(E)-3-Chloro-N-((5-nitrothiophen-2-yl)methylene)aniline: A combined crystallographic, theoretical and antimicrobial activity investigation

Article abstract of DOI:10.1016/j.saa.2012.06.032

The title molecule, (E)-3-chloro-N-((5-nitrothiophen-2-yl)methylene) aniline, (C₁₁H₇ClN₂O₂S), was synthesized and characterized by IR and single-crystal X-ray structure determination. The compound crystallizes in the monoclinic space group P2 ₁/c. In addition, the molecular geometry, vibrational frequencies and frontier molecular orbitals analysis of the title compound in the ground state have been calculated by using the PM3 semi-empirical, HF/6-31G(d) and B3LYP/6-31G(d) ab initio methods. The results of the optimized molecular structure are exhibited and compared with the experimental X-ray diffraction and the calculated results are show that the optimized geometry can well reproduce the crystal structure. The Schiff base compounds are very important in medicinal and pharmaceutical fields because of their wide spectrum of biological activities. Most of them show biological activities such as antimicrobial, antifungal as well as antitumor activity. Therefore, (C₁₁H ₇ClN₂O₂S) was investigated for their antimicrobial activities, Gram-positive and Gram-negative bacteria.

Full text of DOI:10.1016/j.saa.2012.06.032

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 97 (2012) 423–428
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Spectrochimica Acta Part A: Molecular and
Biomolecular Spectroscopy
journal homepage: www.elsevier.com/locate/saa
(E)-3-Chloro-N-((5-nitrothiophen-2-yl)methylene)aniline: A combined
crystallographic, theoretical and antimicrobial activity investigation
a
b
b
c
Ißsıl Yılmaz a, , Canan Kazak , Sümeyye Gümüßs , Erbil Ag˘ar , Yüksel Ardalı
⇑
a Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, Kurupelit, 55139 Samsun, Turkey
b Department of Chemistry, Faculty of Arts and Sciences, Ondokuz Mayıs University, Kurupelit, 55139 Samsun, Turkey
c Department of Environmental Engineering, Faculty of Engineering, Ondokuz Mayıs University, Kurupelit, 55139 Samsun, Turkey
g r a p h i c a l a b s t r a c t
h i g h l i g h t s
"
"
"
Structural properties of (C11H7ClN
2O2S) are characterized by IR and X-
ray diffraction techniques.
Results obtained from experimental
techniques and those from PM3, HF
and B3LYP methods were compared.
(C11H7ClN2O2S) were screened for
antimicrobial activity against Gram-
positive, Gram-negative bacteria and
yeast.
a r t i c l e i n f o
a b s t r a c t
Article history:
The title molecule, (E)-3-chloro-N-((5-nitrothiophen-2-yl)methylene)aniline, (C11H7ClN2O2S), was syn-
thesized and characterized by IR and single-crystal X-ray structure determination. The compound crys-
tallizes in the monoclinic space group P21/c. In addition, the molecular geometry, vibrational
frequencies and frontier molecular orbitals analysis of the title compound in the ground state have been
calculated by using the PM3 semi-empirical, HF/6-31G(d) and B3LYP/6-31G(d) ab initio methods. The
results of the optimized molecular structure are exhibited and compared with the experimental X-ray
diffraction and the calculated results are show that the optimized geometry can well reproduce the crys-
tal structure. The Schiff base compounds are very important in medicinal and pharmaceutical fields
because of their wide spectrum of biological activities. Most of them show biological activities such as
antimicrobial, antifungal as well as antitumor activity. Therefore, (C11H7ClN2O2S) was investigated for
their antimicrobial activities, Gram-positive and Gram-negative bacteria.
Received 21 February 2012
Received in revised form 12 May 2012
Accepted 23 June 2012
Available online 30 June 2012
Keywords:
Schiff base
X-ray diffraction
Antimicrobial activity
Vibrational spectra
PM3
Quantum chemical calculations
Ó 2012 Elsevier B.V. All rights reserved.
Introduction
anti-inflammatory, antiviral, and antipyretic properties [11,12].
Investigation of structural stability of compounds by both experi-
Azomethines (known as Schiff-bases), having imine groups
(CH@N) and benzene rings in the main chain alternately, and being
-conjugated, exhibit interest as materials for wide spectrum
applications, particularly as corrosion inhibitors [1], catalyst
carriers [2,3], thermo-stable materials [4–6], a metal ion complex-
ing agents [7] and in biological systems [8–10]. Schiff bases have
also been shown to exhibit a broad range of biological activities,
including antifungal, antibacterial, antimalarial, antiproliferative,
mental techniques and theoretical methods has been of great inter-
est. Functional material design, theoretical modeling of drug
design and so on, has become possible as results of the develop-
ment of the computational techniques. Many important properties
such as molecular orbitals, electrostatic potentials, dipole moment,
reaction pathways, vibrational frequencies can be predicted by var-
ious computational techniques [13]. In this paper, we present the
synthesis, molecular structure, spectroscopic characterization and
antimicrobial activities of (E)-3-chloro-N-((5-nitrothiophen-2-
yl)methylene)aniline. Calculations were performed by using PM3
semi-empirical, HF and B3LYP ab initio methods with 6-31G(d)
basis set. These calculations are valuable for providing insight into
p
⇑
Corresponding author. Tel.: +90 3623121919; fax: +90 3624576081.
E-mail address: isilylmaz@gmail.com (I. Yılmaz).
1386-1425/$ - see front matter Ó 2012 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.saa.2012.06.032

