Molecular structure, NMR, UV-Visible, vibrational spectroscopic and HOMO, LUMO analysis of (E)-1-(2, 6-bis (4-methoxyphenyl)-3, 3-dimethylpiperidine-4-ylidene)-2-(3-(3, 5-dimethyl-1H-pyrazol-1-yl) pyrazin-2-yl) hydrazine by DFT method

Article abstract of DOI:10.1016/j.molstruc.2015.11.005

We have synthesized (E)-1-(2, 6-bis (4-methoxyphenyl)-3, 3-dimethylpiperidine-4-ylidene)-2-(3-(3, 5-dimethyl-1H-pyrazol-1-yl) pyrazin-2-yl) hydrazine (PM6). It was characterized using FT-IR, FT-Raman, ¹H NMR, ¹³C NMR techniques. To i

Full text of DOI:10.1016/j.molstruc.2015.11.005

Accepted Manuscript
Molecular structure, NMR, UV-Visible, Vibrational spectroscopic and HOMO, LUMO
analysis of (E)-1-(2, 6-bis (4-methoxyphenyl)-3, 3-dimethylpiperidine-4-ylidene)-2-(3-
(3, 5-dimethyl-1H-pyrazol-1-yl) pyrazin-2-yl) hydrazine by DFT method
A.Therasa Alphonsa, C. Loganathan, S.Athavan Alias Anand, S. Kabilan
PII:
S0022-2860(15)30410-5
10.1016/j.molstruc.2015.11.005
MOLSTR 21955
DOI:
Reference:
To appear in: Journal of Molecular Structure
Received Date: 13 September 2015
Revised Date: 30 October 2015
Accepted Date: 2 November 2015
Please cite this article as: A.T. Alphonsa, C. Loganathan, S.A.A. Anand, S. Kabilan, Molecular
structure, NMR, UV-Visible, Vibrational spectroscopic and HOMO, LUMO analysis of (E)-1-(2, 6-bis (4-
methoxyphenyl)-3, 3-dimethylpiperidine-4-ylidene)-2-(3-(3, 5-dimethyl-1H-pyrazol-1-yl) pyrazin-2-yl)
hydrazine by DFT method, Journal of Molecular Structure (2015), doi: 10.1016/j.molstruc.2015.11.005.
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Molecular structure, NMR, UV-Visible, Vibrational spectroscopic and HOMO, LUMO
analysis of (E)-1-(2, 6-bis (4-methoxyphenyl)-3, 3-dimethylpiperidine-4-ylidene)-2-(3-(3, 5-
dimethyl-1H-pyrazol-1-yl) pyrazin-2-yl) hydrazine by DFT method
a
a
a
a*
A. Therasa Alphonsa , C. Loganathan , S. Athavan Alias Anand , S. Kabilan
a
Department of Chemistry, Annamalai University, Annamalainagar - 608002, Tamilnadu, India.
Abstract
We have synthesized (E)-1-(2, 6-bis (4-methoxyphenyl)-3, 3-dimethylpiperidine-4-
ylidene)-2-(3- (3, 5-dimethyl-1H-pyrazol-1-yl) pyrazin-2-yl) hydrazine (PM6). It was
1
13
characterized using FT-IR, FT-Raman, H NMR, C NMR techniques. To interpret the
experimental data, ab initio computations of the vibrational frequencies were carried out using
the Gaussian 09 program followed by the full optimizations done using Density Functional
Theory (DFT) at B3LYP/6-311 G(d,p) level. The combined use of experiments and
computations allowed a firm assignment of the majority of observed bands for the compound.
The calculated stretching frequencies have been found to be in good agreement with the
experimental frequencies. The electronic and charge transfer properties have been explained on
the basis of highest occupied molecular orbitals (HOMOs), lowest unoccupied molecular orbitals
(
LUMOs) and density of states (DOS). The absorption spectra have been computed by using
1
13
time dependent density functional theory (TD-DFT). H and C NMR spectra were recorded and
1
13
H and C NMR chemical shifts of the molecule were calculated using the gauge independent
atomic orbital (GIAO) method. From the optimized geometry of the molecule, molecular
electrostatic potential (MEP) distribution, frontier molecular orbitals (FMOs) of the title
*
Corresponding author: Dr. S. Kabilan
Email: profdrskabilanaa@gmail.com, Tel: 9443924629

