Experimental and Theoretical Studies of 4-(1-benzyl-5-methyl-1H-1,2,3-triazol-4-yl)-6-(2,4-dichlorophenyl)pyrimidin-2-amine: A Potential Antibacterial Agent

Article abstract of DOI:10.1002/jccs.201500010

The title compound (1), 4-(1-benzyl-5-methyl-1H-1,2,3-triazol-4-yl)-6-(2,4-dichlorophenyl)pyrimidin-2-amine (C₂₀H₁₆Cl₂N₆), was synthesized and structurally characterized by elemental analysis, ¹H NMR and ¹³C NMR and single crystal X-ray diffraction. The compound crystallizes as a colourless needle shaped in the triclinic system, space group P-1 with cell constants: a = 10.7557(11) ?, b = 12.7078(17) ?, c = 15.511(2) ?, α = 68.029(4)0, β = 86.637(5)0, γ = 87.869(4)0; V = 1962.4 (4) ?³, Z = 4. There are two structurally similar but crystallographically independent molecules (A and B) in the asymmetric unit of the title compound, which is linked via N-H...Cl hydrogen bond. An intramolecular C-H...N hydrogen also occurs in each molecule. In the crystal, each of independent molecules forms a centrosymmetric dimer with an R²₂(8) ring motifs through a pair of N-H...N hydrogen bonds. These dimers are further connected by intermolecular N-H...Cl and C-H...Cl hydrogen bonds, forming an infinite two dimensional supramolecular network lying parallel to the [010] plane. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311G (d, p) basis set and compared with the experimental data. Mulliken population analyses on atomic charges, HOMO-LUMO energy levels, Molecular electrostatic potential and chemical reactivity of the title compound were investigated by theoretical calculations. The thermo dynamical properties of the title compound at different temperature have been calculated and corresponding relations between the properties and temperature have also been obtained. The in vitro antibacterial activity has been screened against Gram-positive (Bacillus cerus and Staphylococcus epidermidis) and Gram-Negative (Escherichia coli, Acinetobacter baumannii and Proteus vulgaris). The results revealed that the compound exhibited good to moderate antibacterial activity.

Full text of DOI:10.1002/jccs.201500010

JOURNAL OF THE CHINESE
CHEMICAL SOCIETY
Article
Experimental and Theoretical Studies of 4-(1-benzyl-5-methyl-1H-1,2,3-triazol-4-yl)-6-
(2,4-dichlorophenyl)pyrimidin-2-amine: A Potential Antibacterial Agent
S. Murugavel,a* R. Madhanraj,b D. K. Andrew Prasanna Kumar,a Sangaraiah Nagarajanc and
Alagusundaram Ponnuswamyc
aDepartment of Physics, Thanthai Periyar Government Institute of Technology, Vellore-632 002, Tamilnadu, India
bDepartment of Physics, Ganadipathy Tulsi’s Jain Engineering College, Kaniyambadi, Vellore-632102
cDepartment of Organic Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai-625021, Tamilnadu
(Received: Jan. 8, 2015; Accepted: May 27, 2015; Published Online: Jul. 8, 2015; DOI: 10.1002/jccs.201500010)
The title compound (1), 4-(1-benzyl-5-methyl-1H-1,2,3-triazol-4-yl)-6-(2,4-dichlorophenyl)pyrimidin-
2-amine (C20H16Cl2N6), was synthesized and structurally characterized by elemental analysis, 1H NMR
and 13C NMR and single crystal X-ray diffraction. The compound crystallizes as a colourless needle
shaped in the triclinic system, space group P-1 with cell constants: a = 10.7557(11) Å, b = 12.7078(17) Å,
c = 15.511(2) Å, a = 68.029(4)°, b = 86.637(5)°, g = 87.869(4)°; V = 1962.4 (4) Å3, Z = 4. There are two
structurally similar but crystallographically independent molecules (A and B) in the asymmetric unit of
the title compound, which is linked via N-H…Cl hydrogen bond. An intramolecular C-H…N hydrogen
also occurs in each molecule. In the crystal, each of independent molecules forms a centrosymmetric
dimer with an R2 (8) ring motifs through a pair of N-H…N hydrogen bonds. These dimers are further con-
2
nected by intermolecular N-H…Cl and C-H…Cl hydrogen bonds, forming an infinite two dimensional
supramolecular network lying parallel to the [010] plane. The molecular geometry was also optimized us-
ing density functional theory (DFT/B3LYP) method with the 6-311G (d, p) basis set and compared with
the experimental data. Mulliken population analyses on atomic charges, HOMO-LUMO energy levels,
Molecular electrostatic potential and chemical reactivity of the title compound were investigated by theo-
retical calculations. The thermo dynamical properties of the title compound at different temperature have
been calculated and corresponding relations between the properties and temperature have also been ob-
tained. The in vitro antibacterial activity has been screened against Gram-positive (Bacillus cerus and
Staphylococcus epidermidis) and Gram-Negative (Escherichia coli, Acinetobacter baumannii and Pro-
teus vulgaris). The results revealed that the compound exhibited good to moderate antibacterial activity.
Keywords: X-ray structure determination; Hydrogen bonds; DFT calculations; HOMO-LUMO;
MEP; Chemical reactivity; Antibacterial activity.
INTRODUCTION
1,2,3-triazoles have been found a wide range of im-
pound. In recent years, density functional theory (DFT) has
become an increasingly useful tool for theoretical studies.