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I. Yılmaz et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 97 (2012) 423–428
Table 1
molecular properties of Schiff base compounds. In order to provide
templates for molecular modeling studies, experimental results
obtained from X-ray crystallography and those from PM3, HF and
B3LYP methods were compared.
Crystal data and structure refinement for C11H7ClN2O2S.
Formula
C11H7ClN2O2S
Formula weight (g)
Temperature (K)
Wavelength (Mo, Å)
Crystal system
Space group
266.70
293
0.71073
Monoclinic
P21/c
Experimental and theoretical methods
Synthesis
Unit cell dimensions
a, b, c (Å)
22.003(5), 7.457(5), 15.089(5)
b (°)
108.995(5)
2340.9 (18)
8
1.513
0.49
The compound 2-[(3-Chlorophenylimino)methyl]-5-nitrothi-
ophene was prepared by reflux a mixture of a solution containing
5-nitro-2-thiophene-carboxaldehyde (0.134 g, 0.850 mmol) in
20 ml ethanol and a solution containing 3-chloroaniline (0.109 g,
0.850 mmol) in 20 ml ethanol. The reaction mixture was stirred
for one hunder reflux. The crystals of 2-[(3-Chlorolphenylimi-
no)methyl]-5-nitrothiophene suitable for X-ray analysis were ob-
tained from ethylalcohol by slow evaporation (yield: 0.165 g,
68%; m.p 107–110 °C).
Volume (Å3)
Z
Calculated density (g cmÀ3
)
l
(nmÀ1
)
F(0,0,0)
Crystal size (mm)
h ranges (°)
Index ranges
1088
0.71 Â 0.33 Â 0.11
2.0–26.0
À27 6 h 6 27
À9 6 k 6 9
À18 6 l 6 18
32156
Reflections collected
Independent reflections
4606 [R(int) = 0.059]
3642
Integration
Full-matrix least-squares on F2
4606/0/307
1.06
0.036
0.093
0.26 and À0.36
General methods
Reflection observed (>2
Absorption correction
Refinement method
r)
The IR spectrum was recorded in the 4000–400 cmÀ1 region
using KBr pellet on a Schmadzu FTIR-8900 spectrophotometer.
Antimicrobial activity of the title compound was investigated
against standard strains of Gram-negative, Escherichia coli (ATCC
25922) and Salmonella typhi (clinic isolate), Gram-positive Strepto-
coccus pneumoniae (clinic isolate), Staphylococcus aureus (ATCC
25923), Methicillin Resistant Staphylococcus aureus MRSA (clinic iso-
late), Methicillin Sensitive Staphylococcus aureus MSSA (clinic isolate)
and Entrococcus faecalis (ATCC 29212). The compound was dis-
solved in DMSO and sterilized using a millipore membrane filter
Data/restrains/parameters
Goodness-of-fit on F2
Final R indices [I h 2
R indices (all data)
r
(I)]
Largest diff. peak and hole (e ÅÀ3
)
concentration of compounds. Chloramphenicol was used as a refer-
ence inhibitor for bacterial strains.
(0.22 lm). Antibacterial activity was evaluated by minimum inhib-
itory concentration (MIC) using the microdilution method. The
tests were performed according to the Clinical and Laboratory
Standards Institute [14] and National Committee for Clinical Labo-
ratory Standards [15], respectively. All the bacteria mentioned
above were incubated in Muller Hinton Broth at 37 °C for 24 h.
All tests were repeated tree times and average data were taken
as the final result. MICs were determined visually as the lowest
X-ray crystallography
A selected crystal with yellow and dimensions of 0.71 mm
 0.33 mm  0.11 mm was mounted on a STOE IPDS II X-ray dif-
fractometer. Data collection was performed at room temperature
(293 K) using graphite monochromated MoKa radiation (k =
0.71073 Å). A summary of the key crystallographic information is
Fig. 1. The molecular structure of the title molecule, showing the atom-numbering scheme. Displacement ellipsoids are drawn at the %40 probability level and H atoms are
shown as small spheres of arbitrary radii.