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compound have been calculated in the ground state theoretically. The theoretical results showed
good agreement with the experimental values.
Keyword: DFT, VEDA, MEP, NLO, Potential energy scan and Molecular Docking
1
.
Introduction
Nitrogen and oxygen containing heterocyclic compounds have received considerable
attention due to their wide range of pharmacological activity [1]. Pyrazole is an important
aromatic heterocyclic compound containing two bonded nitrogen atoms. It is related to many
compounds such as isoxazole, isothiazole, oxazole and imidazole [2]. Pyrazoles have illustrious
history; in 1883, a German chemist Ludwig Knorr was the first to discover antipyretic action of
pyrazole derivative in man, he named the compound antipyrine. When he attempted to
synthesize quinoline derivatives with antipyretic activity, accidentally obtained antipyrine (2, 3-
dimethyl-1-phenyl-3-pyrazolin-5-one) which has analgesic, antipyretic and antirheumatic
activity; which stimulated interest in pyrazole chemistry. The first natural pyrazole derivative
was isolated by Japanese workers Kosuge and Okeda in the year 1954, till their discovery it was
thought that pyrazoles could not be obtained naturally. They isolated 3-n-nonylpyrazole [3] from
Houttuynia Cordata, a plant of the “piperaceae” family from tropical Asia; which showed
antimicrobial activity. They also isolated levo-β-(1-pyrazolyl) alanine [4] an amino acid from
watermelon seeds (Citrullus Vulgaris).
Many natural products have the pyrazole unit as the core structure [5]. Pyrazoles and its
derivatives, a class of well known nitrogen heterocycles, occupy as the core in a variety of
leading drugs such as Celebrex, Sildenafil (Viagra), Ionazlac, Rimonabant and Difenamizole etc.
Pyrazole analogues have found use as building blocks in organic synthesis for designing
pharmaceutical and agrochemicals; and as bifunctional ligands for metal catalysis. Pyrazole and

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its derivatives have widespread applications in the field of medicine and industry. They are used
as antihypertensive [6], anti thrombotic [7], anti inflammatory [8], anti microbial [9], anti
rheumatic [10], anti tumor [11], anti viral [12] and anti diabetic [13]. Some derivatives are used
as anti corrosion and for coloured photography. These derivatives have attracted significant
attention because of the application in drug development [14]. Particularly, arylpyrazoles are
important in medicinal and pesticidal chemistry [15]; a number of herbicides with pyrazole
moieties have been commercialized [16]. Recent literature shows that, some arylpyrazoles were
reported to have non-nucleoside HIV-1 reverse transcriptase inhibitor activity [17, 18]. They are
also useful intermediates for many industrial products [19–21]. The vibrational spectra of
pyrazole have been thoroughly investigated [22-24], however, there is relatively little
information regarding substituted pyrazoles, and N-substituted pyrazoles in particular [25, 26].
The inclusion of a substituent group in pyrazole leads to the variation of charge distribution in
molecules and consequently this affects the structural, electronic and vibrational parameters. The
methyl and amino groups are generally referred to as electron donating substituents in aromatic
3 2
ring systems [27]. The CH and NH interact with nearby π systems via hyper conjugation,
which implies electronic delocalization and are taken into account by the molecular orbital
approach [28, 29].
Due to the importance of the pyrazole nucleus, we believed it worthwhile to design and
synthesize new pyrazole derivatives. Investigations into the structural stability of these
compounds using both experimental techniques and theoretical methods have been of interest for
many years. With recent advances in computer hardware and software, it is possible to correctly
describe the physico- chemical properties of molecules from first principles using various