It is also computationally less demanding than wave func-
tion based methods with inclusion of electron correla-
tion.8,9 Thus, in order to characterize the correlation be-
tween molecular structure and macroscopic properties in
the studied compound, it seems to be essential to undertake
a detailed comparative study of the isolated molecule and
the solid state unit. In this paper, we report the synthesis,
crystal structure and antibacterial activity of 4-(1-benzyl-
5-methyl-1H-1,2,3-triazol-4-yl)-6-(2,4-dichlorophenyl)
pyrimidin-2-amine (C20H16Cl2N6), as well as theoretical
studies using the DFT(B3LYP) method and 6-311G(d, p)
basis set. The aim of the present work was to describe and
characterize the molecular structure and some electronic
portant applications in the pharmaceutical, polymer, and
material fields.1 In addition, they have shown a broad spec-
trum of biological properties such as anti-bacterial,2 anti-
allergic,3 anti-HIV activity4 and also serve as potential
chemotherapeutic agents for various diseases.5 On the
other hand, substituted pyrimidine nuclei were found anti-
viral,6 anti-tubercular, antineoplastic, anti-inflammatory,
diuretic, antimalarial and cardiovascular.7 In view of these
bioactivities of the individual heterocycles, it was envis-
aged that the synthesis of novel hybrid molecules contain-
ing two of the above said moieties in a single frame is worth
to attempt. Literature survey reveals that so for there is no
experimental and theoretical studies for the title com-
* Corresponding author. Tel: +919790084145; Email: smurugavel27@gmail.com
Supporting information for this article is available on the www under http://dx.doi.org/10.1002/jccs.201500010
974
© 2015 The Chemical Society Located in Taipei & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
J. Chin. Chem. Soc. 2015, 62, 974-983

JOURNAL OF THE CHINESE
CHEMICAL SOCIETY
XRD, DFT and Antibacterial Studies of a Triazole Derivative
structure properties of the title compound, both experimen-
tally and theoretically. We also make comparisons between
experimental and calculated values. The in vitro antibacte-
rial activity has been screened against Gram-positive (Ba-
cillus cerus and Staphylococcus epidermidis) and Gram-
Negative (Escherichia coli, Acinetobacter baumannii and
Proteus vulgaris) at three different concentrations 25, 50
and 75 mg/ml. The results were evaluated by measuring the
inhibition zones diameter in millimeters and were com-
pared with the standard antibiotic ciprofloxacin (25 mg/ml)
ment process of compound (1) are given in Table 1.
The asymmetric unit of the title compound contains
two crystallographically independent molecules (A and B).
The triazole ring(N1A-N4A/C8A/C9A and N1B-N4B/
C8B/C9B) of both molecules Aand B are essentially planar
[maximum deviation -0.004(3) Å for C8A molecule A and
0.005(3) Å for C9B in molecule B] and they form dihedral
angle of 11.8 (2)° and 8.1 (1)°, respectively, with essen-
tially planar pyrimidine ring [maximum deviation C13A
0.004(3) for C13A and 0.003(3) for C14B] as both mole-
cule A and B. The dihedral angle between two benzene
rings is 64.7 (2)° and 65.7 (2)° in molecules A and B, re-
spectively. The benzene ring attached to pyrimidine ring is
in bisection position in molecule A and equatorial position
RESULTS AND DISCUSSION
Description of Crystal structure
The displacement ellipsoid plot and theoretical ge-
ometry structure with the atom-numbering scheme for
compound (1) is shown in Fig. 1. The compound (1) crys-
tallizes as a colourless needle shaped in the triclinic system,
space group P-1 with cell constants: a = 10.7557(11) Å, b =
12.7078(17) Å, c = 15.511(2) Å, a = 68.029(4)°, b =
86.637(5)°, g = 87.869(4)°; V = 1962.4 (4) Å3, Z = 4. De-
tails of the data collection, crystal parameters and refine-
Table 1. Crystal and experimental data for the compound (1)
Empirical formula
C20 H16 Cl2 N6
411.29
Formula weight
Temperature (K)
293(2)
Wavelength (Å)
0.71073
Triclinic
P î
Crystal system
Space group
Unit cell dimensions(Å, °)
a
10.7557(11)
12.7078(17)
15.511(2)
b
c
a
68.029(4)
b
86.637(5)
g
87.869(4)
Volume (Å3)
1962.4(4)
Z
4
Calculated density (Mg/m3)
Absorption coefficient (mm-1)
F(000)
1.392
0.349
848
Crystal size (mm3)
Theta range for data collection (°)
Index ranges
0.30 ´ 0.24 ´ 0.11
1.90 to 28.36
-14 <= h <= 13,
-13 <= k <= 16,
-10 <= l <= 20
11403
Reflections collected
Independent reflections
Completeness to theta = 28.34°
Refinement method
9200 [R(int) = 0.0184]
98.0 %
Fig. 1. (a) View of title compound showing two crys-
tallographically independent molecules (A and
B) with the atom-numbering scheme. Displace-
ment ellipsoids for the non-H atoms are drawn
at the 30% probability level. The H atoms are
presented with spheres with arbitrary radii. (b)
The theoretical geometric structure of the title
compound (B3LYP/6-311G(d,p) level).
Full-matrix least-squares on F2
9200/1/507
Data/restraints/parameters
Goodness-of-fit on F2
1.019
Final R indices [I > 2s(I)]
R indices (all data)
Largest diff. peak and hole (e.Å-3)
R1 = 0.0565, wR2 = 0.1324
R1 = 0.1205, wR2 = 0.1632
0.388 and -0.289
J. Chin. Chem. Soc. 2015, 62, 974-983
© 2015 The Chemical Society Located in Taipei & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.jccs.wiley-vch.de
975

Article
Murugavel et al.
in molecule B. The bond distances for molecule A is
N3–C8, C8–C9, C9–N1, N1–N2 and N2–N3 are 1.368(4),
1.368(4), 1.345(3), 1.345(4) and 1.305 (3) Å, respectively,
which agrees with C=C, N=N, C–N distances found in lit-
erature for compound having triazole heterocycles.10,11 In
pyrimidine ring the N–C bond lengths [1.339(2)–1.357(2)
Å] and bond angles N6–C14–N5 [117.0(2)°] are found
close to the reported values for similar pyrimidine deriva-
tives.12
In view of the bond lengths in Table 3, most predicted val-
ues are longer than experimental ones. We note that the ex-
perimental results are for the solid phase and the theoretical
calculations are for the gas phase. In the solid state, the ex-
istence of a crystal field along with the intermolecular in-
teractions connect the molecules together, which results in
the difference in bond parameters between the calculated
and experimental values.13
When the X-ray structure of the title compound was
compared with its optimized counterpart (see Fig. 1),
conformational discrepancies were observed. The orienta-
tion of the phenyl rings of compound (1) proved the most
notable discrepancy, and is defined with torsion angle
N5–C13–C15–C20 = -54.6° (Molecule A) and -75.7°
(Molecule B) and C5–C6–C7–N1 = 102.4° (Molecule A)
and -42.6° (Molecule B), which is calculated at -40.1° and
-131.9°, respectively, for B3LYP/6-311G(d,p) level.