I. Yılmaz et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 97 (2012) 423–428
425
geometry optimizations of the title compound leading to energy
minima in vacuo was achieved by using PM3 semi-empirical
method, Hartree–Fock(HF) [21], density functional using Becke’s
three-parameter hybrid functional [22] with the Lee, Yang, and
Parr correlation functional methods (B3LYP)[23]. 6-31G(d) basis
set was used for all calculations. The calculation of harmonic
frequencies for the optimized geometry were made at the same
level. After that, by using Gauss-View molecular visualization
program [24], the vibrational bands were assigned.
Result and discussion
Description of crystal structures
The crystal structure of the title compound is monoclinic and
space group is P21/c. The asymmetric unit in the crystal structure
contains two independent molecules (A and B). The displacement
ellipsoid plots with the numbering scheme for the title compound
are shown in Fig. 1. According to experimentalresults; the molecular
structure of the title compound is not planar by torsion angle C4–
C5–N2–C6 [A, 177.60°; B, 179.90°]. The compound is composed of
chlorobenzene and nitrothiophene groups. In this groups, N–O
[N1A–O1A = 1.228 Å; N1B–O1B = 1.223 Å] [25], C–S [C1A–S1A =
1.705 Å; C1B–S1B = 1.706 Å] [25] and C–Cl [C8A–Cl1A = 1.736 Å;
C8B–Cl1B = 1.740 Å] [26] bond lengths are within normal ranges
and are comparable to the related structures. Besides, the molecular
structure adopts E geometry about azomethine C@N [C5A–N2A
= 1.264 Å; C5B–N2B = 1.266 Å] double bond [26]. The orientation
of the nitro group is defined by torsion angle C2/C1/N1/O1 [A,
À177.15°; B, 4.50°] and C2/C1/N1/O2 [A, 2.7°; B, À3.10°]. In the
crystal, there are no directional interactions but interaction forces
between neighboring molecules; such as van der Waals intermolec-
ular and perspective view of the crystal packing in the unit cell is
shown in Fig. 2. Calculational studies were performed by using
PM3 semi-empirical, HF and B3LYP methods with 6-31G(d) basis
set. In order to provide templates for molecular modeling studies,
Fig. 2. Packing diagram of the compound.
given in Table 1. The cell parameters were determined by using
X-AREA software [16]. The crystal structure was solved by direct
methods using SHELXS-97 [17]. All carbon hydrogens of complex
were positioned geometrically and refined by a riding model with
Uiso 1.2 times that of attached atoms and remaining hydrogen
atoms were located from the Fourier difference map. Molecular
plot was prepared with ORTEP-III for Windows [18]. WinGX soft-
ware [19] was used to prepare material for publication.
Computational methods
Calculations performed by using PM3, HF and B3LYP methods
are carried out with the GAUSSIAN03 program package [20]. The
Table 2
Selected structural parameters by X-ray and theoretical calculations for the title compound.
Bond length
X-ray
A
PM3
A
HF
A
B3LYP
A
B
B
B
B
C1–C2
C1–N1
C1–S1
C4–S1
N1–O1
N1–O2
C4–C5
C5–N2
C6–N2
C6–C7
C8–Cl1
1.355(3)
1.436(3)
1.705(2)
1.717(2)
1.228(3)
1.222(3)
1.452(3)
1.264(3)
1.416(3)
1.383(3)
1.736(3)
1.352(3)
1.436(3)
1.706(2)
1.717(2)
1.223(3)
1.224(3)
1.451(3)
1.266(3)
1.416(3)
1.389(3)
1.740(2)
1.385
1.488
1.737
1.722
1.212
1.214
1.459
1.292
1.429
1.399
1.688
1.385
1.488
1.737
1.722
1.214
1.214
1.459
1.291
1.429
1.399
1.686
1.346
1.432
1.723
1.727
1.194
1.193
1.465
1.252
1.408
1.389
1.745
1.347
1.431
1.723
1.726
1.195
1.194
1.465
1.253
1.407
1.390
1.743
1.374
1.437
1.735
1.744
1.234
1.232
1.448
1.282
1.403
1.406
1.762
1.374
1.437
1.734
1.744
1.234
1.231
1.448
1.282
1.403
1.404
1.759
Rmse
0.03
0.03
0.02
0.02
0.05
0.04
Bond angles (°)
O1–N1–O2
O1–N1–C1
N1–C1–S1
C4–C5–N2
C7–C8–Cl1
123.90(2)
118.16(1)
119.45(7)
120.50(2)
119.00(1)
124.50(2)
118.03(1)
118.60(7)
120.28(1)
118.58(1)
121.64
119.81
126.06
120.40
119.13
121.64
119.70
126.12
120.42
119.21
125.54
116.99
120.62
121.21
118.78
125.34
117.07
120.63
121.11
118.93
125.58
117.03
119.84
121.35
118.94
125.50
117.01
119.72
121.10
118.72
Rmse
3.21
3.10
1.09
1.02
0.91
0.90
Torsion angles (°)
O2–N1–C1–S1
C4–C5–N2–C6
C3–C4–C5–N2
C11–C6–N2–C5
À179.84(1)
177.60(3)
174.50(1)
145.50(2)
178.71(1)
179.91(2)
180.00(1)
140.80(1)
À179.91
179.69
177.50
144.50
179.88
178.90
177.48
143.98
À180.91
178.98
179.45
141.14
À179.84
À180.27
179.20
À178.87
177.33
179.02
147.62
177.65
179.88
180.12
141.32
140.42
Rmse
2.01
1.95
2.74
2.45
2.95
2.80

