Synthesis, crystal and molecular structure of 1-(2-chlorobenzyl)-2- methylthio-1H-benzimidazole

Article abstract of DOI:10.1007/s10870-011-9990-0

1-(2-Chlorobenzyl)-2-methylthio-1H-benzimidazole compound has been synthesized and characterized by elemental analysis, IR and ¹H-NMR spectroscopy and single crystal X-ray diffraction. The compound crystallizes in the triclinic space group P-1 with unit cell parameters a = 17.201 A , b = 5.873 A , c = 24.791 A , α = 67.410(10)°, β = 74.083(11)°, γ = 81.858(12)°. In the crystal packing, no classic hydrogen bonds are founded, but C-H...π interactions are being between the molecules. The molecular geometry and vibrational frequencies of (C ₁₅H₁₃ ClN₂S) in the ground state have been calculated by using Hartree-Fock (HF) and Density Functional Method (DFT/ B3LYP) with 6-31G(d) basis set. The optimized geometric bond lengths and bond angles obtained by using HF and DFT (B3LYP) show the best agreement with the experimental data. Springer Science+Business Media, LLC 2011.

Full text of DOI:10.1007/s10870-011-9990-0

J Chem Crystallogr (2011) 41:1968–1975
DOI 10.1007/s10870-011-9990-0
ORIGINAL PAPER
Synthesis, Crystal and Molecular Structure of 1-(2-Chlorobenzyl)-
2-methylthio-1H-benzimidazole
•
•
˘
Mustafa Serkan Soylu C¸ igdem Yu¨ksektepe
¨
•
•
Nezihe C¸ alıs¸kan Sema Ozel Su¨leyman Servi
Received: 16 October 2008 / Accepted: 13 January 2011 / Published online: 22 February 2011
Ó Springer Science+Business Media, LLC 2011
Abstract 1-(2-Chlorobenzyl)-2-methylthio-1H-benzimi-
dazole compound has been synthesized and characterized
Keywords Benzimidazole Á
X-ray structure determination Á HF Á
1
by elemental analysis, IR and H-NMR spectroscopy and
Density functional theory Á Vibrational assignment
single crystal X-ray diffraction. The compound crystallizes
in the triclinic space group P-1 with unit cell parame-
˚
˚
˚
ters a = 17.201 A, b = 5.873 A, c = 24.791 A, a =
67.410(10)°, b = 74.083(11)°, c = 81.858(12)°. In the
crystal packing, no classic hydrogen bonds are founded, but
C–HÁÁÁp interactions are being between the molecules. The
molecular geometry and vibrational frequencies of (C15H13
ClN2S) in the ground state have been calculated by using
Hartree–Fock (HF) and Density Functional Method (DFT/
B3LYP) with 6-31G(d) basis set. The optimized geometric
bond lengths and bond angles obtained by using HF and
DFT (B3LYP) show the best agreement with the experi-
mental data.
Introduction
The benzimidazole nucleus and its derivatives are known to
play extremely crucial roles in the structures and functions of
a number of biologically important molecules, generally by
virtue of their being coordinated to metal ions. The incor-
poration of the benzimidazole nuclei is an important syn-
thetic strategy in drug discovery [1]. The high therapeutic
properties of the related drugs have encouraged the medici-
nal chemist to synthesize the large number of novel che-
motherapeutic agents [2]. Pharmaceutical properties
including: antiviral [3] and antitumoral [4]; antifungal and
antimycotic [5]; antihistaminic and antiallergic [6]; antimi-
crobial [7] and antihelminthic activity [8]; all are unique
characteristics know from benzimidazole derivatives.
The synthesis of heteroarly-substituted 1H- benzimi-
dazoles has become of recent interest to medicinal chemists
owing to the pharmacophoric properties of the heteroaro-
matic rings. In the present paper, we report the crystal
structure, spectral characterizations of a new benzimid-
azole compound (1) together with DFT computational
studies.