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computational techniques [30]. In recent years, density functional theory (DFT) has been the
shooting star in theoretical modeling.
A large number of studies have been made on the synthesis, spectroscopic analysis and
theoretical calculations of pyrazole and its derivatives [31-33]. In this study, we present the
experimental and theoretical studies of the title compound. The interaction energies, NMR
spectral analysis, Molecular electrostatic potential, thermodynamic and nonlinear optical
properties of PM6 were investigated at the B3LYP/6-311G (d, p) level. A detailed interpretation
of the vibrational spectra of PM6 has been made on the basis of the calculated amount of total
energy distribution (TED) [34]. The results of the theoretical and spectroscopic studies are
reported here. The redistribution of electron density (ED) in various bonding and anti-bonding
orbitals and E (2) energies has been calculated by natural bond orbital (NBO) analysis. The UV
spectroscopic studies along with HOMO, LUMO analysis have been used to elucidate
information regarding charge transfer within the molecule. The molecular first
hyperpolarizability and thermodynamic properties have been analyzed by means of vibrational
spectroscopy. The aim of this work is to explore the molecular dynamics and the structural
parameters that govern the chemical behaviour, and to compare predictions made from theory
with experimental observations.
2
2
.
Experimental
.1. Synthesis
, 3-dichloro pyrazine, ammonium acetate, 4-methoxy benzaldehyde, 3-methyl-2-
2
butanone are purchased from Sigma-Aldrich chemical company with a stated purity and are used
as such without further purification. The title compound is synthesized according to Scheme 1.

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2
.2. Instruments
The FT-IR spectrum of the molecule is recorded in the region of 4000-400 cm on
-1
Thermo Scientific Nicolet iS5 (iDl transmission) using KBr pellet. FT-Raman spectrum is
recorded using 1064 nm line of Nd: YAG laser as excitation source with wave length in the
-1
region 3500-50 cm on a Bruker RFS 100/S FT-Raman spectrophotometer. The detector is a
liquefied nitrogen cooled Ge detector. The Ultraviolet absorption spectra of PM6 dissolved in
DMSO are examined in the range of 200-800 nm using a Hitachi model U-2001
spectrophotometer. NMR spectrum is performed in Bruker DPX 400 MHz at 300K. The
compound is dissolved in DMSO-d6. Chemical shifts are reported in ppm relative to
1
13
tetramethylsilane (TMS) for protons and carbons. H and C NMR spectra are obtained at a base
frequency of 400 MHz and 100 MHz respectively.
2
.3. Computational Techniques
All computational studies are carried out at Density Functional theory (DFT) level on a
Dell workstation equipped with V3 quardcore, Xeon quad core processor E3–1240, 3.40 GHz
personal computer with 8 GB total RAM using Gaussian 09W program package [35]. DFT
calculations are less time consuming and include a significant part of the electron correlation
leading to good accuracy. The calculations are carried out with the Becke’s three parameter
exchange functional with the LYP correction (B3LYP) and the basis set, 6-311 G (d, p) are used
in appropriate calculations [36, 37]. The computational work has begun with the conformational
analysis of the compound. The selected geometric parameters of the optimized structure of PM6
are given in Table 1S.

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2
.4. Docking Studies
The molecular docking studies reported in this work were performed on a Dell
workstation equipped with Xeon processor E3–1225, V2 quardcore, 3.20 GHz personal
computer with 8 GB total RAM and with Schrödinger software suite, LLC, New York, 2014
release. The preliminary step for molecular docking is to prepare the protein and ligand to an
optimized and minimized structure. The 3D crystallographic structure of human CYP51 protein
(PDB ID: 3LD6) was downloaded from the protein data bank (www.rcsb.com). The complex
was prepared by protein preparation wizard [38] incorporated in the Maestro [39] of
Schrödinger software, 2014. After pre–processed, the protein complex was optimized and
minimized using Optimized Potential for Liquid Simulations (OPLS–2005) force field [40] until
the root mean square deviation (RMSD) reached the value of 0.3 Å. Further, the grid was
generated for protein complex using receptor grid generation option which is incorporated in the
Glide [41] module of Maestro. The ligand preparation was done by importing the 2D structure of
the compound (mol format) to project table of Maestro. Later, the compound structure was
minimized and possible conformers were generated by OPLS–2005 force field using Ligprep
[42] application. The interactions of the tested ligand in the binding site of the 3LD6 protein
were identified by the extra precision (XP) mode of docking using Glide module.
3
3
.
Results and Discussion
.1. Vibrational analysis
The synthesized PM6 is subjected to FT-IR, FT-Raman spectral analysis. The theoretical
vibrational analysis of the compound PM6 is analyzed using DFT/B3LYP 6-311 G (d, p)