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I. Yılmaz et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 97 (2012) 423–428
frequency calculations and comparisons with experimental values
were performed for A molecule.
Geometry optimization
A logical method for globally comparing the structures obtained
with the theoretical calculations is by superimposing the molecu-
lar skeleton with that obtained from X-ray diffraction, giving a
RMSE of 0.19 Å for PM3, 0.11 Å for HF/6-31G(d), 0.08 Å for
B3LYP/6-31G(d) calculations (Fig. 3). Consequently, the B3LYP
method correlates well for the geometrical parameters when com-
pared with HF and PM3.
Fig. 3. Atom-by-atom superimposition of the structures calculated (red) (a = PM3,
b = HF, c = B3LYP) on the X-ray structure (black) of the title compound hydrogen
atoms have been omitted for clarity. (For interpretation of the references to color in
this figure legend, the reader is referred to the web version of this article.)
Conformational analysis
Based on PM3 optimized geometry, the total energy of the title
compound has been calculated by the method. In order to define
the preferential position of 5-nitro-2-thiophene system with re-
spect to the chlorobenzene system, a preliminary search of low-en-
ergy structures was performed using PM3 computation as a
function of the selected the selected degrees of torsional freedom
T(C11–C6–N2–C5) varied from À180° to and 180° in step of 10°
(Fig. 4). The respective value of the selected torsion angle
145.5(2)° in the X-ray structure analysis (Fig. 5a), whereas the cor-
responding values in PM3 optimized geometry is 140° (Fig. 5b). As
can be seen in Fig. 5c, torsion angle value for maximum energy is
experimental and theoretical results were compared. Using the root
meansquare error (RMSE) for evaluation, HF/6-31G(d) is the ab initio
calculation that best predicts the bond distances for A and B mole-
cule, 0.02 Å and 0.02 Å, respectively. The B3LYP/6-31G(d) calcula-
tion is those that provide the lowest RMSE for bond angles [A,
0.91°; B, 0.90°], whereas PM3 calculation is the best predicts for tor-
sion angles [A, 2.01°; B, 1.95°]. Selected experimental and calculated
bond lengths, bond angles and torsion angles are given Table 2.
Geometry optimization, conformational analysis, vibrational
Fig. 4. Molecular energy profile of the optimised counterpart of the title compound versus selected degrees of torsional freedom.
Fig. 5. Conformational analysis for T(C11–C6–N2–C5) torsion angle on PM3 geometry optimized and comparison with X-ray conformation. (a) T = 145.5°, (b) T = 140° (min.
energy), (c) T = 90° (max. energy).