A global comparison was performed by superimpos-
ing the molecular skeletons obtained from X-ray diffrac-
tion and the theoretical calculations atom by atom (see Fig.
3), obtaining RMSE’s values of 0.544, 0.540 and 0.766 Å
by superimposing molecule Awith molecule B, molecule A
with optimized structure and molecule B with optimized
structure, respectively. This magnitude of RMSE can be
explained by the fact that the intermolecular columbic in-
teraction with the neighboring molecules are absent in gas
phase, whereas the experimental result corresponds to in-
teracting molecules in the crystal lattice.
The two independent molecules A and B are linked
via N6B–H1NB...Cl1A hydrogen bonds. Also, the molecu-
lar conformation is stabilized by intramolecular C10A–
H10B...N4A and C10B–H10A...N4B hydrogen bonds in
molecule A and molecule B, respectively, both forming
S(6) ring motifs. In the crystal packing, each inversion-re-
lated molecules of A and B form a centrosymmetric dimer
through intermolecular N6A–H2NA...N5A and N6B–
H2NB...N5B hydrogen bonds, respectively, each locally
2
creates a R2 (8) ring motifs. This dimers are further con-
nected by intermolecular N6A–H1NA...Cl1B and C19A–
H19A...Cl2B hydrogen bonds forming an infinite two di-
mensional supramolecular network lying parallel to the [0
1 0] plane [Table 2 and Fig. 2]
DFT calculations
The first task of the computational work is to deter-
mine the optimized geometry of the title compound. The
starting coordinates were obtained from X-ray structure
determination. The optimized parameters (bond lengths,
bond angles) of the compound (1) were obtained using
(DFT/B3LYP) method with the 6-311G(d,p) basis set. The
results are listed in Table 3 and compared with the experi-
mental data for the title compound.
As seen from the Table 3, the agreement between the
theoretically calculated and the experimentally obtained
structure parameters for the title compound are very good.
Table 2. Hydrogen bonding geometry for compound (1) (Å, °)
D–H...A
d(D–H) d(H...A) d(D...A) < (DHA)
N6B–H1NB...CL1A
C10A–H10B...N4A
C10B–H10E...N4B
N6A–H2NA...N5A i
N6B–H2NB...N5B ii
N6A–H1NA...Cl1B iii
C19A–H19A...Cl2B iv
0.86
0.96
0.96
0.86
0.86
0.86
0.93
2.55
2.47
2.46
2.23
2.22
2.57
2.67
3.398(3) 169.0
3.082(4) 121.0
3.093(2) 123.0
3.033(3) 154.5
3.011(3) 153.8
3.423(3) 169.8
3.602(3) 176.4
Fig. 2. View of two dimensional supramolecular net-
work parallel to [0 1 0] plane showing N–H…N
(brown and cyan lines), N–H…Cl (purple lines)
and C–H…Cl (yellow lines) interactions. Hy-
drogen atoms not included in the hydrogen
bonding are omitted for clarity.
Symmetry codes (i) -x + 1, -y + 1, -z; (ii) -x + 2, -y + 1, -z + 1;
(iii) x, y, z - 1; (iv) x - 1, y + 1, z - 1.
976
www.jccs.wiley-vch.de
© 2015 The Chemical Society Located in Taipei & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
J. Chin. Chem. Soc. 2015, 62, 974-983

JOURNAL OF THE CHINESE
CHEMICAL SOCIETY
XRD, DFT and Antibacterial Studies of a Triazole Derivative
Table 3. Selected structural parameters by X-ray diffraction and
Mulliken analysis
DFT calculations for compound (1)
The atomic charge in molecules is fundamental to
chemistry. For instance, atomic charge has been used to de-
scribe the processes of electronegativity equalization and
charge transfer in chemical reactions14,15 and to model the
electrostatic potential outside molecular surfaces.16-18 Mul-
liken atomic charges calculated at the B3LYP/6-311G(d,p)
methods are collected in Table 4. It is worthy to mention
that C19, C17, C15, C14, C13, C11 and C9 atoms of title
compound exhibit positive charges, while other carbon at-
oms exhibit negative charges. Nitrogen N4 and N6 has a
negative charge value. The charge values for Nitrogen N4,
N6, Cl1 and C10 atoms are -0.4137, -0.4654, -0.0518 and
-0.2498 a.u., respectively. The positive atomic charge is
obtained for H10B and H6B is 0.1429 and 0.2228 a.u., re-
spectively. However, all the hydrogen atoms exhibit a net
positive charge. These magnitudes are changing between
-0.4659 and 0.2228 a.u. The presence of large negative
charge on Cl1, C10, N6 and N4 atoms and net positive
charge on H10B and H6B atoms may confirms the forma-
tion of C10–H10B…N4 and N6–H6B…Cl1 intramole-
cular interactions in solid forms.