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method. The observed and calculated FT-IR, FT-Raman spectrum of PM6 is given in Figure 1S
and the values are tabulated in Table 2S. The non-negative vibrational frequency obtained from
DFT calculations confirms that the optimized geometry of compound PM6 is located at the
minima on the potential energy state. The calculated vibrational frequencies are found to be in
good agreement with the observed FT-IR frequencies. The theoretical vibrational frequencies
obtained for compound PM6 is interpreted by means of Total energy distribution (TED %)
calculations using SQM method. The normal modes assignment of the theoretical frequencies is
visualized and substantiated with the help of the GaussView 5.0 visualization program. The
synthesized PM6 consists of 74 atoms and hence has 216 normal modes of vibrations which
include 78 stretching, 81 bending and 57 torsional modes of vibration. The molecule PM6
belongs to C1 symmetry. All the modes are IR active modes. The significant normal modes with
TED (10%) are given in order of decreasing wave numbers in Table 2S.
N-H vibrations
-1
The νN-H stretching vibrations normally appear in the range of 3500-3300 cm [43]. The
-1
-1
experimental wave number of 3412 cm in the FT-IR spectrum (FT-Raman at 3425 cm ) of
PM6 is attributed for N-H stretching. The theoretical N-H stretching vibration modes are
-1
-1
visualized in the mode numbers 199 and 198 with the scaled frequencies 3438 cm to 3436 cm
respectively. Both the theoretical and experimental vibrational frequencies are pure vibrations
with TED of 99 %.
Aromatic stretching group vibrations
-
In general, the aromatic C-H stretching frequencies appear in the range of 3100-3000 cm
1
-1
[
44] and the ring C-C stretching vibrations occur in the region 1650-1400 cm [45]. In the
present work, the experimental FT-IR spectrum of PM6 the band appeared in the range of 3132

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-1
-1
cm while in FT-Raman at 3133 cm is assigned to the aromatic C-H stretching. In theoretical
calculation, the mode nos. 197-186 corresponds to theoretical aromatic C-H stretching
vibrations. The theoretical C-C stretching vibration modes are visualized in the mode numbers
-1
1
63-159 with the scaled frequencies of 1611-1559 cm respectively.
Methyl, methylene group vibrations
The symmetric and asymmetric stretching mode of the methyl group appears in the range
-1
-1
of 2935-2860 cm and 2985-2925 cm [46]. The methyl groups present in PM6 undergoes
vibrations like symmetric stretching, asymmetric stretching, symmetric and asymmetric bending
modes. The C-H stretching vibrations of methyl groups in PM6 are observed in the range at
-1
-1
2
983-2924 cm in FT-IR spectrum (FT-Raman at 2983, 2944 and 2923 cm ). The stretching in
the methyl groups is well explained by the mode numbers 178-171 in the theoretical vibrational
study of the compound PM6. The theoretical wave numbers matched well with the experimental
FT-IR and FT-Raman wave numbers. The bending vibrations of the methyl group are found to
-1
-1
appear in the region of 1465-1440 cm and 1390-1370 cm [47]. The bending vibrations of the
-1
methyl groups are observed at 1413 cm in FT-IR spectrum whereas in FT-Raman spectrum at
-1
1
407 cm (mode no. 136). The theoretical study make clear of these bending vibrations as
asymmetric and symmetric bending vibration of the methyl group with the help of the mode
-1
numbers 154-139 and 136 in the scaled frequency range of 1479-1435 and 1414 cm .
The asymmetric and symmetric C-H stretching in methylene group normally appears in
-1
the region of 3100-2900 cm [48]. In the present study, the observations of asymmetric and
symmetric stretching of the C-H in methylene group (C16) in compound PM6 observed at 3059
-1
-1
cm in FT-IR spectrum (FT-Raman at 3053 cm ) are complemented by the theoretical

