘p’
Hydroxybenzaldehyde is found to be almost same the total intrinsic
hyperpolarizability βTOTAL of para isomer is fairly larger as compared to the other
two counterparts (Table 4.2).

4.3.4 Vibrational Assignments:

The experimental and computed vibrational wave numbers and the detailed

description of each normal mode of vibration of three molecules, carried out in

terms of their contribution to the total potential energy are given in table 4.3, 4.4

and 4.5. The calculated harmonic wavenumbers are usually higher than the

corresponding experimental quantities because of the combination of electron

correlation effects and basis set deficiencies. These discrepancies are taken care of

either by computing anharmonic corrections explicitly or by introducing scalar

field or even by direct scaling of the calculated wavenumbers with a proper

scaling factor [18,19].The vibrational wavenumbers are calibrated accordingly

with scaling factor 0.9679 for DFT at B3LYP.The vibrational assignments have

been done on the basis of relative intensities, line shape, the VEDA 4 program and

the animation option of Gaussview 5.0.

4.3.4.1 C=O and C-O vibrations:

The appearance of a strong band in IR spectra around 1650-1800 cm-1 in aromatic

compound shows the presence of C=O stretching motion. The C=O stretch of

aldehyde group in ‘o’-Hydroxybenzaldehyde/ ‘m’-Hydroxy benzaldehyde/ ‘p’-

Hydroxybenzaldehyde is calculated at to be at 1697/1713 /1703 cm-1 and is

103
assigned well with the experimental IR peak at 1672/1728/1779 cm-1. The other

strong band observed at 1227/1290/1241 cm-1 is due to C-O stretching vibration of

the (C-OH) bond whose general position is 1000-1200 cm-1. This band is

calculated at 1224/1289/1250 cm-1 for ‘o’-hydroxybenzaldehyde/ ‘m’-

hydroxybenzaldehyde/ ‘p’-hydroxybenzaldehyde.

4.3.4.2 OH vibrations:
The strong band calculated at 3710 /3711/3705 cm-1 in IR spectra of ‘o’-

hydroxybenzaldehyde/ ‘m’-hydroxybenzaldehyde/ ‘p’-hydroxybenzaldehyde

shows the presence of OH group. These bands contribute 100% to the total PED

(experimental value 3892/3202 for ‘o’-hydroxybenzaldehyde/ ‘m’-

hydroxybenzaldehyde). The small discrepancy between the calculated and the

observed wavenumber may be due to the intermolecular hydrogen bond. The

bands observed at 1178, 1149/1290,1178,1155/1520 cm-1 in IR spectra of ‘o’-

hydroxybenzaldehyde/ ‘m’-hydroxybenzaldehyde/ ‘p’-hydroxybenzaldehyde are

due to H-O-C in-plane bending and are calculated at

1183,1150/1284,1164,1147/1490 cm-1 as mixed modes.

4.3.4.3 Ring modes:

The phenyl ring spectral region predominantly involves the C-H, C-C and C=C

stretching, and C-C-C, H-C-C and bending vibrations. Very intense band are

found in the range 3100-3000 cm-1 which is, in general, observed in the case of

aromatic compounds due to aromatic C-H stretching vibrations. The C-C

stretching modes are observed as mixed modes in the wavenumber range 1600-

104
 Table-4.3 Theoretical and Experimental wave-numbers (in cm-1) of ‘o’-
Hydroxybenzaldehyde

Calc. unsc. Calc. sc. *Exp. Assignment of dominant modes in order of decreasing potential energy
wave no. wave no. Wave distribution (PED)
no.
3833 3710 3892 ν(O7-H14)(100)
3198 3095 ν(C1-H10)(52)+ν(C2-H11)(37)+ν(C3-H11)(11)
3187 3085 ν(C2-H11)(54)+ν(C3-H12)(31)+ν(C1-H10)(13)
3176 3074 3074 ν(C3-H12)(49)+ν(C1-H10)(35)+ν(C2-H11)(10)
3152 3051 ν(C4-H13)(90)
2972 2877 2847 ν(C8-H15)(100)
1753 1697 1672 ν(C8-O9)(87)
1644 1591 1580 ν(C4-C5)(36)+ν(C2-C1)(22)
1627 ν(C3-C1)(26)+ν(C6-C2)(14)+β(C6-C2-C1)(10)+β(C3-C1-C2)(11)+
1575 1551 β(C5-C4-C3)(10)
1520 1471 1488 β(H10-C1-C2)(17)+β(H11-C2-C6)(18)+β(H13-C4-C5)(24)
1488 1440 1459 ν(C6-C20)(12)+β(H10-C1-C3)(20)+β(H12-C4-C5)(21)
1430 1384 1381 β(H15-C8-O9)(81)
1357 1313 1323 ν(C2-C1)(20)+ν(C4-C3)(18)+β(H14-C7—C5)(20)+β(H11-C2-C6)(12)
1328 1285 1280 ν(C6-C2)(16)+β(H11-C2-C6)(15)+β(H13-C4-C5)(12)
1265 1224 1227 ν(C6-C2)(16)+ν(O7-C5)(38)
1222 ν(C2-C1)(17)+ν(C8-C6)(30)+β(C6-C2-C1)(11)+β(H14-O7-C5)(15)+
1183 1178 β(H10-C1-C2)(12)
1188 1150 1149 β(H12-C3-C1)(11)+ν(C5-C4)(10)+β(H14-O7-C5)(27)+β(H13-C4-C5)(25)
1181 1143 1115 β(H13-C4-C5)(12)+β(H10-C1-C3)(24)+β(H11-C2-C6)(13)+β(H12-C3-C4)(30)
1107 ν(C5-C4)(11)+β(C6-C2-C1)(18)+β(H14-C7-C5)(10)+β(H10-C1-C3)(11)
1071 +β(H12-C3-C4)(12)
1058 1024 1033 ν(C4-C3)(14)+ν(C3-C1)(40)+β(H11-C2-C6)(12)+β(H133-C4-C5)(20)
1028 995 1009 ω(C-H)ring(80)
993 961 980 ω(C-H)ring(91)
960 929 946 ω(C-H)ring (85)+ρ(C5-C4-C3-C1)(12)
856 828 883 ν(O7-C5)(16)+ν(O8-C6)(14)+β(C3-C1-C2)(24)+β(C5-C4-C3)(10)
851 824 859 ω(C-H)ring (76)+ρ(C5-C4-C3-C1)(10)
815 789 ν(C6-C2)(11)+β(C6-C2-C1)(10)+β(O9-C8-C6)(21)+β(C3-C1-C2)(10)
765 740 757 ρ(H10-C1-C3-C4)(34)+ρ(H12-C3-C4-C5)(27)+ρ(H13-C4-C5-C6)(19)
701 ρ(H13-C4-C5-C6)(13)+ρ(C5-C4-C3-C1)(18)+ρ(C6-C2-C3-C1)(19)+
678 665 ρ(O7-C5-C6-C8)(23)
641 620 641 β(O9-C8-C6)(23)+β(C4-C3-C1)(34)+β(C5-C4-C3)(17)
556 538 ν(C7-C5)(13)+β(O9-C8-C6)(25)+β(C5-C4-C3)(16)+β(07-C5-C4)(19)
534 517 ρ(C6-C2-C1-C3)(28)+ρ(O7-C5-C4-C3)(18)+ρ(O7-C5-C6-C6)(19)