M. S. Soylu (&)
Department of Physics, Faculty of Arts and Sciences,
Giresun University, 28100 Giresun, Turkey
e-mail: mssoylu@omu.edu.tr
C¸ . Yu¨ksektepe
Department of Physics, Faculty of Science, Cankiri Karatekin
University, Ballica, 18100 Cankiri, Turkey
N. C¸ alıs¸kan
Department of Physics, Faculty of Arts and Sciences,
Ondokuz Mayis University, Kurupelit, 55139 Samsun, Turkey
Density functional theory calculations are reported to
provide excellent vibrational frequencies of organic com-
pounds if the calculated frequencies are scaled to com-
pensate for the approximate treatment of electron
correlation, for basis set deficiencies and for the anhar-
monicity [9, 10]. Rauhut and Pulay calculated the vibra-
tional spectra of 31 molecules by using B3LYP method
with 6-31G(d) basis set [11]. In their work, they calculated
¨
S. Ozel
Adil Karaaqac¸ Anatolian Technical High School, Konya, Turkey
S. Servi
Department of Chemistry, Faculty of Arts and Sciences,
Firat University, 23169 Elazıg, Turkey
123

J Chem Crystallogr (2011) 41:1968–1975
1969
vibrational frequencies of 20 smaller molecules whose
experimental vibrational frequencies are well assigned, and
derived transferable scaling factors by using least-square
method. The scaling factors are successfully applied to
other 11 larger molecules. Thus, the vibrational frequen-
cies calculated by using the B3LYP functional with
6-31G(d) basis set could be utilized to eliminate the
uncertainties in the fundamental assignments in infrared
and Raman vibrational spectra [12].
Result and Discussions
X-Ray Crystallography
X-ray data collection was carried out an X-AREA dif-
fractometer [15]; with a graphite monochromatized Mo-Ka
radiation. Cell refinement: X-AREA [15]; data reduction:
X-RED32 [15]; program(s) used to solve structure:
SHELXS97 [16]; program(s) used to refine structure:
SHELXL97 [16]; molecular graphics ORTEP-3 for Win-
dows [17] and demonstrated version of DIAMOND [18].
The positions of H atoms bonded C atoms geometrically
were calculated and refined a riding model with C–H dis-
In previous publications, the crystal structure, vibra-
tional spectra and computational study of the similar
compound (C16H12N2S2) had been studied.[13, 14]. How-
ever, there are no theoretical and experimental results for
the title compound in the literature. In this study, we report
the crystal structure, spectral characterizations of a new
benzimidazole compound (1) together with DFT compu-
tational studies. These calculations are valuable and pro-
viding insight into the vibrational spectrum and molecular
parameters.
´
˚
tances of 0.93–0.97 A. The H atoms displacement param-
eters were restricted to 1.2 Ueq (1.5 Ueq for methyl atoms)
of parent atom.
Table 2 Optimized and experimental selected geometric parameters
of title compound (C15H13ClN2S) in the ground state
Parameters
Experimental Calculated
HF/6-31G(d) B3LYP/6-31G(d)
Table 1 Crystallographic data of (1)
˚
Bond lengths (A)
Formula
C15H13ClN2S
N1–C1
1.310(4)
1.386(4)
1.379(4)
1.379(4)
1.461(3)
1.739(3)
1.736(3)
1.784(4)
1.288
1.3118
1.3904
1.3935
1.3871
1.4518
1.7662
1.7642
1.8266
CCDC deposit no.