X-ray
Parameters
DFT
Molecule A Molecule B
Bond lengths (Å)
C12-C13
1.381(4)
1.335(3)
1.343(3)
1.343(3)
1.348(4)
1.373(4)
1.385(4)
1.736(3)
1.365(4)
1.364(5)
1.732(3)
1.374(4)
1.373(4)
1.331(3)
1.335(3)
1.351(3)
1.347(3)
1.375(4)
1.375(4)
1.727(3)
1.358(4)
1.369(5)
1.733(3)
1.379(4)
1.392
1.341
1.342
1.340
1.368
1.402
1.393
1.759
1.387
1.390
1.756
1.387
C13-N5
C14-N4
C14-N5
C14-N6
C15-C16
C16-C17
C16-Cl1
C17-C18
C18-C19
C18-Cl2
C19-C20
Bond angles (°)
N5-C13-C12
N4-C14-N5
N4-C14-N6
N5-C14-N6
C15-C16-C17
C15-C16-Cl1
C17-C16-Cl1
C18-C17-C16
C19-C18-C17
C19-C18-Cl2
C17-C18-Cl2
C18-C19-C20
C19-C20-C15
C13-N5-C14
Torsion angles (°)
N5-C13-C15-C20
C5–C6–C7–N1
C15-C13-N5-C14
N6-C14-N4-C11
122.6(2)
126.1(3)
117.0(3)
117.0(2)
123.1(2)
119.7(2)
117.1(2)
117.7(3)
121.5(3)
118.9(2)
119.6(3)
119.2(3)
121.9(3)
116.2(2)
122.2(2)
126.2(2)
117.5(2)
116.4(2)
123.2(3)
119.3(2)
117.4(2)
117.7(3)
121.6(3)
119.2(3)
119.1(3)
119.6(3)
120.7(3)
116.1(2)
121.80
126.54
116.91
116.53
121.70
122.06
119.15
119.15
121.10
119.75
119.15
118.63
122.43
116.53
Table 4. Mulliken atomic charges of compound (1) at DFT level
Atoms
Cl1
Cl2
N1
Atomic charges
-0.0518
-0.0593
-0.3279
-0.0296
-0.2396
-0.4137
-0.3862
-0.4654
-0.0443
-0.0908
-0.0846
-0.0920
-0.0712
-0.1348
-0.0122
-0.0634
0.2801
Atoms
C15
C16
C17
C18
C19
C20
H6A
H1
Atomic charges
0.0543
-0.2359
0.1421
-0.2372
0.0242
-0.0220
0.2228
0.1126
0.2248
0.1023
0.0998
0.0981
0.0875
0.1275
0.1606
0.1381
0.1429
0.1198
0.1395
0.1405
0.1209
0.1094
N2
N3
N4
N5
-54.6(4)
- 102.4(4)
178.7(2)
-179.4(1)
-75.7(4)
-42.6(1)
-179.1(2)
-179.0(3)
-40.1
-131.9
177.6
177.5
N6
C1
H6B
H2
C2
C3
H3
C4
H4
C5
H5
C6
H7A
H7B
H10A
H10B
H10C
H12
H17
H19
H20
C7
C8
C9
C10
C11
C12
C13
C14
-0.2498
0.1425
Fig. 3. Atom-by-atom superimposition of the calcu-
lated structure (red) on the X-ray structure
(Molecule A – Black; Molecule B - blue) for
compound (1).
-0.0465
0.1208
0.4470
J. Chin. Chem. Soc. 2015, 62, 974-983
© 2015 The Chemical Society Located in Taipei & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.jccs.wiley-vch.de
977

Article
Murugavel et al.
Molecular orbital studies
Chemical hardness is associated with the stability and reac-
tivity of a chemical system. In a molecule, it measures the
resistance to change in the electron distribution or charge
transfer. On the basis of frontier molecular orbitals, chemi-
cal hardness corresponds to the gap between the Highest
Occupied Molecular Orbital (HOMO) and Lowest Unoc-
cupied Molecular Orbital (LUMO). Chemical hardness is
approximated using equation h = (ELUMO - EHOMO)/2, where
ELUMO and EHOMO are the LUMO and HOMO energies, re-
spectively. The larger the HOMO–LUMO energy gap, the
molecule will be harder, more stable and less reactive. Ta-
ble 5 (row 4) contains the computed chemical hardness
value for title compound.
The most widely used theory by chemists is the mo-
lecular orbital (MO) theory. The frontier molecular orbitals
play an important role in the electronic and optical proper-
ties, as well as in UV-VIS spectra and chemical reactions.19
The DFT calculated electronic absorption spectra, the max-
imum absorption wavelength corresponding to the elec-
tronic transition is from the highest occupied molecular or-
bital (HOMO) to the lowest unoccupied molecular orbital
(LUMO). The frontier molecular orbital energies of the ti-
tle compound are shown in Fig. 4.
The energy gap between HOMO and LUMO is a criti-
cal parameter in determining molecular electrical transport
properties.20,21 The lowest unoccupied molecular orbital
(LUMO) energy is -1.7557 eV and the highest occupied
molecular orbital (HOMO) energy is -6.2222 eV. The en-
ergy gap of HOMO–LUMO explains the ultimate charge
transfer interaction within the molecule, and the frontier or-
bital energy gap of title compound is found to be -4.4665
eV obtained at DFT method using 6-311G(d,p) basis set.
Lower the HOMO–LUMO gap explains the eventual
charge transfer interactions taking place within the mole-
cule, which influences the biological activity of the mole-
cule.
The concept of electronegativity put forward by
Pauling22 is defined as “the power of an atom in a molecule
to attract electrons towards itself”. Higher is the electro-
negativity of the species, greater is its electron accepting
power or rather the electrophilicity. Electronegativity is de-
termined using equation c = -(EHOMO + ELUMO)/2, Table 5
(row 6) contains the computed electronegativity values for
the title compound.
Electronic chemical potential is defined as the nega-
tive of electronegativity of a molecule23 and determined us-
ing equation m = (EHOMO + ELUMO)/2. Physically, m de-
scribes the escaping tendency of electrons from an equilib-
rium system.24 The value of m for the title compound is pre-
sented in Table 5 (row 5).
Chemical reactivity
Chemical reactivity indices like chemical hardness
(h), electronegativity (c), electronic chemical potential (m),
and electrophilicity Index (w), are calculated using DFT.