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427
Table 3
calculations of the title compound are compared to the experimen-
tal results. Some primary theoretical and experimental results of
the title compound are shown in Table 3. The two bands attributed
to the C@N stretching vibrations obtained at 1619 cmÀ1, were cal-
culated for PM3, B3LYP and HF. This calculated values 1700, 1686
and 1635 cmÀ1, respectively. Essential characteristic vibrations of
nitrothiophene group are NO2 and C–S. The stretching NO2 vibra-
tion gives at 1593 cmÀ1 [27] in the infrared experimental spec-
trum, while the calculated values are 1610, 1625 and 1631 cmÀ1
for PM3, B3LYP and HF. C–S stretching mode was observed to be
695 cmÀ1[28] as experimentally; 694, 703 and 715 cmÀ1 for PM3,
B3LYP and HF. This difference between experimental and calcu-
lated vibrations frequency can be due to van der Waals intermolec-
ular forces between neighboring molecules, that calculations do
not take into consideration. As can be seen from Table 3, there is
also given between experimental and theoretical vibration data
for the others. The correlation graphics in Fig. 6 shows that exper-
imental fundamentals are found to have a good correlation with
calculations.
Comparison of the observed and calculated vibrational spectra of the title compound.
Assignments (cmÀ1
)
Experimental
PM3
B3LYP
HF
m
m
m
m
m
m
m
as(CH)(cb)
s(CH)(cb)
as(NO2)
(C@N)
s(NO2)
3114
–
–
1619
1593
–
1542
–
3085
3015
1850
1700
1610
1573
1482
1380
1086
816
3092
3020
1820
1686
1625
1580
1584
1356
1101
825
3111
3024
1837
1635
1631
1600
1581
1368
1115
820
(ring)(thp)+
s(C@C)(thp)
m
(NO2)
ring breathing (cb)
m
c
m
(C–Cl)
(C–H)(cb + thp)
(C–S)
1093
823
695
694
703
715
m: Stretching, s: symmetric, as: asymmetric,
c: rocking, chlorobenzene: cb, thio-
phene: thp.
90°. This calculated the low energy value is in good agreement
with the experimental value.
Vibrational frequency
Antimicrobial activity
Frequency calculations at the same levels and basis set of theory
revealed no imaginary frequencies, indicating that an optimal
geometry at these levels of approximation was found for the title
compound. The vibrational bands assignments have been made
by using Gauss-View molecular visualization program [24]. Our
MIC values were evaluated for gram negative and gram positive
bacteria and they were found to be decreased significantly after the
title compound(I) added to medium inoculated with bacteria. So,
changes in MIC values were changed between 64–128
cept for S. aureus. As can be seen in Table 4, the compound has
l
g mLÀ1 ex-
Fig. 6. Correlation graphics of calculated and experimental frequencies of the title compound.
Table 4
The results of antimicrobial studies of the title compound.
MIC (l )
g mLÀ1
Bacteria
I
E. coli
S. pneumonia
E. faecalis
S. aureus
MRSA
128
MSSA
64
S. typhi
Standard
-c
64
64
128
512
128
c: Chloramphenicol; –: no turbidity.

428
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creased for E. coli (64
g mLÀ1) among than gram positive bacteria
and for S. pneumonia and MSSA (64
g mLÀ1) among gram negative
bacteria. From these results obtained, it comes out that the anti-
bacterial activity decreases as the length of the carbon chain in-
creases. This could be due to bulkiness of the carbon chain,
which renders the molecule unable to penetrate through the cell
wall of the bacteria. The compound demonstrated potent inhibi-
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Conclusions
In this study, we have synthesized a novel compound 5-nitro-2-
thiophene-carboxaldehyde derivate, (C11H7ClN2O2S), and charac-
terized by spectroscopic IR and X-ray single-crystal diffraction.
The theoretical calculations performed by PM3, HF and B3LYP sup-
port the solid state structure. To fit the theoretical frequency re-
sults with experimental ones for HF and B3LYP levels, we have
multiplied the data. Multiplication factors results gained seemed
to be in a good agreement with experimental ones. The conforma-
tional analysis study is considerably successful in determining the
conformational preferring obtained from X-ray of the title com-
pound. The geometry of the solid state structure is subject to inter-
molecular forces, such as van der Waals interactions and crystal
packing forces. According to antimicrobial activities result, the title
compound exhibited antibacterial activity for bacteria studied.
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Appendix A. Supplementary material
CCDC 860578 contains the supplementary crystallographic data
for the compound reported in this paper. Copies of the data can be
obtained, free of charge, on application to CCDC, 12 Union Road,
Cambridge, CB12 1EZ, UK, fax: +44 1223 366 033. Web: http://
www.ccdc.cam.ac.uk.
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