105
 Table–4.4 Theoretical and Experimental wave-numbers (in cm-1) of
‘m’-Hydroxybenzaldehyde

Calc. Calc. sc. *Exp. Assignment of dominant modes in order of decreasing potential energy
unsc. wave no. wave distribution (PED)
wave no. no.
3834 3711 3203 ν(O4-H12)(100)
3203 3100 2973 ν(C3-H11)(99)
3189 3087 ν(C8-H15)(75)+ν(C6-H13)(15)+ν(C2-H10)(10)
3170 3068 ν(C6-H13)(79)+ν(C8-H15)(17)
3153 3052 ν(C2-H10)(91)
2893 2800 2737 ν(C7-H14)(99)
1770 1713 1728 ν(C7-O9)(89)
1648 1595 ν(C1-C3)(36)+ν(C6-C8)(10)+ν(C8-C2)(10)+β(H12-O4-C1)(15)
1627 1574 1584 ν(C8-C2)(18)+ν(C6-C5)(30)+β(C2-C8-C6)(11)+β(C1-C3-C5)(10)
1513 1464 1504 β(H11-C3-C5)(14)+β(H13-C6-C5)(16)+β(H15-C8-C6)(27)
1501 1452 ν(C1-C3)(11)+ν(C8-C6)(11)+ν(C5-C3)(18)+β(H10-C2-C8)(17)
1419 1373 1365 β(H14-C7-O9)(78)
1361 1317 ν(C1-C3)(13)+ν(C2-C8)(20)+ν(C8-C2)(18)+ν(C5-C3)(21)
1327 ν(O4-C1)(11)+β(C2-C8-C6)(10)+β(H12-C4-C1)(17)+β(H10-C2-C8)(17)
1284 1290 +β(H11-C3-C5)(11)+β(H13-C6-C8)(20)
1285 1244 1250 ν(C6-H5)(11)+ν(C4-C1)(24)+β(H11-C3-C5)(11)+β(H13-C6-C8)(12)
1203 1164 1178 ν(C1-C3)(13)+β(H12-O4-C1)(38)+β(H15-C8-C6)(29)
1185 1147 1155 ν(C8-C6)(10)+β(H12-O4-C1)(19)+β(H10-C2-C8)(23)+β(H15-C8-C6)(18)
1153 1116 ν(O4-C1)(12)+ν(C7-C5)(23)+β(H11-C3-C5)(31)+β(H13-C6-C8)(13)
1108 1072 1086 ν(C8-C6)(12)+ν(C8-C2)(23)+β(H13-C6-C8)(31)+β(H10-C2-C8)(13)
1023 990 1000 ω(C-H)ring(65)+ρ(O9-C7-C5-C3)(32)
1012 β(C6-C5-C3)(32)+β(C6-C8-C2)(13)+β(C2-C1-C3)(14)+ν(C1-C3)(14)+
980 ν(C6-C5)(10)
979 948 948 β(C8-C6-C5)(17)+ν(C7-C5)(15)+ν(O4-C1)(13)+β(H11-C3 C5)(11)
964 933 897 ω(C-H)ring(72)+ ρ(C2-C8-C6-C5)(13)
906 877 874 ω(C-H)ring(71)
883 855 ω(C-H)ring(89)
778 753 782 ρ(H15-C8-C6-C5)(28)+ρ(H10-C2-C8-C6)(25)+ρ(H13-C6-C8-C2)(21)
764 739 707 β(C8-C6-C5)(25) +β(O9-C7-C5)(15)+ ν(O4-C1)(10)
662 641 656 ρ(C1-C2-C3-C6)(29)+ρ(C2-C8-C6-C5)(29)+ρ(C6-C8-C5-C3)(18)
657 636 β(C6-C5-C3)(36)+ β(C2-C8-C6)(29)+β(O9-C7-C5)(18)
555 537 ρ(O4-C1-C2-H10)(54)+ρ(C3-C5-C7-O9)(18)
540 523 β(C5-C6-C8)(42)+ β(C2-C1-C3)(33)
457 442 β(C7-C5-C6)(39)+ β(O4-C1-C2)(37)

