Neeraj Misra etal Der Pharma Chemica; 2009, 1 (1): 196-209

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Comparative vibrational spectroscopic investigation of benzonitrile

derivatives using density functional theory

Neeraj Misraa*, Shamoon Ahmad Siddiquib, Anoop Kumar Pandeya, Sanjeev Trivedi

a
Department of Physics, Lucknow University, Lucknow-226007, India
b
Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
__________________________________________________________________

Abstract

Comparative studies of the vibrational spectra of 4-methyl 3-nitrobenzonitrile and 2-formyl

benzonitrile have been made. The spectra are interpreted with the aid of normal mode analysis
following full structure optimization based on the density functional theory and different basis
set combination. While making complete assignment of vibrational wavenumbers, some
interesting facts were noticed for example, how modes of vibrations, bond angles and bond
lengths are affected by different groups attached to the benzene ring. The main aim of the present
study is to investigate in detail the vibrational spectra and thermo dynamical properties of 4-
methyl 3-nitrobenzonitrile and 2-formyl benzonitrile by B3LYP/6-311+G(2df,2p) method and
basis set combination, which can presumably help in understanding its behavior i.e. effect on
reactivity, stability, nature of state due to the different groups attached to the benzene ring. These
effects are also correlated with the chemistry of attached groups.

Keywords: Geometry optimization; Vibrational spectra; DFT

______________________________________________________________________________
Introduction
Benzonitrile (BN), is derived mainly from the reaction of benzoic acid with theocyanate, by
heating at 1910C. It, reacts violently with strong acid to produce toxic fumes [1]. Nitrile
derivatives have found a wide range of application in industry For example, Phthalonitrile have
been used as starting materials for phtalocyanide [2], which is an important component for dyes,
pigment, gas sensor, optical limiter, and liquid crystal and is also used in medicine as a singlet
oxygen photosensitizer for photodynamic therapy. Nitrile compounds are precursors of tetrazole
complexes [3], and benzonitrile is an aprotic polar solvent with a dipole moment of 4.18D, and
hence, it is extensively used as a solvent [4].
It can also be mentioned that Benzonitrile has been used as an enriched precursor for the
introduction of isotopes into l-tyrosine and has been used in the electrochemical preparation of
polydidodecyle terthiphenes from a mixture of acetonitrile and benzonitrile. Cyanide compound
can be degraded by pseudomonas species and BN biotransformed directly to benzoic acid by

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Der Pharma Chemica, 2009, 1(2): 162--169
(http://derpharmachemica.com/archive.html)
ISSN 0975-413X

FTIR Spectra and Vibrational Spectroscopy of Lantadene A

Apoorva Dwivedi1, Shamoon.A.Siddiqui1, Namita Misra2, Kanwal Raj2*

Onkar Prasad1, Leena Sinha1, Neeraj Misra1*

1
Department of Physics, Lucknow University, Lucknow, India
2
Medicinal and Process Chemistry Division, Central Drug Research Institute, Lucknow, India

_______________________________________________________________________________

Abstract
The molecular geometry and vibrational frequencies of Lantadene A in the ground state have
been calculated by Semi-empirical AM1 and PM3 parametrizations. Semi-empirical methods can
produce reasonable results on relatively large molecules (near 100s of atoms) in a reasonable
amount of time. The experimental frequencies of Lantadene A and the frequencies calculated by
AM1 and PM3 methods are nearly the same. Quantum chemical calculations have been carried
out to understand the dynamical behaviour of the bioactive molecule Lantadene A.

Keywords- Lantadene A, FTIR Spectra, Vibrational analysis

______________________________________________________________________________

Introduction

Natural products have been the subject of investigation for many reasons. They have got wide
applications, such as antibiotics, pharmacologically active agents or otherwise of interest in
human or animal medicine. They hold great potential as probes of the cellular processes in which
they interfere. Structural and conformational studies lead to hypothesis concerning target ligand
interactions while synthesis is a means to test these hypotheses by eventual total synthesis of
derivatives [1, 2]. Lantadene A, [22fl(Z)]-2-methylisocrotonoyloxy-3-oxoolean-12-en-28-oic
acid, is the major triterpenoid constituent of L. Camara, red variety. Mixed toxin preparation
from lantana leaves has been found to exist in two molecular forms, of which only one was
found to be hepatotoxic to guinea pigs [3]. Lantana plant has been reported to possess a number
of medicinal properties [4, 5]. Some metabolites isolated from their leaves possess antitumor
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Der Pharma Chemica, 2009, 1(2): 258-268
(http://derpharmachemica.com/archive.html)
ISSN 0975-413X