Molecular weight
Temperature (K)
705368
N1–C2
1.3842
1.3860
1.3681
1.4446
1.7510
1.7587
1.8100
288.78
N2–C7
296
N2–C1
˚
Wavelength (A)
0.71073
N2–C8
Crystal system
Crystal size (mm3)
Space group
Triclinic
Cl1–C14
0.480 9 0.347 9 0.140
P-1
S1–C1
S1–C15
˚
Unit cell dimensions (A, °)
Bond angles (°)
C1–S–C15
C1–N1–C2
C7–N2–C1
C7–N2–C8
C1–N2–C8
N1–C1–N2
N1–C1–S1
N2–C1–S1
N1–C2–C7
N1–C2–C3
Dihedral angles (°)
C2–N1–C1–N2
C2–N1–C1–S1
C7–N2–C1–N1
a = 8.1980(12)
b = 8.6890(12)
c = 11.1162(15)
a = 67.410(10)
b = 74.083(11)
c = 81.858(12)
702.47(17)
2
99.73(17)
104.2(3)
106.7(2)
125.7(3)
127.6(3)
113.2(3)
126.4(2)
120.5(2)
111.3(3)
129.5(3)
99.698
105.016
105.476
126.160
128.327
114.321
124.854
120.824
109.927
129.868
99.311
104.881
105.774
126.279
127.916
113.853
125.640
120.507
110.274
129.817
Volume, V
Z
Calculated density (Mg m-3
)
1.365
T
min, Tmax
l (mm-1
max. (°)
0.8248; 0.9495
0.407
)
h
25.00
0.1(4)
180.0(2)
-0.3(4)
0.139
179.879
0.001
0.067
179.935
0.137
Index ranges
h = -9 ? 9, k = -10 ? 10,
l = -13 ? 12
Reflections collected
12144
2472
C8–N2–C1–N1 -179.7(3)
177.862
179.751
2.387
177.930
179.861
2.072
Independent reflections
C7–N2–C1–S1
C8–N2–C1–S1
C15–S1–C1–N1
C15–S1–C1–N2
179.8(2)
0.4(4)
Observed reflections (I [ 2r)
1522
S
0.983
0.0532
0.132
-5.9(3)
174.0(3)
3.691
5.964
R1 (I [ 2r)
wR2 (I [ 2r)
176.585
174.038
123

1970
J Chem Crystallogr (2011) 41:1968–1975
DFT and HF Calculations
˚
Table 3 C–HÁÁÁp (Cg) interactions of (1) (A, °)
D–HÁÁÁA
D–H
HÁÁÁCg
DÁÁÁCg
D–HÁÁÁCg
Starting geometries of compound (1) were taken from X-ray
refinement data. The molecular structures of the title com-
pound (C15H13ClN2S) in the ground state (in vacuo) are
optimized by Hartree–Fock (HF) and Density Functional
Theory (DFT) methods to include correlation corrections
with the 6-31G(d) basis set. In DFT calculation, hybrid
functional are also used, the Becke’s three-parameter
C15–H15AÁÁÁCg(3)i
C8–H8AÁÁÁCg(1)ii
C8–H8BÁÁÁCg(2)ii
C15–H15CÁÁÁCg(2)iii
0.96
0.97
0.97
0.96
2.9145
2.9405
3.0297
2.7849
3.776(4)
3.664(4)
3.452(4)
3.579(5)
150
132
108
141
Symmetry codes: i: 1 ? x, y, z; ii: 2 - x, -y, 1 - z; iii: 2 - x, 1 - y,
1 - z
Table 4 Comparison of the observed and calculated vibrational spectra of title compound (C15H13ClN2S)
Assignments
Experimental IR
with KBr
Calculated
B3LYP
6–31G(d)
HF
6–31G(d)
C–H (chlorobenzene) str.
3087/3054
3066/2989
3031–2959
2933–2912
2873
3149/3140
3145/3120
3133–3113
3110–3100
3029
3072/3058
3066/3037
3051–3027
3029–3011
2935
C–H (chlorobenzene) asym. str.
C–H (benzimidazole) asym. str.
CH3 asym. str.
CH2 asym. str.
CH3 sym. str.
2854
3011
2928
CH2 sym. str.
2840
2993
2935
C–C (benzimidazole) str.
1611/1578
1593/1571
1477–1473
1459
1621/1595
1609/1587
1486–1481
1471
1635/1610
1623/1599
1484–1475
1515
C–C (chlorobenzene) str.
CH2 sci. ? C–H (benzimidazole) rock
CH3 sci. ? C=N str.
CH3 sci.
1450
–
1448
CH3 sci. ? CH2 sci.
1445
1463
1471
C–H (chlorobenzene) rock ? C–H aliph. rock
CH3 twist
1433
1452
1452
1425
1446
1448
CH2 twist ? C–N str.
1410
–
1391
CH2 wag
1405
1375
1379
CH3 wag. ?CH2 wag. ? C–N–C str.
CH3 sci.
1380
1358
–
1371
1351
1367
CH2 twist ? C–N str. ? C=N str. ? C–H ? C–C (benzimidazole) str
CH2 wag ? C–C (chlorobenzene) sci.
C–H (benzimidazole) rock ? CH2 twist.
C–H (chlorobenzene) rock
CH2 twist ? C–H (benzimidazole) rock
CH2 twist ? C–H (benzimidazole) rock ? C–N str.