106
Table-4.5 Theoretical and Experimental wave-numbers (in cm-1) of
‘p’-Hydroxybenzaldehyde

Calc. Calc. * Exp. Assignment of dominant modes in order of decreasing potential energy
unsc. sc. wave distribution (PED)
wave wave no.
no. no.
3828 3705 ν(O8-H15)(100)
3199 3096 ν(C1-H10)(94)
3194 3091 ν(C5-H12)(95)
3163 3061 ν(C3-H12)(95)
3153 3052 3047 ν(C7-H14)(96)
2884 2791 ν(C6-H13)(99)
1759 1703 1779 ν(O9-C6)(85)
1642 1589 1596 ν(C5-H7)(30)+ν(C1-C2)(20)
1625 1573 ν(C1-C2)(25)+ν(C4-C3)(22)
1539 β(H11-C3-C4)(14)+β(H12-C5-C7)(14)+β(H15-O8-C2)(12)+β(H14-C7-C5)(17)
1490 1520 +β(C1-C2-C7)(13)
1470 1423 1419 ν(C3-C1)(15)+ν(C5-C7)(11)+β(H10-C1-C3)(12)
1418 1372 1388 β(H13-C6-O9)(73)
1372 ν(C3-C1)(12)+ν(C5-C7)(19)+ν(C4-C3)(12)+ν(C7-C2)(13)+β(H15-O8-C2)(20)
1328 1317 +β(H11-C3-C4)(10)
1328 1285 1287 ν(C4-C3)(12)+β(H11-C3-C4)(17)+β(H12-C5-C7)(17)+β(H14-C7-C5)(16)
1291 1250 1241 ν(C2-O8)(52)+ν(C3-C1)(10)
1233 1193 1216 ν(C6-C4)(32)+ β(H10-C1-C3)(12)+ β(C4 –C3-C1)(10)
1193 1155 1165 β(H15-O8-C2)(55)+ β(H14-C7-C5)(13)+ν(C7-C2)(12)
1177 1139 β(H10-C1-C3)(19)+ β(H11-C3-C4)(19)+ β(H12-C5-C7)(20)
1123 ν(C3-C1)(14)+ν(C5-C7)(10)+ β(H10-C1-C3)(18)+ β(H11-C3-C4)(12)+
1087 1109 β(H12-C5-C7)(21)+ β(H14-C7-C5)(12)
1024 991 ρ(H13-C6-C4-C3)(74)+ρ(O9-C6-C4-C3)(10)
1023 990 β(C3-C1-C2)(41)+β(C4-C5-C7)(39)
979 948 ω(C-H)ring(84)
951 920 ω(C-H)ring(63)+ρ(C4-C3-C1-C2)(15)
865 837 835 β(C1-C2-C7)(19)+β(C4-C5-C7)(19)+ν(C4-C5)(18)
836 809 785 ω(C-H)ring(88)
828 801 719 ω(C-H)ring(80)
794 769 ν(C8-C2)(15)+β(O9-C6-C4)(18)+β(C1-C2-C7)(10)+β(C4-C3-C1)(25)
690 ρ(C3-C1-C2-C7)(12)+ ρ(C5-C7-C2-C1)(16)+ ρ(C4-C3-C2-C1)(34)+
668 ρ(O8-C2-C7-C5)(16)
653 632 648 β(C2-C1-C3)(32)+β(C4-C5-C7)(40)
614 594 602 β(C5-C7-C2)(11)+β(O9-C6-C4)(37)+β(C1-C2-C7)(11)
513 497 511 ρ(H11-C3-C4-C5)(12)+ρ(C3-C1-C2-C7)(11)+ρ(O8-C2-C1-C3)(41)

Note : Abbreviations used here have following meaning- : stretching; β: in plane bending; ρ :
torsion; ω: wagging.

107
cm-1 to 1000 cm-1 for three molecules and are in good agreement with general

appearance of C-C stretching modes. The modes appearing below 1000 cm-1 are

mixed modes. The torsional modes appear in general in the low wavenumber

regions.

4.4 Conclusion

In the present work we have calculated the geometric parameters, the vibrational

frequencies, frontier orbital band gap, MESP surfaces and the non-linear optical

properties of ‘o’, ‘m’ and ‘p’ Hydroxybenzaldehyde using DFT/ B3LYP method.

The higher frontier orbital energy gap and the lower dipole moment values make

the ‘p’-Hydroxybenzaldehyde less reactive and less polar, hence most stable

among the three isomers. A good agreement between experimental and calculated

normal modes of vibrations has been observed.

NLO behavior of the title molecules were investigated by the determination of the

polarizability and the first hyperpolarizability using the DFT/B3LYP/6-311G(d,p)

method. The polarizability values are almost the same but the para isomer has

significantly higher values for the total hyperpolarizability.

108
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110
5.1 Introduction
Benzothiazoles and its derivatives are heterocyclic chemicals that contain a

benzene ring fused with a thiazole ring. Thiazoles are one of the most rigorously

investigated classes of aromatic five membered hetrocycles and find a variety of

applications in the treatment of allergies, inflammation, hypnotics, bacterial

and HIV infections [1-5]. Benzothiazole, together with 2(3H)-Benzothiazolone

(HBT), is produced as a by-product from the industrial production of rubber

vulcanization accelerators [6] and is used as a pesticide [7]. Both compounds

are present in antifreeze [8] to which they could have been added as corrosion

inhibitors or by leaching out from the rubber hoses in cooling systems [9].

These are released into the environment by various industrial applications and

their presence can be detected in various environmental and other types of

samples. Currently, there is a rising interest in the studies of this class of

compounds especially since the pharmacological profile of one of its derivative,

as a Glutamate neurotransmission inhibitor was discovered [10-14]. Recently

nonlinear optical properties of a series of benzothiazole derivatives have also

been studied [15-16]. A comprehensive study and better knowledge of the

structural properties and spectroscopic profile of benzothiazoles and its

derivatives is crucial and can assist significantly to get major advances in their

diverse applications and the help lessen the environmental harm. The present

chapter deals with the investigation of the structural, electronic and

spectroscopic investigation of monomeric and dimeric form of 2(3H)-

111
Benzothiazolone with the long term objective of gain a better insight of such

compounds.

5.2 Experimental

The pure single crystal of the HBT was obtained from TCI chemicals, and was

used as such for the spectroscopic measurements. The FTIR spectra was

recorded on Brucker spectrophotometer in the wavenumber range 4000–400

cm- 1
with the spectral resolution of 4 cm-1. The pellet in solid phase was

prepared using 10 mg of the sample in the fine powder form with KBr. The UV

absorption spectra of HBT were examined in the range 200–600 nm using the

Hewlett Packard 8453 UV-VIS spectrophotometer. These spectroscopic

investigations were performed at I.I.T, Kanpur, India.

5.3 Results and Discussion

5.3.1 Molecular Geometry

The compound can occur in two tautomeric forms, the thiol and keto forms

[Fig. 5.2]. It has been reported that in solution as well as in the crystalline state,

the equilibrium is almost completely on the keto side of 2-benzothiazolone [17].

112
Figure: 5.1 Optimized dimer of HBT at MP2 level.

Figure: 5.2: Tautomeric forms of 2(3H)-Benzothiazolone (HBT).