Quantum chemical study and the effect of substitution of

amino group on the reactivity of 4-Aminopyridine and 3,4-
Diaminopyridine by Density Functional Theory
Apoorva Dwivedia, S. A. Siddiquia, Anoop Kumar Pandeya, Onkar Prasada, Leena Sinhaa,
Neeraj Misraa*
a
Department of Physics, Lucknow University, Lucknow, India
______________________________________________________________________________

Abstract
Present work deals with the quantum mechanical study of the molecular structure of two well-
known voltage sensitive potassium channel blockers: 4, Aminopyridine and 3, 4 Diaminopyridine.
The equilibrium geometry, harmonic vibrational frequencies and HOMO-LUMO gap have been
calculated by the density functional theory (DFT), employing 6-311++G (2d, 2p) as the basis set.
A detailed interpretation of the infrared and Raman spectra of 4, aminopyridine and 3, 4
Diaminopyridine in terms of the potential energy distribution (P.E.D) is reported. The similarities
and differences between the vibrational spectra of the two molecules studied have been
highlighted. The thermodynamic calculations related to the title compounds were also performed
at B3LYP/6-311++G (2d, 2p) level of theory.

Keywords: Vibrational Spectra; Density functional theory; P.E.D; HOMO-LUMO

___________________________________________________________________

Introduction
The compound 3,4-Diaminopyridine (3,4-DAP), a derivative of 4, Aminopyridine, is soluble in
cold water and is used in the symptomatic treatment of fatigue in multiple sclerosis as well as
Lambert–Eaton myasthenia syndrome. It is capable of reducing morphine-induced respiratory rate
depression in doses, which did not produce signs of toridty and also used to treat downbeat
nystagmus (DBN) syndrome. [1-7].

Whereas the parent compound 4-AP is used as an acetylcholine-releasing drug, in serum, saliva,
and urine [8]. The pre-synaptic effects of 4-AP and 3, 4-DAP have also been investigated on rat
diaphragm neuromuscular junction using intracellular recording techniques. The effects of 4-AP
and 3, 4-DAP on quantal release indicates that these drugs enhance calcium entry indirectly by
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Der Pharma Chemica, 2010, 2(4): 342-360
(http://derpharmachemica.com/archive.html)
ISSN 0975-413X

Vibrational spectra and assignment of 3-(2-Nitrophenoxy)

phthalonitrile by Ab initio Hartree-Fock and Density Functional
Methods

Neeraj Misra1*, Anoop Pandey1, Apoorva Dwivedi1, Sanjeev Trivedi1,

Shamoon Ahmad Siddiqui1
1
Department of Physics, University of Lucknow 226007, India
______________________________________________________________________________

ABSTRACT

This work deals with a theoretical study of the molecular structure of 3-(2-Nitrophenoxy)
phthalonitrile. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities
in scattering activities was calculated by the ab initio Hartree-Fock method and the Density
Functional B3LYP method employing 6-311g (d, p) as the basis set. A detailed interpretation of
the infrared spectra of 3-(2-Nitrophenoxy) phthalonitrile is reported. The scaled theoretical
wave numbers are in perfect agreement with the experimental values.

Keywords: FTIR Spectra, Molecular structure, 3-(2-Nitrophenoxy) phthalonitrile, Vibrational

spectra.
______________________________________________________________________________

INTRODUCTION

In recent years the synthesis of near infrared absorbing dyes has been an increasingly active
field. Phthalonitriles (1,2-dicyanobenzenes) are used as synthetic precursors for large
macrocyclic organic semiconductors, particularly for phthalocyanines [1,2] with strong
absorption in the near infrared region of the spectrum. For the synthesis of substituted
phthalocyanines, halogen substituted phthalonitriles are used. Vibrational studies of these
precursor molecules are of interest in their own right and they are extremely valuable when
performing vibrational studies of larger composite molecular systems. In the present work we are
discussing on 3-(2-Nitrophenoxy) phthalonitrile. Several vibrational studies of different
phthalonitriles have been carried out [3–7]. Phthalonitriles are among the most important
precursors of phthalocyanine materials (Leznoff, 1989–1996). Monophneoxyphthalonitriles have