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investigation which well explains the asymmetric and symmetric stretching in the methylene
-1
group in the respective scaled frequencies at 3012 cm (mode no.188).
C=N Vibrations
-1
The C=N vibration normally appears in the region 1689-1471 cm [49]. The strong band
-1
-1
observed at 1612 cm in FT-IR spectrum besides in FT-Raman spectrum at 1612 cm (mode no.
1
1
64) of PM6 is assigned to C=N vibration. The mode no. 164 and 158 with the scaled frequency
-1
612 and 1541 cm visualizes to the C=N stretching.
N-N Vibrations
The wave number of 1120 and 1076 cm in the FT-IR spectrum whereas in FT-Raman
-1
-1
spectrum at 1123 and 1079 cm (mode nos.101 and 97) is attributed for N-N stretching in
pyrazine ring and in NH-N bond. The N-N stretching vibration modes are visualized in the
-1
mode nos. 96, 97 and 100-102 with the scaled frequency 1064, 1089, 1107, 1124 and 1129 cm
respectively.
1
13
3
.2.
H and C NMR spectral analysis.
1
1
The H NMR spectrum of PM6 has been given in Figure 2S. In the H NMR spectrum of
the compound PM6 Table 1 in which H (4) signal appears as triplet at 0.85 ppm. The singlet at
1
1
1
.20 ppm in the H NMR indicates the presence of H (3). The doublet at 2.54 ppm in the H
1
NMR spectrum of the compound PM6 shows the presence of H (16) protons. The H NMR
spectrum of PM6 reveals a multiplet at 4.78 ppm for H (5), H (15) attached to a phenyl ring. The
aromatic protons are observed in the range for 6.92 to 7.59 ppm. The doublet observed at 9.92
and 10.03 ppm are attributed to the presence of H (26) and H (14) ppm.

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1
3
The C NMR spectrum of the compound PM6 has been displayed in Figure 3S. The
13
carbon chemical shifts are presented in Table 1. The C NMR spectrum of the synthesized
compound PM6 has been recorded in DMSO. The low field signal observed at 20.1 and 20.9
1
3
ppm in C NMR spectra of PM6 is due to the carbons C 38, C39. The C (16) carbon is identified
1
3
at 47.7 ppm in C NMR of PM6. The carbons in the azine linkage are exposed by the up-field
1
3
signals 159.6 ppm to 160.1 ppm. The signals at 58.1 ppm and55.2 ppm in the C NMR spectrum
of PM6 are due to the carbons C (15) and C (2) respectively.
NMR spectroscopy is the key to reveal the conformational analysis of organic molecules.
Good quality geometries must be taken into consideration for the quantum calculation of the
absolute isotropic magnetic shielding tensors to yield more reliable results. There are many
reports on NMR isotropic magnetic shielding tensor calculations employing the GIAO method
1
13
associated with the Density functional theory (DFT) [50]. The GIAO H NMR and C NMR
chemical shift calculations of the stable conformer is made in DMSO [scrf= (solvent=DMSO)]
using B3LYP / 6-311G (d, p) basis set. The isotropic values in the calculations are subtracted
1
3
1
from a scaling factor of 182.4656 and 31.882 to obtain the chemical shifts for C and H NMR
respectively. The obtained chemical shift values were compared with the experimentally
observed values. The observed and the calculated chemical shift values are found to be in good
agreement. The calculated values are given in the Table 1 along with the observed values. The
relationship between the experimental chemical shift and computed chemical shift values are
given in Figure 2. The relation between the observed and computed values predicts that the
conformation deducted theoretically should be the favorable conformation of the synthesized
PM6.