113
Table 5.1: Parameter corresponding to optimized geometry at B3LYP
and MP2 level of theory for HBT

B3LYP MP2
Parameters 6-311+G(d,p) 6-311+G(d,p)

Monomer

Ground state energy (in Hartree) -798.08320 -796.41129

Frontier orbital energy gap (in

0.19925 0.26533
Hartree)

Dipole moment (in Debye) 4.1119 4.7402

Polarizabilitya in a.u. 108.453 -

Dimer
Parameters B3LYP MP2
6-311+G(d,p) 6-311+G(d,p)

Counterpoise: corrected energy (in -1596.18918 -1592.84647

Hartree)
Counterpoise: BSSE energy (in 0.00113 0.00517
Hartree)
Interaction Energy 0.015769/ 0.026272/
(in Hartree/ in kcal/mol) 9.8952 16.48593

a
In atomic units. Conversion factor to the SI units,

1e2 a o2 E h-1 = 1.648778 x 10-41 C2 m2 J

114
Table 5.2: The optimized geometric parameters of HBT and comparison with experimental results, bond lengths in
angstrom (A˚), bond angles
* T. Henryk, Flakus, A.Miros, P. G. Jones, J. Mol. Struc, 604 (2002) 29-44.

Definition B3LYP MP2 Exp.* Definition B3LYP MP2 Exp.

Monomer Dimer Monomer Dimer Monomer Dimer Monomer Dimer
C1-C3 1.392 1.393 1.397 1.398 1.358 C5-C6-H14 119.9 119.9 119.8 119.7 119.5
C3-H11 1.085 1.083 1.087 1.086 0.949 H14-C6-C7 119.5 119.5 119.5 119.4 119.5
C3-C5 1.394 1.394 1.398 1.397 1.391 C6-C7-H15 120.6 120.7 120.8 120.8 120.9
C5-H13 1.085 1.084 1.086 1.086 0.949 H15-C7-C2 120.5 120.7 120.4 120.6 120.8
C5-C6 1.395 1.397 1.404 1.405 1.397 C3-C1-N4 127.0 126.6 127.0 126.6 126.7
C6-H14 1.085 1.084 1.086 1.086 0.950 C9-N4-C1 117.8 116.7 117.2 116.3 116.1
C6-C7 1.395 1.395 1.398 1.398 1.384 N4-C1-C2 112.3 112.7 111.8 112.2 112.4
C7-H15 1.085 1.084 1.086 1.086 0.950 C1-C2-S8 111.2 110.7 111.2 110.8 110.7
C7-C2 1.389 1.390 1.398 1.399 1.392
C2-S8 1.767 1.767 1.750 1.749 1.748 C3-C1-C2-C7 0.0 0.0 0.0 0.2 0.5
C2-C1 1.404 1.403 1.407 1.407 1.401 C3-C1-C2-S8 180.0 180.0 179.9 179.9 179.1
C1-N4 1.390 1.390 1.388 1.387 1.391 N4-C1-C2-C7 180.0 180.0 179.9 179.8 179.6
N4-H12 1.009 1.028 1.012 1.028 0.802 C2-C1-C3-C5 0.0 0.0 0.0 0.1 0.4
N4-C9 1.379 1.362 1.382 1.366 1.358 C3-C1-N4-C9 180.0 180.0 179.9 179.9
C9-O10 1.201 1.221 1.211 1.227 1.227 C1-C2-C7-C6 0.0 0.0 0.0 0.2 0.3
C9-S8 1.825 1.806 1.798 1.786 1.776 C2-S8-C9-N4 0.0 0.0 0.0 0.0 1.1
C7-C2-S8-C9 180.0 180.0 179.9 179.8 179.4
C1-C3-C5 118.5 118.4 118.4 118.2 118.3
C3-C5-C6 120.8 121.0 120.7 120.8 120.8
C5-C6-C7 120.5 120.6 120.7 120.8 121.0
C6-C7-C2 118.8 118.6 118.7 118.5 118.4
C7-C2-C1 120.4 120.7 120.3 120.4 120.6 Intermolecular H bond lengths
C2-C1-C3 120.7 120.7 121.0 121.1 120.9 O-------H 1.854 1.870 2.030
C1-C3-H11 120.6 120.4 120.6 120.3 120.8 N-------O 2.872 2.890 2.833
H11-C3-C5 120.8 121.2 121.0 121.4 120.9
C3-C5-H13 119.3 119.3 119.4 119.3 119.6
H13-C5-C6 119.9 119.7 119.8 119.7 119.7

115
The analysis of the two possible tautomers was carried out using the density

functional theory and employing the 6-311+G(d) basis set. The present

calculations show that in gas phase the keto conformer (HBT) is lower in energy

from thiol form by 0.01965 Hartree and hence used for theoretical

investigations. HBT consists of a 5-membered 1,3-thiazole ring fused to a benzene

ring with C=O group in between the nitrogen and sulphur atoms of the thiazole

ring. The skeleton of the molecule is planer. The C-C bond lengths in the benzene

ring vary in the range 1.389–1.395 Å, except C1-C2 at the largest 1.404 Å value

which is due to the fusion of heterocyclic ring. The C-H bond lengths are found at

constant value of 1.085 Å. The C=O bond lengths at 1.200 Å lie within the

standard range 1.196 to 1.211 Å [18]. The C2–S8 bond length is calculated to be

1.767 Å, which is close to the typical C-S bond distance for benzothiazoles [19],

while C9-S8 bond (1.825 Å) is larger than the average distance for C-S single

bond due to the electronegative oxygen atom attached to C9. The C1-C3-C5 and

C2-C7-C6 angles both involving a common C atom of the two fused rings are

reduced at 118.5 and 118.8 while all other C-C-C angle of the benzene ring are

between 120-121 [Table5.2].

In crystal structure the molecules are linked in centro-symmetric dimers by N-

HO hydrogen bond [20]. Optimized molecular structure of hydrogen-bonded

dimer is shown in Fig. 1. The counterpoise corrected energy for the HBT dimer

structure calculated by the MP2/B3LYP method is -1592.84647/-1596.18918

116
Hartree, respectively. Novoa and Sosa [21] have shown that density functional

theory is not a good model for the study of the energetics of hydrogen-bonded

systems. Our results are in line with Novoa and sosa [21] as the interaction energy

provided by the DFT/B3LYP method is (9.8952 kcal/mol) about 60% smaller than

the value, which is obtained using the MP2 method (16.4859 kcal/mol). The

counterpoise corrected interaction energy is calculated for the HBT dimer by

taking the energy difference between the fragments and the super-molecule. The

large value of interaction energy shows that the H-bonds in the super-system are

strong.