342
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 ISSN : 0974 - 7524 Volume 5 Issue 2

Physical CHEMISTRY
An Indian Journal
Trade Science Inc.
Full Paper
PCAIJ, 5(2), 2010 [37-49]

Vibrational spectroscopic investigation of ipolamiide using QM/MM method

Shamoon Ahmad Siddiqui1, Ruby Srivastava2, Sudha Jain3, Neeraj Misra2#*
1
Molecular Biophysics Unit, Indian Institute of Science, Bangalore - 560 012, (INDIA)
2
Department of Physics, Lucknow University, 226 007, (INDIA)
3
Department of Chemistry, Lucknow University, 226 007, (INDIA)
#
B-981,sector-A, Mahanagar, Lucknow - 226 006, (INDIA)
E-mail : neerajmisralu@rediffmail.com
Received: 26th April, 2010 ; Accepted: 6th May, 2010

ABSTRACT KEYWORDS
The combination of Quantum Mechanics (QM) and Molecular Mechan- QM/MM method;
ics (MM) methods has become an alternative tool for many applications FT-Raman spectra;
for which pure QM and MM are not suitable. The QM/MM method has Ipolamiide;
been used for different types of problems, for example: structural biology, Vibrational spectra;
surface phenomena, and liquid phase. In this paper we have used this DFT;
method on the molecular structure of ipolamiide. The equilibrium geom- UFF.
etry, harmonic vibrational frequencies and Raman activities were calcu-
lated by QM/MM method with B3LYP/6-31G(d,p) and universal force field
(UFF) combination using ONIOM code. We found the geometry obtained
by the QM/MM method to be very accurate, and we can use this rapid
method in place of time consuming ab initio methods for large molecules.
A detailed interpretation of the Raman spectra of ipolamiide is reported.
The scaled theoretical wave numbers are in perfect agreement with the
experimental values. The FT-Raman spectra of ipolamiide has been taken
from the literatures.  2010 Trade Science Inc. - INDIA

INTRODUCTION Here in the present communication, the experimental

The iridoid glycosides represent a large group of
cyclopentano[c]pyran monoterpenoids and are found as
natural constituents in a large number of plant families.
They have been shown to possess various biological ac-
tivities such as antimicrobial, antitumoral, hemodynamic,
choleretic, and hepatoprotective, as well as being anti-
inflammatory agents[1]. Ipolamiide is isolated from
Stachytarpheta indica VAHL, which is used locally as an
anti-inflammatory agent[2]. Ipolamiide has been also re-
ported to be antinociceptive, anti ulcerogenic,
antidiarrheoal as well as sedative and hypotensive[3-8].
FT-Raman frequencies of the title molecule are com-
pared with the theoretical frequencies obtained by QM/
MM method with B3LYP/6-31G(d,p) and universal
force field (UFF) combination using ONIOM code.
To gain a better understanding of the performance and
limitation of QM/MM method, as a general approach
to the vibrational problems of organic molecules, we
calculated harmonic frequencies of ipolamiide by this
method and compared these results with the observed
fundamental vibrational frequencies. Thus the evalua-
tion of the advantages of this method is useful for ob-
taining a reliable assignment of the vibrational spectra.
 Available on line www.jocpr.com

Journal of Chemical and Pharmaceutical Research

__________________________________________________

J. Chem. Pharm. Res., 2010, 2(4):835-850

ISSN No: 0975-7384

CODEN(USA): JCPRC5
______________________________________________________________________________

Comparative conformational, structural and vibrational study on

the molecular structure of tyrosine and L-DOPA using density
functional theory
Shamoon Ahmad Siddiqui1, Anoop Kumar Pandey2, Apoorva Dwivedi2, Sudha Jain3,
Neeraj Misra2*