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3
.3. Natural Bond orbital analysis
The natural bond orbital analysis provides an efficient method for studying intra-and
intermolecular bonding and interaction among bonds, and also provides a convenient basis for
investigating charge transfer or conjugative interaction in molecular systems; it could enhance
the analysis of the delocalization of charge in the system.
The donor bonding orbitals, the acceptor antibonding orbitals, the donor lone pair atoms
are given in Table 2 along with the E (2) values which estimates the interaction between the
donor (filled) and acceptor (vacant) orbitals. The E (2) energy is the lowering energy that occurs
during the hyperconjugative electron transfer process and hence E (2) can be referred to as
stabilization energy. Larger the E (2) values, greater is the stability of the molecule. In the NBO
analysis of the compound PM6, the E (2) values are greater for the delocalization of the electrons
between the bonds present in the phenyl ring. The lone pair of electrons present in the Nitrogen
atom N25, N26, N33, N32, N29, O12, O23 are delocalized to C1-C16, C1-N25, C27-N32, C28-
N29, C37- C36, C35- N34, C27- C28, C27-C28, C10- C9 and C21-C20 antibonding orbitals.
The delocalization energy for lone pair electrons delocalization to π* antibonding orbital is
higher than the delocalization of lone pair electrons to σ* antibonding orbitals.
3
.4. Charge Analysis
The charge quantifies the electronic structure changes under atomic displacement. It is
related directly to the chemical bonds present in the molecule, it influences dipole moment,
polarizability, electronic structure and more properties of molecular systems. The Mulliken and
natural charge distribution of the molecule calculated on B3LYP level with 6-311G (d, p) basis
set are shown in Table 3. The Mulliken charge distribution in the compound PM6 is found to be

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the distribution of charges considering the atomic orbitals alone and the natural charge
distribution considers the polarization of the orbitals too and hence some atoms like C2, C3, C4,
C13, N14C16, C21C24, C35, C37, C38 and C39 possess great differences between Mulliken and
natural charges Figure 3. The carbon atoms 5C, 6C, 15C, 17C, 30C, 31C possess positive
Mulliken charge and negative natural charge. All the hetero atoms in the compounds possess
negative Mulliken and negative charges.
3
.5. Molecular electrostatic potential (MEP) surfaces
The reactive behavior of the molecule is visualized with the help of three dimensional
MEP surface. MEP surface describes the charge distribution in the molecule and helps in
predicting the sites for nucleophilic and electrophilic attack in the molecule. The MEP surface
has been plotted for the molecules PM6 in Figure 4. Region of negative charge is pictured out in
red colour and it is found around the electronegative N in the azine linkage and O12, O23 atoms
in the methoxy groups in the molecule PM6. The red colour region is susceptible to electrophilic
attack. The blue colour region represents strong positive region and is prone to nucleophilic
attack. The green colour region corresponds to a potential half way between the two extremes
red and blue region.
3
.6. HOMO-LUMO of PM6
HOMO-LUMO pictures of molecule PM6 is presented in Figure 5. The p orbitals of
z
O23, O12, C13, C24, C22, C17, C18, C19, C20, C21, N14, C5, C6, C7, C8, C9, C10, C11, C15
carbon atoms do not involve in the formation of the HOMO orbitals in the molecule PM6. The
z
p orbitals of O23, O12, C13, C24 ,C22, C17, C18, C19, C20, C21, C7, C8, C9, C10, C11, C4

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carbon atoms alone do not involve in the formation of the LUMO orbital. The band gap between
the HOMO and LUMO orbital energy is found to be 4.140 eV.
3
.7. Polarizability calculations of PM6
The calculated values of the dipole moment (µ), the polarizability (α ) and first
0
hyperpolarizability (β ) by finite field approach are given in Table 4 along with the
tot
corresponding components. The field independent and field dependent dipole moment µ values
of PM6 are calculated to be 4.84 and 1.64 respectively. The highest value of dipole moment is
X
observed for the component µ for both the field independent and dependent conditions. The
compound PM6 is found to be polar molecule having non – zero dipole moment components.
The calculated polarizabilities α have non – zero values and are dominated by the
ij
-30
diagonal components. The β value of PM6 is found to be 10.81 x 10 esu. Delocalization of
tot
charges in particular directions is indicated by large values of those particular components of
polarizability and hyperpolarizability. First order hyperpolarizability is dominated by βxxx value.
This shows that the delocalization of the charges in presence of external field is endorsed in βxxx
direction. The first hyperpolarizability of PM6 (βtot) is 29 times greater than that of urea (0.3728
-30
x 10 esu); hence this molecule can have considerable NLO activity.
3
.8. UV spectrum and electronic properties
On the basis of fully optimized ground-state structure, TD-DFT// B3LYP/6-311 G (d, p)
calculations have been used to determine the low-lying excited states of PM6. The experimental
max value is obtained from the UV/Vis spectra recorded in DMSO is given in Figure 4S. The
calculations were also performed with DMSO solvent effect. The calculated results involving the
λ