As interaction energy corresponds to two hydrogen bonding interactions and both

hydrogen bonds are equivalent due to the formation centrosymmetric dimer, the

interaction energy should be divided by 2 to have the hydrogen bond strength. The

strength of a H-bond may also be found from the elongation of dX-H (X=O, N or

F) and the red shifts of υXH. The OH distance in hydrogen bonded dimer is

found to be 1.854 Å. The N–H and C=O distances involved in the hydrogen

bonds are lengthened by 0.016 and 0.018Å respectively upon dimerization. The

N-HO angle is calculated to be 170.7 while C=OH angle is 123.4. The

bond lengths and angles mentioned here corresponds to the MP2 calculations.

5.3.2 UV–VIS Studies and Electronic Properties

On the basis of a fully optimized ground-state structure, the TD-DFT method has

been used to determine the low-lying excited states of HBT. The calculations

involving the vertical excitation energies, oscillator strength (f) and wavelength
117
have been carried out and compared with experimental data (Table 5.3). The

calculation predicts one sharp electronic transition at 219.71 (oscillator strength f

= 0.1452)/ 219.77 nm (oscillator strength f =0.1757) in ethanol and chloroform

respectively, in good agreement with the measured experimental data (λexp. = 210

nm in ethanol and 216 nm in chloroform) as shown in Figure 5.3. This electronic

absorption corresponds to the transition from Molecular orbital (MO) 38→40,

where the highest occupied molecular orbital (HOMO) is the molecular orbital 39

and the lowest unoccupied molecular orbital (LUMO) is MO no. 40.

This transition is assigned as π → π* type. The HOMO lying at −6.45944 eV is

distributed over the entire molecule whereas LUMO lies largely over the benzene

ring and slightly over rest of the molecule except the nitrogen atom. The atomic

orbital compositions of the frontier molecular orbital are sketched in Figure.5.4.

From Table 5.3, it is evident that the experimentally measured broad region

around 254 nm in chloroform arises primarily due to the electronic transitions

given by HOMO → LUMO and reflects the transfer of electron cloud mainly

from nitrogen and sulphur atoms of penta-ring to the benzene ring and is also

assigned as π → π* type, the corresponding transition in ethanol is at 245 nm.

The 3D plot of the molecular electrostatic potential map (MESP) surface for the

HBT is shown in Figure.5.5. The MESP [22-28] contains information about the

entire electronic constitute of the molecule and defines regions of nucleophilicity

and electrophilicity on the molecular surface and has been plotted for HBT.

118
Figure: 5.3 : Experimental and simulated UV absorption spectra of HBT.

119
 Table 5.3: Experimental and calculated absorption spectral values
Experimental TD-DFT/B3LYP/6-311++G(d,p)
λ (nm) E (eV) Abs. λ (nm) E (eV) f
Ethanol
297.00 4.1745 4.11
245.00 5.0605 2.33 259.53 (39→40) 4.7773 0.0706
250.20 (39→42) 4.9554 0.0002
240.67 (39→41) 5.1516 0.0521
223.15 (38→42) 5.5561 0.0016
220.05 (39→43) 5.6342 0.0029
210.00 5.9040 2.36 219.71 (38→40) 5.6430 0.1452
Chloroform
316.00 3.9235 3.60
254.00 4.8812 3.75 260.74 (39→40) 4.7550 0.0816
251.04 (39→42) 4.9387 0.0003
241.09 (39→41) 5.1427 0.0481
223.38 (38→42) 5.5503 0.0017
216.00 5.7400 2.30 219.98(38→40) 5.6362 0.1757
219.77 (39→43) 5.6416 0.0026
Gas
263.13 (39→40) 4.7118 0.0594
254.28 (39→42) 4.8760 0.0004
241.36 (39→41) 5.1369 0.0231
225.97 (39→43) 5.4868 0.0010
220.25 (38→42) 5.6293 0.0007
218.13 (38→40) 0.1194 0.0066

Table 5. 4 All βb components and β total of HBT at B3LYP/6-311+G(d,p)

βXXX 410.1
βXXY -24.6
βXYY 23.7
βYYY 6
βXXZ 0.05
βXYZ 0
βYYZ 0.02
βXZZ 68.6
βYZZ -39
βZZZ 0
βTOTAL 505.7

b
In atomic units. Conversion factor to the SI units-
1e3a03Eh-2= 3.206 361 × 10-53C3 m3 J-2