Global electrophilicity index (w), introduced by Parr,
is calculated using the electronic chemical potential and
chemical hardness as shown in equation w = m2/2h.
Electrophilicity index measures the propensity or capacity
of a species to accept electrons.25,26 It is a measure of the
stabilization in energy after a system accepts additional
amount of electronic charge from the environment.27,28 The
electrophilicity values of the title compound is presented in
(Table 5, row 7).
Table 5. Calculated energy values of compound (1)
Basis set
B3LYP/6-311G(d, p)
-6.222
EHOMO (eV)
ELUMO (eV)
-1.756
E
HOMO - ELUMO gap (eV)
-4.466
Chemical hardness (h)
Chemical potential (m)
Electronegativity (c)
2.233
-3.989
3.989
Fig. 4. The molecular orbital’s and energies for the
HOMO and LUMO of the title compound.
Electrophilicity index (w)
3.563
978
www.jccs.wiley-vch.de
© 2015 The Chemical Society Located in Taipei & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
J. Chin. Chem. Soc. 2015, 62, 974-983

JOURNAL OF THE CHINESE
CHEMICAL SOCIETY
XRD, DFT and Antibacterial Studies of a Triazole Derivative
The HOMO and LUMO orbital energies are related to
gas phase ionization energies (I) and electron affinities (A)
of the isomers according to the Koopmans’ theorem
through equations A = - ELUMO, I = - EHOMO. Electron affin-
ity refers to the capability of a ligand to accept precisely
one electron from a donor.
Thermodynamic properties
The thermodynamics parameters of the compound
have also been computed in order to get reliable relations
among energetic, structural and reactivity characteristics of
the molecules. Knowledge of permanent dipole moment of
a molecule allows us to determine molecule’s conforma-
Molecular electrostatic potential
The molecular electrostatic potential (MEP) is a plot
of electrostatic potential mapped onto the constant electron
density surface. The MEP has been used primarily for pre-
dicting sites and relative reactivity towards electrophilic at-
tack, in studies of biological recognition and hydrogen
bonding interactions.29,30 The negative electrostatic poten-
tial corresponds to an attraction of the proton by the con-
centrated electron density in the molecule (and is coloured
in shades of red on the EPS surface), the positive electro-
static potential corresponds to repulsion of the proton by
atomic nuclei in regions where low electron density exists
and the nuclear charge is incompletely shielded (and is col-
oured in shades of blue). Potential increases in the order red
< orange < yellow < green < blue.
Fig. 5 shows the molecular electrostatic potential
(MEP), was determined using B3LYP/6-311G(d, p) me-
thod. The different values of the electrostatic potential at
the surface are represented by different colours. As can be
seen in Fig. 6, the negative (red) region is localized on the
unprotonated atom of N5 and Cl1, with a minimum value of
-0.034 and -0.0204 a.u., respectively. However, maximum
positive (blue) region is localized on atom N6 and C19
probably due to hydrogen H6 and H19 with a value of
0.046 and 0.035 a.u., respectively and green represents re-
gion of zero potential. Therefore, Fig. 5 confirms the exis-
tence of an intermolecular N–H…N, N–H…Cl and
C–H…Cl interactions.
Fig. 5. Molecular electrostatic potential map calcu-
lated using B3LYP/6-311G(d, p) level.
Fig. 6. Variation of thermodynamic parameters with
temperature for compound (1).
J. Chin. Chem. Soc. 2015, 62, 974-983
© 2015 The Chemical Society Located in Taipei & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.jccs.wiley-vch.de
979

Article
Murugavel et al.
tion. The values of thermodynamic parameters such as
zero-point vibrational energy, thermal energy and dipole
moment of title compound by Hartree-Fock(HF) and DFT
methods with same 6-311G (d,p) basis set at 298.15 K and
1 atm pressure were calculated and listed in Table 6. From
Table 6, the high value of dipole moment of title compound
obtained by HF and DFT methods signifies high delocal-
ization of charges, resulting in the formation of relatively
loose structured and charge separated species.
These equations could be used for further studies on
the title compound. For instance, when the interaction of ti-
tle compound with another compound is studied, these
thermodynamic properties could be obtained from the
above equation and then can be used to calculate the
change in Gibbs free energy of the reaction, which will in
turn help to judge the spontaneity of the reaction.
Interpretation of antibacterial activity
Each zone size is interpreted by reference to the Table
2G (Zone Diameter Interpretative Standards and equiva-
lent Minimum Inhibitory Concentration Breakpoints) of
the NCCLS M100-S12: Performance Standards for Anti-
microbial Susceptibility Testing: Twelfth Informational
Supplement.31 Results indicated that target compound ex-
hibited significant antimicrobial activity against selected
pathogens, Bacillus cerus, Escherichia coli, Acinetobacter
baumann, Staphylococcus epidermidis and Proteus vul-
garis when compared with the standard antibiotic cipro-
floxacin (25 mg).
The temperature dependence of the thermodynamic
properties such as heat capacity at constant pressure (C°p ,m ),
entropy (S°m ) and enthalpy (H°m ) for the title compound have
been determined by B3LYP/6-311G(d,p) method in tem-
perature range 100–500 K and listed in Table 7. From Table
7, it can be observed that these thermodynamic parameters
increase with rise of temperature due to the fact that the mo-
lecular vibrational thermal energies increase with tempera-
ture. The correlation equations between heat capacities,
entropies, enthalpy changes and temperatures were fitted by
quadratic formulas given in equations. Below, and the corre-
sponding fitting factors (R2) for these thermodynamic
properties were found to be 0.999. The temperature de-
pendence correlation graphs are shown in Fig.7.
The compound exhibits good antibacterial activity
against Escherichia coli and Acinetobacter baumannii and
exhibits moderate activity against Bacillus cereus, Staphy-
lococcus epidermidis and Proteus vulgaris as shown in Ta-
ble 8.