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vertical excitation energies and wavelength are carried out and compared with measured
experimental wavelength. Typically, according to the Franck-Condon principle, the maximum
absorption peak (max) corresponds in an UV-Vis spectrum to vertical excitation. The TD-DFT//
B3LYP/ 6-311 G (d, p) [51] method predicts one intense electronic transition at 280 nm in good
agreement with the measured experimental data (exp=283nm). The deviation between
experimental and theoretical results may be due to solvent effects. This electronic absorption
corresponds to the transition from the ground to the first excited state and is mainly described by
one electron excitation from the highest occupied molecular orbital (HOMO) to the lowest
unoccupied molecular orbital (LUMO). The HOMO-LUMO energy gap of PM6 was calculated
at the B3LYP/6-311 G (d, p) level. LUMO as an electron acceptor represents the ability to obtain
an electron; HOMO represents the ability to donate an electron. The gap between HOMO and
LUMO characterizes the molecular chemical stability [52]. The energy gap between the HOMOs
and LUMOs is a critical parameter in determining molecular electrical transport properties
because it is a measure of electron conductivity.
3
.9. Docking studies
Molecular docking studies were performed to investigate the binding affinities of the
newly synthesized compound PM6 and the human CYP51 protein, PDB ID: 3LD6 [53]. The
ligand−protein complex stability was successfully made by some features such as hydrogen bond
interactions, vander Waals forces, π−π stacking, hydrophilic and hydrophobic interactions. These
interactions between the drug and receptor depend upon the nature of functional groups present
in the ligand. On ligand preparation (by ligprep module) of compound PM6, twelve structures
were obtained as different conformers. Each conformer was docked into the binding pocket of

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the 3LD6. The conformer with high docking score -8.41 is displayed in Fig. 6. The imidazole
and pyrazine nucleus of the tested compound PM6 have two π−π stacking interactions with TYR
1
31 and PHE 234 amino acids respectively. The docking studies were also showed weak
hydrogen bond interaction with length 2.27 Å between the pyrazine nitrogen atom of PM6 and
the water molecule (HOH 8) present in the active site of 3LD6. The statistical parameters of top
five conformers of compound PM6 were tabulated in Table 5.
4
.
Conclusions
A novel compound PM6 was synthesized and characterized by FT-IR, UV, FT-Raman,
1
13
H and C NMR techniques. The theoretical vibrational frequencies are found to be in good
agreement with the observed vibrational frequencies of PM6. The compound PM6 is subjected
to NBO analysis, the E(2) values are greater for the delocalization of the electrons between the
bonds present in the phenyl ring. The delocalization energy for lone pair electrons delocalization
to π* antibonding orbital is higher than the delocalization of lone pair electrons to σ*
antibonding orbitals. The first hyper polarizability of PM6 is 29 times greater than of urea
-30
(
0.3728 x 10 esu), hence this molecule can have considerable NLO activity and can find its
application in material science field too. The docking results clearly indicate that the imidazole
and pyrazine nucleus of the tested compound PM6 have two π−π stacking interactions with TYR
1
31 and PHE 234 amino acids present in the active site of 3LD6.
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1] P.M.G. Swamy, Y.S. Agasimundin, Rasayan J. Chem. 1 (2) (2008) 421–428.
[