120
 Table 5.5: Theoretical and experimental wave numbers (in cm-1) of HBT
Experimental Calculated B3LYP Assignment of dominant mode in order of decreasing
FTIR potential energy distribution (PED)
Monomer Dimer IR Intensity
scaled scaled
3308 3504 3198, 3162 61.28 ν(N-H)P(100)
3155 overtone + combination
3110 3097 3096, 3096 9.26 νS(C-H)R(95)
- 3088 3088,3088 10.37 νas(C-H)R(98)
- 3079 3081,3081 4.16 νas(C-H)R(97)
3058 3071 3072,3072 1.33 νas(C-H)R(96)
1663 1737 1684,1684 928.59 ν(C=O)P(85)
1590 1585 1586,1586 14.71 ν(C-C)R(54)+ β(H-C-C)R(16)+ β(H12-N4-C9)P(14)
1580 1569 1571,1570 3.46 ν(C-C)R(44)+ β(H12-N4-C1)P(20)
1478 1456 1474,1473 10.72 β(H-C-C)R(26)+ β(H12-N4-C9)P(13)+ ν(C-C)R(11)
1463 1450 1450,1450 61.48 β(H-C-C)R(52)+ ν(C1-C2)(12)
1414 1376 1411,1408 23.04 ν(C1-N4)P(39)+ β(H-C-C)R(20)
1305 1293 1298,1297 11.29 ν(C-C)R(70)+ β(H-C-C)R(12)
1285 1251 1259,1256 9.33 β(H-C-C)R(34)+ β(C9-N4-C1)P(20) )+ ν(C-C)R(10)
1215 1220 1250,1253 10.01 ν(C1-N4)P(33)+ β(C-C-C)R(23)+ β(H-C-C)R(16)
1150 1148 1184,1191 28.81 β(H-C-C)R(47)+ ν(C9-N4)P(24)
1123 1138 1146,1146 91.89 ν(C9-N4)P(47)+ β(O10-C9-S8)P(12)+ β(H-C-C)R(11)
- 1112 1113,1112 13.23 β(H-C-C)R(38)+ ν(C2-S8)(26)
1070 1042 1045,1046 2.64 β(C-C-C)R(31)+ ν(C2-S8)P(16)+ β(H-C-C)R(14)
1017 1010 1009,1009 9.25 Phenyl ring breathing (71)
966 950 954,954 0.00 ω(C-H) R (77)
930 908 912,912 1.81 ω(C-H) R (65)
898 870 877,882 4.77 Trigoanl phenyl ring bending (68)
850 827 831,832 0.69 ω(C-H) R (76)
771 728 802,764 76.99 ω(C-H) R (83)
745 690 732,732 2.84 β(C-C-C)R(52)+ ν(C2-S8)P(23)
707 689 692,692 5.50 ρ(C-C-C-C)R(48)+ ρ(S8-C2-C1-N4)P(18)
700 659 691,691 8.85 β(C-C-C)R(32)+ ν(C9-S8)P(23)
641 614 673,679 14.47 βOUT(S8-C9-N4)(46) +βOUT(O10-C9-S8)(31)
629 614 628,626 40.25 β(O10-C9-S8)P(30)+ ν(C9-S8)P(23)
- 534 611,615 7.36 ρ(C-C-C-C)R(48)+ ρ(C2-C1-N4-H12)(16)
494 478 532,532 3.46 β(C2-S8-C9)P(34)+ β(C3-C1-N4)(32)
488 472 483,484 85.71 ω(N-H) P (78)
442 466 476,480 2.45 β(S8-C9-N4)P(42)+ β(C-C-C)R(19)
Abbreviation: ν- stretching; νs- symmetric stretching; νas- asymmetric stretching; β-in plane bending; ρ- torsion; βOUT - out of plane bending; ω – wagging.

121
Figure 5.4: Patterns of the principle highest occupied and lowest unoccupied
molecular orbitals of HBT obtained with TD-DFT method in
vacuum.

Figure: 5.5 3D MESP surface and 2D contour map of HBT.

122
An approaching electrophile/nucleophile will initially be attracted to those regions

in which potential is negative/positive and particularly to the points with most

negative/positive values. The MESP of HBT shows clearly the three major

negative potential regions around oxygen atom of carbonyl group (represented

by red colour), around sulphur atom of the heterocyclic ring and around the

central region of benzene ring characterized by yellow colour.

All H atoms bear the brunt of positive potential (blue colour). The sliced 2D

MESP contour map plotted in Fig. 5.5 provides complete information concerning

molecular electrostatic potential distribution, by showing the values in a manifold

of spatial position around the molecule. The 2D contour map drawn in the

molecular plane reveals maximum values of positive potential and negative

potential corresponding to the electrophilic and nucleophilic region and are 0.4

a.u. and 0.04 a.u. respectively.

5.3.3 Electric Moments

The calculated value of dipole moment for HBT by B3LYP/MP2 method is found

to be 4.1119/4.7402 Debye. The mean polarizability is calculated to be 123.715

a.u.(B3LYP). The high value of dipole moment and polarizability is also reflected

from the MESP surface as the more red/blue colour difference, the more polar is

the molecule. This is also in line with the small frontier orbital gap of HBT as

from second-order perturbation theory it follows that a small gap between

occupied and unoccupied orbitals will give a large contribution to the

polarizability [29], i.e. softness is a measure of how easily the electron density can
123
be distorted by external fields, generated by nearby molecules. The thiazole ring

has long been recognised as a potential candidate in nonlinear optics (NLO). The

first static hyperpolarizability β value is calculated to be 505.7 a.u. (or 4.4 x 10-30

e.s.u.) [Refer to Table 5.4], which is almost 23 times higher than that of urea. Urea

is the classical molecule used in the study of the NLO properties of the molecular

systems and is used often as a threshold value for comparative purposes. The large

β value calculated by the B3LYP method confirms that the studied compound is a

potential NLO material. The theoretical calculation of β components is very useful

as this clearly indicates the direction of charge delocalization. The largest βxxx

value indicates charge delocalization is along the bond axis and the involvement

of σ orbitals in intra-molecular charge transfer process.

5.3.4 Vibrational analysis

The experimental and computed vibrational wave numbers, their IR intensities

and the detailed description of normal modes of vibration of HBT, carried out in

terms of their contribution to the potential energy are given in Table 5. The

experimental FT-IR and theoretical IR spectra have been shown in Figure.5.6.

Comparison of calculated wavenumbers at B3LYP/6-311+G(d,p) level with

experimental values reveals an overestimation of the vibrational wavenumbers

due to neglect of the anharmonicity present in the actual system. For complete

vibrational analysis the vibrational modes are discussed under four heads - (i)

Phenyl ring vibration (ii) N-H group vibration (iii) C=O group vibration (iv) C-

S vibration.
124
Figure: 5.6 Comparison of Experimental FT-IR and Theoretical (DFT)
wavenumbers for monomer and dimer of HBT.

125
5.3.4.1 Phenyl ring vibration –

The phenyl ring spectral region chiefly involves the C–H, C–C stretching, and C–

C–C as well as H–C–C–bending vibrations. The bands due to the ring C–H

stretching vibrations are observed as a collection of weak-to-moderate bands in

the region 3100–3000 cm−1. The calculated wavenumber for the CH-stretching

modes are found in the range 3097–3071 cm−1 and have been matched with the

experimental FTIR spectra. The in-plane C-H bending vibrations of aromatic

compounds classically occur in the region 1150–950 cm-1 [30] but are not

considered as investigative for many compounds because of inconsistency and

overlap with other functional group absorptions, including some skeletal

(backbone) vibrations. The aromatic C–H in-plane bending modes of benzene and

its derivatives are observed in the region 1300–1000 cm−1 [31]. In the case of HBT

vibrations involving C-H in-plane bending are found throughout the region 1585–

1042 cm−1. Due to the fused thiazole ring, benzene ring breathing and trigonal

bending modes are modified and are computed at 1010 and 870 cm−1. These are

matched well with experimentally observed bands at 1012 cm−1 and 898 cm−1

respectively in FTIR spectra. The C–H wagging mode starts appearing from 950

cm−1 and has contributions up to 728 cm−1 and are assigned well in the spectra.