CH2 wag ? C–H (chlorobenzene) rock
C–H (chlorobenzene) sci.
1352
1335
1355
1321
1301
–
1315
1287
1288
1280
1272
1275
1276
1251
1255
1222
1196
1194
1200
1189
1180
1194
1167
1134
C–H (benzimidazole) sci.
1176
1158
1116
C–H (benzimidazole) ? C–H (chlorobenzene) sci. C–C asym str.
C–H (benzimidazole) ? C–H (chlorobenzene) sci.
C–H (benzimidazole) sci.
1157
1137
1089
1137
1122
–
1108
1097
1089
C–H (chlorobenzene) sci.
1069
1047
1039
C–C (chlorobenzene) in plane str
C–H (benzimidazole) sci.
1045
1026
1025
1036
1014
–
C–H aliph. twist
1020
997
–
C–H aliph. twist
1009
986
995
123

J Chem Crystallogr (2011) 41:1968–1975
1971
Table 4 continued
Assignments
Experimental IR
with KBr
Calculated
B3LYP
6–31G(d)
HF
6–31G(d)
CH3 twist
995
989
976
944
920
890
862
843
826
807
771
759
752
742
704
695
686
669
600
577
571
552
509
–
976
974
954
936
912
883
854
836
822
797
762
747
745
732
695
690
688
654
595
572
567
550
502
444
441
413
394
1001
1010
993
968
954
875
768
870
815
788
–
C–H (chlorobenzene) in plane bend
C–H (benzimidazole) in plane bend
C–H (chlorobenzene) out of plane bend
C–H (benzimidazole) out of plane bend
Ring str. ? C = N–C str. ? CH2 rock
C–H (chlorobenzene) twist
C–H (benzimidazole) twist
CH2 rock ? Ring (benzimidazole) str.
CH2 rock ? Ring (chlorobenzene) str.
CH2 bend
C–H (chlorobenzene) wag.
768
765
759
705
–
Ring (benzimidazole) out of plane bend
C–H (benzimidazole) out of plane bend
C–S str.
Ring (chlorobenzene) out of plane bend
Ring (chlorobenzene) out of plane bend
C=N–C twist
703
680
592
575
565
545
506
486
489
450
444
Ring (benzimidazole) rock
Ring (benzimidazole) bend ? C–H bend
Ring (benzimidazole) twist ? C–H bend
Ring (benzimidazole) rock ? CH2 rock
Ring (chlorobenzene) rock ? CH2 rock
Ring (chlorobenzene) ? C–H wag.
Ring (benzimidazole) ? C–H wag.
C–Cl str.
–
–
C–S str.
–
functional (B3) [19] which defines the exchange functional
as the linear combination of Hartree–Fock, local and gradi-
ent-corrected exchange terms. The B3 hybrid functional was
used in combination with the correlation functionals of Lee,
Yang and Parr [20]. Two sets of vibrational frequencies for
these species are calculated with these methods and then
scaled by 0.9012 and 0.9776, respectively. Molecular
geometry is restricted and all the calculations are per-
formed by using Gauss-View molecular visualization pro-
gram [21] and Gaussian 98 program package on personal
computer [22].
Cl
H2
C
N
N
S
Me
Scheme 1 Chemical diagram of the title compound
Details of crystal parameters, data collection, structure
solution and refinement are given in Table 1. Selected bond
distances and angles for X-ray, DFT and HF models are
listed in Table 2. Hydrogen bonds geometries are described
in Table 3. The calculated IR frequencies with the exper-
imental data of (1) are compared in Table 4. Chemical
diagram of (1) is introduced in Scheme 1. ORTEP drawing
diagram of the molecular structure and the theoretical
geometric structure of the title compound (1) are shown in
Fig. 1a, b. Packing diagram with C–HÁÁÁp interactions is
presented in Fig. 2. Correlation graphics of the calculated
and experimental molecular bond lengths, bond angles,
dihedral angles and frequencies of the title compound
123

1972
J Chem Crystallogr (2011) 41:1968–1975
(C15H13ClN2S) are shown in Fig. 3a, b, c and Fig. 4,
respectively.