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[2]
B.K.Wibreg "Aromaticity of Heterocyclic Chemistry; pyrazole, pyrazolines,
pyrazolidines imidazoles and condensed ring" 3, 20 (1967); B.K.Wibreg “Aromaticity
and its chemical Manifestation" (1999) 519.
[
3]
4]
Da-Qing Shi, Jing-Wen Shi, Hao Yao, J Chinese Chem. Soc 56 (2009) 504-509.
Hai-Ling Liu, Huan-Feng Jiang, Min Zhang, Wen-Juan Yao, Qiu-Hua Zhu, Zhou Tang,
Tetrahedron Lett 49 (2008) 3805-3809.
[
[
[
[
[
[
[
[
[
5]
6]
7]
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Figure and Scheme Captions
Scheme 1.
Fig. 1. Numbering of PM6 used in this study
1
13
Fig. 2. Comparison of observed and theoretical chemical shifts values of H and C spectrum of
PM6
Fig. 3. Comparison of Mulliken charges and NBO charges of PM6
Fig. 4. MEP plot of PM6
Fig. 5. HOMO-LUMO pictures of PM6
Fig. 6. 2D and 3D docking poses of compound PM6 with 3LD6

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(i) Synthesis of hydrazine
H C
3
O
O
H
N
N
Cl
Cl
N
N
N
CH3
NH NH H O
NH
2
N
2
2.
2
MeOH
EtOH
N
1
N
2
Cl
N
3
Cl
NH NH H O
2
2. 2
THF/ammonia
H C
3
CH3
N
N
N
N
4
NH
NH2
(ii) Synthetic route of PM6
O
CH3
H C
3
O
CH3
CH3
CH3
O
O
EtOH
Warm
N
H
H H
H C
3
CH3
H C
3
CH3
O
O
O
O
5
NH OAc
4
4
MeOH/HCl
H C
3
CH3
N
N
N
N
NH
N
CH3
CH3
N
H
H C
3
CH3
O
O
6
Scheme 1

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3
0
C
2
9 N
C 31
N 32
34
C
N
3
9
3
5
C
N
28
C
H C
3
3
3
27
2
6
C
HN
C
N 25
3
7
CH3
3
3
6
3
8
CH3
C
4
C
C
1
C
C
CH3
1
6 2
22
7
C
15
5
C
17
6
14
2
1 C
C
N
C
C 8
H C
C
C 18
H
C
C
CH3
3
O
20
C
19
C
9
O
12
13
2
4
1
1
2
3
1
0
Fig. 1. Numbering of PM6 used in this study

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1
13
Fig. 2. Comparison of observed and theoretical chemical shifts values of H and C spectrum of
PM6

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Mulliken charges
0
0
0
0
.6
.4
.2
.0
Natural charges
C1C2C3C4C5C6C7C8C9C1 0C 1 O1 1 2C 1 3N 1 4C 1 5C 1 6C 1 7C 1 8C 1 9C 2 0C 2 1C 2 2O 2 3C 2 4N 2 5N 2 6C 2 7C 2 8N 2 9C 3 0C 3 1N 3 2N 3 3N 3 4C 3 5C 3 6C 3 7C 3 8C 39
-
-
-
-
0.2
0.4
0.6
0.8
Fig. 3. Comparison of Mulliken charges and Natural charges of PM6

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Fig. 4. MEP plot of PM6

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a) HOMO
b) LUMO
Fig. 5. a) HOMO and b) LUMO pictures of PM6

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Fig. 6 2D and 3D docking poses of compound PM6 with 3LD6

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Table captions
1
13
Table 1. Experimental and computational H and C NMR spectral analysis of PM6 in DMSO
solution by DFT method
Table 2. Second order perturbation theory analysis of fock matrix in NBO basis for PM6
Table 3. Mulliken charges and NBO charges of PM6
-24
0
Table 4. Dipole moment µ (D), mean polarizability α (x 10 esu) and first hyperpolarizability
-33
β
tot (x10 esu) of PM6 by DFT method
Table 5. Molecular docking data of PM6 conformers with 3LD6