The torsional modes appear in general in the low-wave-number regions. In the

present case, the calculated normal modes below 700 cm−1 wavenumbers are

mainly the torsional modes.

126
5.3.4.2 N-H group vibration-
The intermolecular hydrogen bonding is simply revealed in the deviation of

theoretical wave-numbers of N- H stretching modes. For heterocyclic compounds

containing an N-H group, an N-H stretching band is observed in the 3500-3200

cm−1 region, the position of which depends upon the degree of hydrogen bonding.

The hydrogen-bonded N-H stretching is calculated at 3504 cm−1 while the

corresponding observed mode is at 3320 cm−1. The N-H stretch of HBT dimer is

calculated at 3198, 3162 cm−1, more closer to the experimental value [Fig.5.7]. A

weaker band at 3160 cm−1 in FT-IR is a Fermi resonance-enhanced overtone of

the 1580 cm−1 band [32,33]. The N-H in-plane bending vibrations are calculated at

1585, 1569, 1456 cm−1 and match well with the experimental FT-IR peaks. The

out-of-plane NH wag assigned at 472 cm−1 theoretically and is observed at 486

cm−1 experimentally.

5.3.4.3 C=O group vibrations

The appearance of strong bands in the FT-IR around 1800 – 1650 cm-1 in aromatic

compounds shows the presence of carbonyl group and is due to the C=O-

stretching motion. Formation of hydrogen bonding lowers the bond strength and

thus ν (C=O) absorption occur at lower wavenumbers. The strong band in the FT-

IR spectra at 1673 cm-1 is due to C=O-stretching vibrations while the calculated

value for monomer shows a positive deviation of 64 cm-1 and is calculated at 1737

cm-1, the corresponding mode in case of dimer is nearer the experimental value.

127
The dominant in-plane C=O-bending vibrations in the case of HBT is calculated at

614 cm-1 in complete conformity with Rastogi et. al. [33].

5.3.4.4 C-S stretching vibration

Since HBT contains thiazole moiety having two hetero atoms and the conjugated -

C=C-N=C- system, vibrations of these hetero atoms are themselves influenced

and modified. The stretching vibration assigned to the C-S linkage occurs in the

region 700- 600 cm-1 [34]. For HBT C-S stretching has been calculated as mixed

mode at 1112, 1042, 690 and 614 cm-1.

5.3.5 Atomic Charges

Atomic charges presents a vital insight in the understanding of several kinds of

chemical reactions, and they are crucial to the elucidations of a number of other

phenomena, for instance dipole moments and nuclear magnetic resonance (NMR)

chemical shifts. They also are important factors in molecular structure–activity

and structure–property relations. The atomic charges were calculated using the

Mulliken Population Analysis (MPA) [35]. The results are plotted in Fig.8. It is

generally accepted that atomic charges yielded by MPA are basis set dependent

and their absolute magnitude have little physical meaning, [36], however, with a

consistent basis set used for calculation, their relative values can yield useful

information [37]. MPA charges have been calculated both at B3LYP/6-

311+G(d,p) and MP2/6-311+G(d,p) level[Figure 5.5]. Both the methods show

similar charge pattern although with different magnitude. According to MPA, C2

128
Figure: 5.7 Experimental FT-IR and Theoretical IR spectra of HBT in 4000-
400 cm-1 range.

129
is positive while S8 is negative. The rest of the benzene C atoms show usual

negative charge due to π → π* interaction of the electron cloud.

5.4 Conclusions
In the present study, we have carried out the theoretical vibrational analysis of

HBT for the first time. In general, a good agreement between available

experimental and calculated normal modes of vibrations has been observed. The

hydrogen bonded interaction between the two monomeric units of HBT molecule

and consequently the counterpoise corrected interaction energy has been

calculated. The hydrogen bond strength in HBT dimer calculated from

counterpoise correction method (8.24297 kcal/mol) is close to that calculated from

topological parameters at the MP2 level. NLO behavior of the title molecule was

investigated by the determination of the dipole moment, the polarizability and the

first static hyperpolarizability using the B3LYP/6-311+G(d,p) methods. The β

value is calculated to be 4.4 x 10-30 e.s.u. which is almost 23 times higher than

that of urea. The experimental and theoretical UV–vis spectral analysis has also

provided insight into the excitation energy and oscillator strength and predicted

mainly the π → π* type electronic transitions which are intra-molecular charge

transfer type. The molecular orbitals, MESP contour/surface and NBO analysis

may lead to the understanding of properties and activity of HBT and may also aid

the use of HBT in various advanced pharmaceutical applications.

130
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31. T. Miyazawa, J. Mol. Spectrosc. 4 (1960) 155–167.
32. V.K. Rastogi, M.A. Palafox, K. Lang, S.K. Singhal, R.K. Soni, and R.
Sharma, Ind. J. Pure Appl. Phys. 44 (2006)653–660.
33. R. M. Silverstein and F. X. Webster, D. Kiemle Spectrometric
Identification of Organic Compounds 2nd edition Jon-Wiley & Sons Inc.
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35. E.R. Davidson, S.Chakravorty, Theoretica Chimica Acta 83(1992) 319-330
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(1996) 571- 577.

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High speed computers and efficient computer programs have made the

electronic structure calculation, an important module for theoretical and

experimental chemical researches. The electronic structure of materials, in

general sense determines all the molecular properties accurately by ab initio

calculations i.e. from fundamental quantum theory. The simplest type of ab

initio electronic structure calculation is the Hartree–Fock (HF) method, but

Density Functional Theory (DFT) has become a widely used class of quantum

chemical methods, because of its capability to predict relatively precise

molecular properties with comparatively less computational cost [1-5]. In the

Hartree-Fock method, electron correlations beyond a mean field picture are

entirely neglected, whereas in DFT they are included approximately via a

functional Exc. The work reported in this thesis is based on the calculation of

ground state properties and the vibrational analysis of finite molecules using

DFT method. The calculation involves full geometry optimization and thereafter

calculation of total energy, vibrational frequencies and nonlinear optical

properties. Three small molecules namely of 5-nitro-2-furaldehyde-

semicarbazone, Hydroxybenzaldehyde, 2(3H)-Benzothiazolone have been

studied. In general, good agreements between experimental and calculated

normal modes of vibrations have been observed for the molecules under

investigation.