Description of the Crystal Structure
The title compound (1), crystallizes in the triclinic, space
˚
group P-1 with unit cell parameters a = 17.201 A, b =
˚
˚
5.873 A, c = 24.791 A, a = 67.410(10)°, b = 74.083(11)°,
c = 81.858(12)°. A view of the asymmetric unit with the
atom labelling scheme is shown in Fig. 1a. Selected geo-
metric parameters are listed in Table 2 and hydrogen
bonding geometry is listed in Table 3. As can be seen from
Fig. 1a, the title compound contains chlorobenzene ring and
1H-benzimidazole moiety. The chlorobenzene ring(A) and
1H-benzimidazole (B) moiety of the molecule (except fort
he methyl group) are planarity and the dihedral angle
between these moieties is 85.78(10)°. These moieties are
linked by CH2 group each other.
˚
The C1–N1 distance is a 0.07 A shorter than the C1–N2
distance (see Table 2), similar to the literature values [23],
consistent with the partial double-bond character of the
former bonds. In the crystal packing, no classic hydrogen
bonds are founded, but C–HÁÁÁp interactions are being
between the molecules. These interactions are tabulated in
Table 3 with symmetry codes. The atom C(8) of CH2 group
at (x, y, z) acts as a hydrogen bond donor, via the atoms H(8A)
and H(8B), to Cg(1)(C1/N2) and Cg(2)(C2/C7) rings at
(2 - x, -y, 1 - z) molecule, respectively.
Additionaly, the atom C(15) of methyl group at (x, y,
z) acts as a hydrogen bond donor, via atom H(15C), to Cg(2)
ring at (2 - x, 1 - y, 1 - z) molecule and via the atom
H(15A), to Cg(3)(C9/C14) ring at (1 ? x, y, z) molecule
(see Fig. 2). As a result propagation of C15–H15AÁÁÁp
bonds lie along c-axis, while C15–H15CÁÁÁp bonds lie along
b-axis and the crystal packing is polymeric form.
Fig. 1 a The experimental geometric structure of the title compound
(C15H13ClN2S). Displacement ellipsoids are drawn at the 50%
probability level and H atoms are shown as small spheres of arbitrary
radii. b The theoretical geometric structure of title compound
(C15H13ClN2S)
Geometry Optimization and FT-IR Spectra of (1)
Owing to the overlaps of absorption bonds, it is difficult to
identity to vibration modes in the IR spectra and this case,
Fig. 2 C–HÁÁÁpinteractions of (1)
123

J Chem Crystallogr (2011) 41:1968–1975
1973
the frequencies derived from the DFT calculations may be
helpful to distinguish the vibration modes more directly.
We have calculated the vibrational frequencies and
geometric parameters of title compound in the ground state
to distinguish the fundamentals from the experimental
vibrational frequencies and geometric parameters by using
B3LYP and HF methods 6-31G(d) basis set. The optimized
molecular geometry of the title compound is shown in
Fig. 1b. These calculations valuable and providing insight
into the vibrational spectrum and molecular parameters.
The optimized geometric parameters (bond lengths and
angles) by HF and B3LYP with 6-31G(d) as the basis set
are listed in Table 2 and compared with the experimental
crystal geometry for the title compound. The bond
angles of C15–S1–C1 and N1–C1–N2 were observed at
99.73(17)° and 113.2(3)°, these angles have been calcu-
lated at 99.698° and 114.32° for HF and at 99.311° and at
113.85° for B3LYP with using 6-31G(d) basis set. The C–S
bonds were observed/calculated at: 1.784(4)/1.8100/1.8266
[for C15–S1], 1.736(3)/1.7587/1.7642 [for S1–C1] as can
be seen from Table 2. For the optimized geometric
parameters, various methods including HF method estimate
some bond lengths well to some extent [24–27]. We noted
that the experimental results belong to solid phase and
theoretical calculations belong to gaseous phase. The cor-
relation between the experimental and calculated geometric
parameters obtained by the several methods is shown in
Fig. 3. According to our calculations, HF and B3LYP
methods correlate well for the bond length compare
(Table 2, Fig. 3, 4). The largest differences between
˚
experimental and calculated bond length are about 0.026 A
˚
for HF and 0.0426 A for B3LYP. The B3LYP method
leads to geometric parameters (angles), which are much
closer to experimental data. The largest difference is about
1.026° for the second one. As a result, the optimized bond
lengths obtained by HF method and bond angles by DFT
(B3LYP) method show the best agreement with the
experimental values. We have not found theoretical results
for the title compound (C15H13ClN2S) in the literature.