C°p ,m = 7.1982 + 0.30962 T - 8.47571 E ´ 10-5 T2
(R2 = 0.9993)
EXPERIMENTAL
S°m = 70.5082 + 0.38189 T - 1.038E ´ 10-4 T2
(R2 = 0.9999)
H°m = 207.2974 + 0.01258 T + 1.3155E ´ 10-4 T2
(R2 = 0.999)
Synthesis of (1): The title compound (1) was obtained ac-
cording to the reaction Scheme 1.32 A mixture of (E)-1-(1-benzyl-
5-methyl-1H-1,2,3-triazol-4-yl)-3-(2,4-dichlorophenyl)prop-2-
en-1-one(0.2 g, 0.53 mmol), guanidine hydrochloride (0.15 g,
1.57 mmol) and NaOH (0.04 g, 1.0 mmol) in ethanol (10 mL) was
refluxed for 40 min. Then, the reaction mixture was poured onto
excess crushed ice and neutralized with dilute hydrochloric acid.
The precipitated 4-(1-benzyl-5-methyl-1H-1,2,3-triazol-4-yl)-
6-(2,4-dichlorophenyl)pyrimidin-2-amine was filtered and recry-
stallized from ethanol. Needle like colourless single crystals of
the title compound used in X-ray diffraction studies were grown
Table 6. Thermodynamical parameters of compound (1) at 298K
Parameters
HF/6-311G(d, p) B3LYP/6-311G(d, p)
Total energy (Hartree)
Zero point energy
(K cal.mol-1)
-2012.26
222.706
-2020.99
207.568
Rotational constants
(GHz)
0.34544
0.05590
0.05398
85.500
0.34189
0.05570
0.07176
Table 7. Thermodynamic properties at different temperatures of
compound (1) at B3LYP/6-311G(d, p) level
Specific heat (Cv)
(cal.mol-1K-1)
Entropy (cal.mol-1K-1)
Total
91.961
Cop,m
Som
Hom
Temperature (K)
(cal.mol-1K-1) (cal.mol-1K-1) (Kcal.mol-1)
100
200
300
400
500
37.800
64.755
92.469
118.449
140.338
107.427
143.259
175.558
206.369
235.679
209.900
215.025
222.886
233.460
246.437
169.735
43.925
36.976
88.834
6.6392
174.975
43.925
37.000
94.050
6.6033
Translational
Rotational
Vibrational
Dipole moment (Debye)
980
www.jccs.wiley-vch.de
© 2015 The Chemical Society Located in Taipei & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
J. Chin. Chem. Soc. 2015, 62, 974-983

JOURNAL OF THE CHINESE
CHEMICAL SOCIETY
XRD, DFT and Antibacterial Studies of a Triazole Derivative
tained by a least-squares fit of several high angle reflections in the
ranges 1.90° < q < 28.36° for the title compound. The unit cell pa-
rameters were determined for 36 frames measured (0.5° phi-scan)
from three different crystallographic zones and using the method
of difference vectors. The intensity data were collected with an
average four-fold redundancy per reflection and optimum resolu-
tion (0.75 Å). The intensity data collection, frames integration,
Lorentz-polarization correction and decay correction were done
using SAINT-NT (version 7.06a) software. Empirical absorption
correction (multi-scan) was performed using SADABS33 pro-
gram. The structure was solved by direct methods using
SHELXS-97 implemented in WinGX34 program suit. The refine-
ment was carried out by full-matrix least-square method on the
positional and anisotropic temperature parameters of the non-hy-
drogen atoms, using SHELXL-97.35 All the H atoms were posi-
tioned geometrically and constrained to ride on their parent atom
with C–H = 0.93–0.97 Å and N–H = 0.86 Å, and with Uiso(H) =
1.5 Ueq for methyl H atoms and 1.2 Ueq(C) for other H atoms. Ow-
ing to poor agreement, the reflection [1 1 0], was omitted from the
final cycles of refinement. The general-purpose crystallography
tool PLATON,36 ORTEP37 and MERCURY38 were used for struc-
ture analysis and presentation of the results. Crystallograhic data
for the structure reported in this article have been deposited in the
Cambridge Crystallographic Data Center with a supplementary
publication number of CCDC 1001329. Copies of these informa-
tion can be obtained free of charge from the Director, CCDC, 12
Union Road, Cambridge CB2 1EZ, UK (fax: +44 1223 336 033;
e-mail: deposit@ccdc.cam.ac.uk).
Table 8. Antibacterial activity of compound (1) at different
concentrations against bacterial pathogens
Zone of inhibition (mm)
Compound concentration
Microorganisms
Positive control
(25
(50
mg/ml)
(75
mg/ml)
CIPX (25 mg)
mg/ml)
Bacillus cereus
(MTCC 430)
24
18
30
21
18
30
20
36
24
21
36
23
42
28
27
38
24
30
18
30
Staphylococcus
epidermidis
(MTCC 10623)
Escherichia coli
(MTCC 443)
Acinetobacter
baumannii
(MTCC 1425)
Proteus vulgaris
(MTCC 742)
in an ethanolic solution by slow evaporation of the solvent at
room temperature and collected in 79% yield.
Reaction scheme and chemical diagram of
Scheme 1
the title compound (1)
Computational details: The molecular structure of the
compound in ground state (in vacuo) was optimized using density
functional theory DFT (B3LYP)39,40 method with the 6-311G(d,p)41
basis set. All the calculation was performed without specifying
any symmetry for the title molecule by using GaussView molecu-
lar visualization program42 and Gaussian 03 program package.43
The optimized geometrical parameters, energy, atomic charges
and dipole moments were calculated using Gaussian 03W pack-
age. GaussView 03 program has been using to construct opti-
mized molecular geometry, Mullikan charges, HOMO-LUMO
energy gap,44,45 Molecular electrostatic potential, chemical reac-
tivity and thermodynamic properties.