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Chapter I and Chapter II gives a brief introduction and theoretical details of

quantum chemical methods. Chapter III presents the geometry, electronic

properties, polarizability, and hyperpolarizability of 5-nitro-2-furaldehyde

semicarbazone (5N2FSC) using density functional theory with the hybrid

functional B3LYP. A complete vibrational analysis of the molecule has been

performed and assignments are made on the basis of potential energy

distribution. In general, a good agreement of calculated modes with the

experimental ones has been obtained at DFT/(B3LYP)/6-311++G(d,p) level of

theory. Both the dipole moment (10.55 Debye) and hyperpolarizabilty (21.2 x

10-30 e.s.u.) of 5N2FSC is found to be very high. Ultraviolet–visible spectrum of

the title molecule has also been calculated using TD-DFT method. The

calculated energy and oscillator strength almost exactly reproduces reported

experimental data.

Chapter IV, focuses on the comparison of molecular structural properties,

vibrational and energetic data of „o‟-Hydroxybenzaldehyde, „p‟-

Hydroxybenzaldehyde and „m‟-Hydroxy-benzaldehyde, in gas phase, due to

their commercial importance. The structure and the ground state energy of the

molecules under investigation has been analyzed employing DFT / B3LYP

level. The higher frontier orbital energy gap and the lower dipole moment

values make the „p‟-Hydroxybenzaldehyde less reactive and most stable among

the three isomers. A good agreement between experimental and calculated

normal modes of vibrations has been observed. NLO behavior of the title

135
molecules were investigated by the determination of the polarizability and the

first hyperpolarizability using the DFT/B3LYP/6-311G(d,p) method. The

polarizability values are almost the same but the para isomer has significantly

higher values for the total hyperpolarizability.

In Chapter V, the theoretical vibrational analysis of 2(3H)-Benzothiazolone

(HBT) has been carried out for the first time. In general, a good agreement

between available experimental and calculated normal modes of vibrations has

been observed. The hydrogen bonded interaction between the two monomeric

units of HBT molecule and consequently the counterpoise corrected interaction

energy has been calculated. The hydrogen bond strength in HBT dimer

calculated from counterpoise correction method (8.24297 kcal/mol) is close to

that calculated from topological parameters at the MP2 level. The β value is

calculated to be 4.4 x 10-30 e.s.u. which is almost 23 times higher than that of

urea. The experimental and theoretical UV–vis spectral analysis has also

provided insight into the excitation energy and oscillator strength and predicted

mainly the π → π* type electronic transitions which are intra-molecular charge

transfer type. The molecular orbitals, MESP contour/surface and NBO analysis

lead to the understanding of properties and activity of HBT and may also aid the

use of HBT in various advanced pharmaceutical applications.

The work reported in the thesis is primarily based on the calculation of

molecular properties using DFT method. All these studies are based on certain

assumptions and as such have their own limitations. The experimental data,

136
which have been used, also have their dependability within certain limits.

Density functional theory (DFT) calculations are the most common type of

calculations, though they are subject to limitations in the accuracy of the

functional employed, and the ability to chemically interpret the result. These are

briefly discussed as follows - DFT methods require careful calibration to

establish their accuracy (or inaccuracy) on a case by case basis. These methods

are not systematically improvable like wavefunction based methods and so it is

impossible to assess the error associated with the calculations without reference

to experimental data or other types of calculation. The choice of functionals is

intimidating and can have a real impact on the calculations. Thus one of the

prime limitations of density functional theory is that it doesn't correctly treat the

exchange interaction. Developing better approximations for the electron-

electron coulomb and exchange terms is still an area of active research. The

geometric differences between the optimized molecules and the molecule in

solid state are due to the fact that the molecular conformation in the gas

phase is different from that in the solid state, where inter molecular

interactions play an important role in stabilizing the crystal structure.

Another important limitation to density functional theory is DFT's

characteristically poor treatment of long-range noncovalent interactions.

Although DFT is enjoying ever increasing popularity in Solid State Physics and

Quantum Chemistry but it is generally known that HF overestimates the

HOMO-LUMO gap whereas DFT/ B3LYP underestimates it [6,7]. Hence

137
methods like MP2 should be used to get a better estimate of HOMO-LUMO

gap. This has been done in the case of Benzothiazolone only, but not for all the

molecules studied as it is very computationally costly and beyond the scope of

the present work.

In the present work one of the important limitations in the evaluation of

spectroscopic data lies in the fact that an isolated model has been used in place

of three dimensional systems. This leads to a shift of few wave numbers in the

calculated frequencies. Calculations on a three dimensional system together

with intermolecular interactions will fully interpret the vibrational modes, but

the calculation with three dimensional system becomes computationally very

costly and cumbersome.

The experimental work reported here is based on the FT-IR and FT-

Raman spectra. It is to be noted that the FT-IR and FT-Raman spectra have their

own limitations. Their interpretation may not be simple. Sometimes,

fluorescence of impurities or of the sample itself can hide the Raman spectrum.

In case of bands separated by small energy, the information contained in them

may be masked by overlapping. Other features which limit the information can

be because of over tones and shifting of bands due to structural features.

Unlike Infrared or Raman study, neutron scattering does not involve

electromagnetic interaction [8, 9] and there is no restriction on selection rules.

Thus it can give information on the entire range of vibrational spectra of a

138
molecule besides giving density-of-states directly. It is specially suitable in the

low frequency spectral region for lattice modes and chain vibrations.

On the other hand there are still many “white areas” stimulating future research,

which must be mentioned here. The future research scope involves the quantum

chemical study of a series of derivatives of Hydroxybenzaldehyde, so that the

trend in electronic properties may be used to interpret the dynamics of such

compounds and their use as NLO materials. UV and NBO analysis can be done

through quantum chemical methods to have a better understanding of the

dynamics of these compounds.

The present work can also be extended for time-dependent density functional

theory (TDDFT) studies. TDDFT is a quantum mechanical method to

investigate the properties of many-body systems beyond the ground state

structure. It is an extension of density functional theory (DFT) to the time-

dependent domain as a method to describe such systems when a time dependent

perturbation is applied and as DFT, it is becoming one of the most popular and

versatile methods available in condensed matter physics, computational physics

and computational chemistry [10].

139
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Narayan, O. Prasad, L. Sinha, Journal of Molecular Structure 1022 (2012)
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