In general, the calculated IR frequencies are compared
well with the experimental data of compound (1) (see
Table 4). As can be seen from the C–H symmetric and
asymmetric stretching vibrations, the experimental and
calculated vibration frequencies of the title compound were
shown between 3087–2959/3149–3113(B3LYP)/3072–
3027 cm-1(HF), respectively. Also the C–H vibrations of
the title compound are calculated in the same range and
there is a good agreement between experimental and
Fig. 3 a Correlation graphics of calculated and experimental molec-
ular bond lengths of the title compound (C15H13ClN2S). b Correlation
graphics of calculated and experimental molecular bond angles of the
title compound (C15H13ClN2S). c Correlation graphics of calculated
and experimental molecular dihedral angles of the title compound
(C15H13ClN2S)
123

1974
J Chem Crystallogr (2011) 41:1968–1975
Experimental Section
Measurement
All reagents were commercially obtained and used without
any further purification. Elemental analyses were performed
by a Vario EL elemental analyzer for C, H, N and S. FT-IR
spectra were recorded on a MATTSON1000 spectropho-
tometer, KBr pellets; 4000–400 cm-1 range. 1H-NMR
spectra were obtained by using a Bruker 400 MHz spec-
trometer.
Synthesis of 1-(2-Chlorobenzyl)-2-methylthio-1H-
benzimidazole
To a mixture of 2-methylthio-1H-benzimidazole (0.91 g,
3.14 mmol) and finely powdered NaOH (0.5 g, 12.5 mmol)
in DMSO (7 mL) was added drop wise 1-chloro-2-chlor-
omethylbenzene (0.35 mL, 3.45 mmol). The resulting
solution was stirred at 35–40 °C for 1 h. Then water was
added to the reaction mixture, and the solid that precipi-
tated was collected crystallization from ethanol. m.p.:
125–126 °C (Ethanol), IR (KBr) tmax
:
3054–3021
(aromatic C–H stretching), 2928–2862(aliphatic C–H
stretching), 1607(C=C stretching), 1572(C=N stretching),
973(C–Cl stretching) 746(SCH3 stretching); 1H-NMR
(DMSO-d6, 400 MHz): d 2.71 (s, 3H, S–CH3), 5.47 (s, 2H,
N–CH2), 7.62–6.59 (m, 8H, Ar–H).
Conclusions
Fig. 4 Correlation graphics of calculated and experimental frequen-
cies of the title compound (C15H13ClN2S)
The crystal structure of C15H13ClN2S, (I), is investigated
with X-ray diffraction and the observed values as bond
lengths and angles are compared with the calculated val-
ues. The theoretical vibrational spectrum assignments of
C15H13ClN2S have been calculated and the experimental
vibrational spectrum assignments of (1) are compared with
theoretical results, besides of these, the optimized molec-
ular geometry of this compound has been calculated by
using ab initio calculations as Hartree–Fock and Density
Functional Theory (DFT/B3LYP) with 6-31G(d) basis set.
As a consequence, all the calculated spectra, bond lengths
and angles of this structure are in good agreement with the
experimental data.
theoretical values, in Table 4. The S–C symmetric vibra-
tions have been observed at 704 cm-1, this band has been
calculated at 695 cm-1 for HF and at 705 cm-1 for B3LYP
with using 6-31G(d) basis set. As can be seen from
Table 3, there is a good agreement between experimental
and theoretical vibration values.
In conclusion, the geometric parameters and the vibra-
tional frequencies of the title compound were calculated by
using B3LYP and HF methods with 6-31G(d) basis set. To
fit the theoretical results with experimental ones for
B3LYP, we have multiplied by 0.9776, whereas for HF
method the number of 0.9012 was used with these. Mul-
tiplication factor results gained seemed to be in a good
agreement with experimental ones. In particular, the results
of B3LYP method have shown better fit to experimental
ones than HF in evaluating vibrational frequencies and
calculation of bond angles.
Supplementary Data
Crystallographic data for the structural analysis have been
deposited with the Cambridge Crystallographic Data Cen-
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obtained free of charge from the Director, CCDC, 12
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