White solid; m.p. 181 °C, Yield: 79%. 1H NMR (300 MHz,
CDCl3): d 7.80 (1H, s, =CH), 7.56-7.50 (2H, m, ArH), 7.35-7.33
(4H, m, ArH), 7.26 (1H, s, ArH), 7.26-7.20 (1H, m, ArH), 5.56
(2H, s, C6H5-CH2), 5.14 ( 2H, brs, NH2), 2.62 (3H, s, CH3); 13C NMR
(75 MHz, CDCl3): d 165.67, 163.15, 160.10, 139.05, 134.56,
134.02, 129.68, 129.11, 129.06, 128.40, 127.19, 119.74, 116.82,
112.09, 104.60, 51.62, 9.73.
X-ray Crystallography: The Crystal of the title compound
having approximate dimension 0.30 ´ 0.24 ´ 0.11 mm3 was
mounted on a glass fiber using cyanoacrylate adhesive. All mea-
surement were made on a Bruker AXS Kapppa Apex II single
crystal X-ray diffractometer using graphite mono-chromated
MoKa (l = 0.71071 Å) radiation and CCD detector. Diffraction
data were collected at room temperature by the w-scan technique.
Accurate unit cell parameters and orientation matrix were ob-
Antibacterial test: Antibacterial susceptibility test was
carried out using Kirby-bauer disk diffusion method as per CLSI
M38-A guidelines.46
The synthesized compound was dissolved in DMSO at var-
ious concentrations (25, 50 and 75 mg/ml) and tested against se-
lected bacterial pathogens. Suspension of bacterial isolates was
adjusted to 0.5 McFarland standards in 0.85% saline (suspension
J. Chin. Chem. Soc. 2015, 62, 974-983
© 2015 The Chemical Society Located in Taipei & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.jccs.wiley-vch.de
981

Article
Murugavel et al.
will contain approximately 4 ´ 108 CFU/ml) and lawn culture was
spread using sterile swabs on Muller Hinton agar media (Hi-me-
dia, Mumbai). Wells (6 mm/dm, 2 cm apart) were bored upon the
lawn culture of the agar media using a sterile borer. Test com-
pound (25, 50 and 75 mg/ml) were loaded to the wells under asep-
tic conditions and the plates were incubated at 37 °C for 24 hours.
Presence of inhibition zones surrounding each well evidenced
antimicrobial activity. The antimicrobial activity was evaluated
by measuring the inhibition zones diameter in millimeters. Each
experiment was repeated three times and the mean of inhibitory
zones were recorded. Tests strains were procured from MTCC,
INTECH, Chandigarh, India. They include Bacillus cerus
(MTCC 430), Escherichia coli (MTCC 443), Acinetobacter
baumannii (MTCC 1425), Staphylococcus epidermidis (MTCC
10623), and Proteus vulgaris (MTCC 742). Standard antibiotic
ciprofloxacin (25 mg) was used as positive control to perform the
test.
dicate that the compound exhibit good to moderate activity
against tested pathogens.
ACKNOWLEDGEMENTS
The authors thank Dr. Shibu M. Eapen, STIC, Co-
chin, India, for his help with the data collection.
REFERENCES
1. Morales-Sanfrutos, J.; Ortega-Munoz, M.; Lopez-Jaramillo,
J.; Hernandez-Mateo, F.; Santoyo-Gonzalez, F. J. Org.
Chem. 2008, 73, 7768-7771.
2. Genin, M. J.; Allwine, D. A.; Anderson, D. J.; Barbachyn,
M. R.; Emmert, D. E.; Garmon, S. A.; Graber, D. R.; Grega,
K. C.; Hester, J. B.; Hutchinson, D. K.; Morris, J.; Reischer,
R. J.; Ford, C. W.; Zurenko, G. E.; Hamel, J. C.; Schaadt, R.
D.; Stapert, D.; Yagi, B. H. J. Med. Chem. 2000, 43, 953-970.
3. Buckle, D. R.; Rockell, C. J. M.; Smith, H.; Spicer, B. A. J.
Med. Chem. 1986, 29, 2262-2267.
4. Giffin, M. J.; Heaslet, H.; Brik, A.; Lin, Y. C.; Cauvi, G.;
Wong, C. H.; McRee, D. E.; Elder, J. H.; Stout, C. D.;
Torbett, B. E. J. Med. Chem. 2008, 51, 6263-6270.
5. Wang, S.; Wang, Q.; Wang, Y.; Liu, L.; Weng, X.; Zhang, G.
L. X.; Zhou, X. Bioorg. Med. Chem. Lett. 2008, 18, 6505-
6508.
CONCLUSIONS
The title compound was synthesized and has been
confirmed by NMR and structural (single-crystal X-ray
diffraction) techniques. To support the solid state structure,
the geometric parameters of the title compound have been
calculated using density functional theory DFT (B3LYP)
method with the 6-311G(d,p) basis sets, and compared with
the experimental findings. It was noted here that the experi-
mental results belong to solid phase and theoretical calcula-
tions belong to gaseous phase. In the solid state, the exis-
tence of the crystal field along with the intermolecular in-
teractions have connected the molecules together, which
result in the differences of bond parameters between the
calculated and experimental values. The small HOMO-
LUMO gap value shows that the molecule is biologically
active. The MEP map shows that the negative potential
sites are on nitrogen and chlorine atoms as well as the posi-
tive potential sites are around the hydrogen atoms and
hence MEP map confirms the existence of intermolecular
N–H…N, C–H…Cl and N–H…Cl interactions. The calcu-
lated HOMO and LUMO energies can be used to semi
quantitatively estimate the ionization potential, electron af-
finity, electronegativity, electrophilicity index, hardness,
and chemical potential. The correlations between the statis-
tical thermodynamics and temperature are also obtained. It
is seen that the heat capacities, entropies and enthalpies in-
crease with the increasing temperature owing to the intensi-
ties of the molecular vibrations increase with increasing
temperature. The obtained antibacterial activity results in-
6. El-Subbagh, H. I.; Abu-Zaid, S. M.; Mahran, M. A.; Badria,
F. A.; Al-Obaid, A. M. J. Med. Chem. 2000, 43, 2915-2921.
7. Trivedi, A. R.; Dodiya, D. K.; Ravat, N. R.; Shah, V. H.
Arkivoc 2000, XI, 131-141.