1
Shri Ramswaroop Memorial College of Engg. and Management, Lucknow, India
2
Department of Physics, Lucknow University, Lucknow, India
3
Department of Chemistry, Lucknow University, Lucknow, India
__________________________________________________________
ABSTRACT
A brief conformational, structural and vibrational study has been performed on the molecular
structure of two well known amino acids tyrosine and L-DOPA. The equilibrium geometry,
harmonic vibrational frequencies, infrared intensities and Raman scattering activities were
calculated by the Density Functional B3LYP method employing 6-311G(d,p) as the basis set and
the vibrational studies were interpreted in terms of potential energy distribution (P.E.D.). The
internal coordinates were optimized repeatedly to maximize the P.E.D. contributions. A detailed
interpretation of the infrared and Raman spectra of tyrosine and L-DOPA is reported in the
present work. The similarities and differences between the vibrational spectra of the two
molecules studied have been highlighted. The calculations are in agreement with experiment.
The thermodynamic calculations related to the title compounds were also performed at
B3LYP/6-311G(d,p) level of theory. The FT-Raman and FT-IR spectra of tyrosine and L-DOPA
have been taken from literature.

Keywords: FT-IR and FT-Raman Spectra; Density functional theory; P.E.D.; Tyrosine and L-
DOPA; Vibrational study.
______________________________________________________________________________

INTRODUCTION

Tyrosine (4-hydroxyphenylalanine) also known as L-tyrosine is a non essential amino acid that is
a building block of protein. It is a precursor of the neurotransmitter dopamine, as well as a

835
International Journal of Pure and Applied Physics
ISSN 0973-1776 Volume 6, Number 1 (2010), pp. 15–30
© Research India Publications
http://www.ripublication.com/ijpap.htm

Hybrid QM/MM Study on the Molecular Structure of

Cinnamoyl Shikonin

Ruby Srivastavaa, Shamoon Ahmad Siddiquib Kanwal Rajc and Neeraj Misraa*
a
Department of Physics, Lucknow University, Lucknow, 226007, India
b
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
c
Medicinal and Process Chemistry Division, Central Drug Research Institute,
Lucknow, 226001, India
a*
Corresponding Author E-mail: neerajmisralu@rediffmail.com

Abstract

The combination of Quantum Mechanics (QM) and Molecular Mechanics

(MM) methods has become an alternative tool for many applications for which
pure QM and MM are not suitable. The QM/MM method has been used for
different types of problems, for example: structural biology, surface
phenomena, and liquid phase. In this paper we have used this method on the
molecular structure of cinnamoyl shikonin. The equilibrium geometry,
harmonic vibrational frequencies and infrared intensities were calculated by
QM/MM method with B3LYP/6-31G(d,p) and universal force field
combination (UFF) using ONIOM code. We found the geometry obtained by
the QM/MM method to be very accurate, and we can use this rapid method in
place of time consuming ab initio methods for large molecules. A detailed
interpretation of the infrared spectra of cinnamoyl shikonin is reported in the
present work. The scaled theoretical wave numbers are in perfect agreement
with the experimental values. The FT-IR spectra of cinnamoyl shikonin in the
region (4000-500) cm-1 was recorded in solid phase.

Keywords: QM/MM method; FT-IR Spectra; Cinnamoyl shikonin;

Vibrational spectra.

Introduction
Bioassay directed fractionation extract of Arnebia euchroma led to the isolation of
Alkanin [1], Shikonin [2] and their derivatives [3-4] as the active principles against
methicillin resistant staphylococcus aureus (MRSA) and vancomysin resistant
enterococci (VRE). The toxic effect of this compound restricted its further
Send Orders of Reprints at reprints@benthamscience.net
14 Micro and Nanosystems, 2013, 5, 14-21

Quantum Chemical Study of Fe Doped ZnO Nanoclusters

Shamoon Ahmad Siddiquia,b* and M.M. Abdullaha,b

a
Department of Physics, College of Arts and Sciences, Najran University, Najran, KSA; bAdvanced Materials and Nano
Research Centre, Najran University, Najran, KSA