8. Koch, W.; Holthausen, M. C. A. A Chemistry Guide to Den-
sity Functional Theory; Wiley-VCH: Weinheim, New York,
Chichester, 2000
9. Parr, R. G.; Yang, W. T. Density Functional Theory of Atoms
and Molecules; Oxford University Press: New York, 1989.
10. Huang, C.-C.; Wu, F.-L.; Lo, Y. H.; Lai, W.-R.; Lin, C.-H.
Acta. Cryst. 2010, E66, o1690.
11. Sarmiento-Sánchez, J. I.; Aguirre, G.; Rivero, I. A. Acta
Cryst. 2011, E67, o1856.
12. Bukhari, M. H.; Siddiqui, H. L.; Chaudhary, M. A.;
Hussaina, T.; Parvezc, M. Acta Cryst. 2008, E64, o963.
13. Jian, F. F.; Zhao, P. S.; Bai, Z. S.; Zhang, L. Struct. Chem.
2005, 16, 635-639.
14. Jug, K.; Maksic, Z. B. Theoretical Model of Chemical Bond-
ing; Springer: Berlin, 1991.
15. Fliszar, S. Charge Distributions and Chemical Effects;
Springer: Berlin, Heidelberg, New York, 1933.
16. Smith, P. E.; Montgomery Pettitt, B. J. Am. Chem. Soc. 1991,
113, 6029-6037.
17. Gao, J. J. Chem. Phys. 1993, 98, 1975-1981.
18. Cieplak, P.; Kollman, P. J. Comput. Chem. 1991, 12, 1232-
1236.
19. Fleming, I. Frontier Orbitals and Organic Chemical Re-
actions; Wiley: London, 1976.
982
www.jccs.wiley-vch.de
© 2015 The Chemical Society Located in Taipei & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
J. Chin. Chem. Soc. 2015, 62, 974-983

JOURNAL OF THE CHINESE
CHEMICAL SOCIETY
XRD, DFT and Antibacterial Studies of a Triazole Derivative
20. Fukui, K. Science 1982, 218, 747-754.
21. Udhayakala, P.; Rajendiran, T. V.; Seshadri, S.; Gunasekaran,
S. J. Chem. Pharm. Res. 2011, 3(3), 610-625.
22. Pauling, L. The Nature of Chemical Bond; Cornell Univer-
sity Press: Ithaca, 1960.
2002, B58, 389.
39. Becke, A. D. J. Chem. Phys. 1993, 98, 648.
40. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. 1998, B37, 785.
41. Ditchfield, R.; Hehre, W. J.; Pople, J. A. J. Chem. Phys.
1971, 54, 724-728.
23. Parr, R. G.; Pearson, R. G. J. Am. Chem. Soc. 1983, 105,
7512.
42. Dennington, II., R.; Keith, T.; Millam, J. GaussView (Version
4.1.2.) Semichem Inc.: Shawnee Mission, 2007.
24. Chattaraj, P. K.; Maiti, B. J. Am. Chem. Soc. 2003, 125,
2705.
43. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.;
Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.;
Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.;
Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi,
M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.;
Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.;
Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.;
Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.;
Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.;
Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski,
J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.;
Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels,
A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A.
D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.;
Baboul, A. G. Clifford, S.; Cioslowski, J.; Stefanov, B. B.;
Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R.
L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.;
Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson,
B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A.
Gaussian 03, Revision B.05. 2004 Gaussian Inc.: Pittsburgh.
44. Frisch, A. E.; Nielsen, A. B.; Holder, A. J. Gaussview
Gaussian Inc.: Pittsburgh, 2003.
25. Vektariene, A.; Vektaris, G.; Svoboda, J. ARKIVOC 2009, 7,
311.
26. Parr, R. G.; Szentpaly, L.; Liu, S. J. Am. Chem. Soc. 1999,
121, 1922.
27. Koopmans, T. Physica 1933, 1, 104.
28. Liu, S. J. Chem. Sci. 2005, 117, 477.
29. Murray, J. S.; Sen, K. Molecular Electrostatic Potentials,
Concepts and Applications; Elsevier: Amsterdam, 1996; pp
7-624.
30. Scrocco, E.; Tomasi, J. Adv. Quant. Chem. 1978, 11, 115.
31. National Committee for Clinical Laboratory Standards
(NCCLS). Performance Standards for Antimicrobial Sus-
ceptibility Testing; 2002 Twelfth Informational Supplement,
Wayne, PA, M100-S.
32. Nagarajan, S.; Shanmugavelan, P.; Sathishkumar, M.; Selvi,
R.; Ponnuswamy, A.; Harikrishnan, H.; Shanmugaiah, V.
Chin. Chem. Lett. 2014, 25, 419-422.
33. Bruker, APEX-II, SAINT-Plus (Version 7.06a), (BrukerAXS
Inc. Madion, Wisconsin, USA, 2004).
34. Farrugia, L. J. J. Appl. Cryst. 1999, 32, 837.
35. Sheldrick, G. M. Acta Cryst. 2008, A64, 12.
36. Spek, A. L. J. Appl. Cryst. 2003, 36, 7.
37. Farrugia, L. J. J. Appl. Cryst. 1997, 30, 565.
38. Bruno, I. J.; Cole, J. C.; Edgington, P. R.; Kessler, M.;
Macrae, C. F.; McCabe, P.; Pearson, J.; Taylor, R. Acta Cryst.
45. Young, D. C. Computational Chemistry: A Practical Guide
for Applying Techniques to Real-World Problems; John
Wiley & Sons Inc.: New York, 2001.
46. Bauer, A. W.; Kirby, W. M. M.; Sherris, J. C.; Turck, M. Am.
J. Clin. Pathol. 1966, 45, 493.
J. Chin. Chem. Soc. 2015, 62, 974-983
© 2015 The Chemical Society Located in Taipei & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.jccs.wiley-vch.de
983