Abstract: Quantum chemical calculations have been carried out using Density Functional Theory (DFT) analysis with
B3LYP method and Lanl2dz basis set to investigate (ZnO)n nano structures (n = 4–12) with substitution of Iron (Fe) as an
impurity. We deeply investigated the effects after the substitution of one Fe atom in place of one Zn atom for each (ZnO)n
nano structures. All the structures have been analyzed in detail and the relationship of the structural effects has also been
discussed after the Fe substitution. The variation in Binding Energy (BE) as well as electronic properties have also been
discussed. For the different cluster families relative energies were also calculated and the results obtained were compared
to the previous works. In all cluster families, Binding Energy was found to increase when Fe was substituted and HOMO–
LUMO energy gap was found to decrease when compared to the results of the pure form.
Keywords: Quantum chemical calculation, nanostructures, iron, density functional theory.

1. INTRODUCTION Here Density Functional Theory (DFT) analysis has been

Modification of electrical and magnetic properties of
semiconductor opens up a possibility of creating new and
advanced materials for the next era in Electronics, Spintron-
ics and Energy applications. At present, scientists are trying
to improve the performance and customization of existing
materials depending as per demand of industry. The desired
modification in semiconductor properties can be achieved by
combination of materials [1-5]. For instance, some specific
applications such as to improve optical and electronic prop-
erties; and to suppress degradation; surface coatings is found
to be very effective [6-8]. Other research groups are involved
in investigation of different properties such as magnetic
properties by adding impurities in various percents and loca-
tions [9-11].
A lot of theoretical studies have also been conducted to
investigate the electronic and atomic properties of various
semiconducting nanomaterials [12-16] because nanomaterial
with new structures may offer interesting and novel features
for various applications in electronics. Researchers are par-
ticularly interested in diverse forms of ZnO nanostructures,
like nanotubes [17], nanobelts [10], nanowires [18], nanor-
ings [19], nanosprings [20], nanocages [21] and nanohelixes
[22], which have resulted in new nanomaterials available for
optical, electronic and many other applications. Many other
researchers have used doping on ZnO and, many of them
concluded that the impurity induced in pure ZnO modifies its
optical and electronic properties [23,24]. For example, in flat
panel displays and photovoltaic devices, impurities on ZnO
have been used to create highly transparent conducting lay-
ers rather than using some expensive films [11].
*Address correspondence to this author at the Department of Physics,
College of Arts and Sciences, Najran University, Najran, KSA;
Tel: 00966508047809; E-mail: shamoonasiddiqui@gmail.com
performed by adding of iron as a substitutional impurity
which resulted in a modification of electronic properties of
novel (ZnO)n nanoclusters as studied by prior workers [17-
22,25,26]. In this work we have selected (ZnO)n, n = 4–12
nanostructures, as reported in [25,26]. In our study only
(ZnO)4, (ZnO)6, (ZnO)8 and (ZnO)12 nanoclusters have been
included, but in literature some more nanostructures are also
available, such as novel small ZnO nanoclusters [27], as well
as medium size ZnO clusters [28-32]. We have compared
our own results with their results and made further discus-
sion and conclusions.
In this study, we used best results from a geometric and
an energetic perspective as the criteria for cluster selection as
used by Cheng et al. [25] and Wang et al. [26]. The clusters
(ZnO)4, (ZnO)6, (ZnO)8 and (ZnO)12 as chosen for our study
were reported by these authors. Here we are trying to com-
pare the planar and three dimensional structures which are
similar in shape but have different count of atoms. Sunaidi et
al. [33] also worked with similar type of (ZnO)n nano-
clusters, and reported metastable structures of low energy
with n = 1–32. Two (ZnO)4 nanoclusters selected in present
work were also reported by Al Sunaidi et al. [33] and corre-
late with those reported by other workers [28-31].
Pure form of (ZnO)n nanoclusters is already reported by
many researchers, but our literature survey reveals that to the
best of our knowledge, the (ZnO)n clusters with substitu-
tional impurity of Fe have not been reported so far. In this
work an important and additional feature is that all the calcu-
lations were performed by considering relativistic effects
using Density Functional B3LYP method in combination
with Lanl2dz basis set which gives accurate results, although
these clusters contain Zn and Fe which are the transition
metals and one of these elements is present in each clusters
in its pure form as well as after Fe substitution. The effect of
Fe substitution in pristine form of ZnO is analyzed in detail

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