Synthesis and characterization of 2,2′-(pyridine-2,6-diyl)bis(1H- benzo[d]imidazol-3-ium) 2,4,6-trimethylbenzenesulfonate chloride by experimental and theoretical methods

Article abstract of DOI:10.1016/j.saa.2014.04.148

The title molecular salt (2), 2,2′-(pyridine-2,6-diyl)bis(1H-benzo[d] imidazol-3-ium) 2,4,6-trimethylbenzenesulfonate chloride (C₁₉H ₁₅N₅²⁺·C₉H₁₁O ₃S^-·Cl^-), was synthesized unexpectedly from the reaction of 2,6-bis(benzimidazol-2-yl)pyridine (1) with 2-mesitylenesulfonyl chloride. Spectroscopic techniques (FT-IR, NMR and UV-vis.) were used to characterize compounds 1 and 2. Solid-state structure of compound 2 was identified by X-ray crystallography. Theoretical characterization of the spectroscopic properties of compounds 1 and 2 was achieved using the density functional theory (DFT) method with the 6-311G(d,p) basis set, and the results were checked against the experimental data. Electronic absorption spectra of the compounds have also been obtained.

Full text of DOI:10.1016/j.saa.2014.04.148

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 131 (2014) 145–152
Contents lists available at ScienceDirect
Spectrochimica Acta Part A: Molecular and
Biomolecular Spectroscopy
journal homepage: www.elsevier.com/locate/saa
Synthesis and characterization of 2,20-(pyridine-2,6-diyl)bis
(1H-benzo[d]imidazol-3-ium) 2,4,6-trimethylbenzenesulfonate
chloride by experimental and theoretical methods
b,
b
c
Namık Özdemir a, , Osman Dayan , Melek Tercan Yavasßog˘lu , Bekir Çetinkaya
⇑
⇑
a Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, 55139 Samsun, Turkey
b Laboratory of Inorganic Synthesis and Molecular Catalysis, Çanakkale Onsekiz Mart University, 17020 Çanakkale, Turkey
c
_
Department of Chemistry, Faculty of Science, Ege University, 35100 Izmir, Turkey
h i g h l i g h t s
g r a p h i c a l a b s t r a c t
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
A novel benzimidazole compound
was synthesized unexpectedly.
The compound was crystallized as
salt.
The structure of the compound was
determined by X-ray crystallography.
The compound was characterized by
FT-IR, NMR and UV–vis. spectroscopy.
The structure and spectroscopic
properties were examined by DFT
method.
a r t i c l e i n f o
a b s t r a c t
The title molecular salt (2), 2,20-(pyridine-2,6-diyl)bis(1H-benzo[d]imidazol-3-ium) 2,4,6-trimethylben-
zenesulfonate chloride (C19H15N25+ꢁC9H11O3SꢂꢁClꢂ), was synthesized unexpectedly from the reaction of
2,6-bis(benzimidazol-2-yl)pyridine (1) with 2-mesitylenesulfonyl chloride. Spectroscopic techniques
(FT-IR, NMR and UV–vis.) were used to characterize compounds 1 and 2. Solid-state structure of
compound 2 was identified by X-ray crystallography. Theoretical characterization of the spectroscopic
properties of compounds 1 and 2 was achieved using the density functional theory (DFT) method with
the 6-311G(d,p) basis set, and the results were checked against the experimental data. Electronic absorp-
tion spectra of the compounds have also been obtained.
Article history:
Received 11 November 2013
Received in revised form 2 March 2014
Accepted 23 April 2014
Available online 5 May 2014
Keywords:
Crystal structure
FT-IR
Ó 2014 Elsevier B.V. All rights reserved.
NMR
UV-vis.
DFT calculations
Introduction
benzimidazole, which is very attractive with its weak
p-receptor
and strong -donor property. One of the unpaired electron pairs
p
N-heterocylic ligands have recently become more attractive in
applied chemistry [1–3]. The most common of these is a group of
contributes the aromatic ring and the other one gives molecule
basic character [4]. So that, nitrogen atom enables substitution
and changing electronic and steric properties of the molecule [5].
Benzimidazole derivatives have been investigated intensively in
view of application of biological activity such as inhibition of topo-
isomerase I, antifungal, antiparasitic, anticancer and antimicrobial
effect [6–14].
⇑
Corresponding authors. Tel.: +90 362 3121919/5256; fax: +90 362 4576081
(N. Özdemir). Tel.: +90 286 2180018/1860; fax: +90 28621805333 (O. Dayan).
E-mail addresses: namiko@omu.edu.tr (N. Özdemir), osmandayan@comu.edu.tr
(O. Dayan).
http://dx.doi.org/10.1016/j.saa.2014.04.148
1386-1425/Ó 2014 Elsevier B.V. All rights reserved.

146
N. Özdemir et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 131 (2014) 145–152
On the other hand, tridentate N-compoundsbearing benzimidaz-
olyl/pyridine rings are very stable because of their electrons. The
temperature (296 K) using graphite monochromated Mo K
a radia-
p
tion (k = 0.71073 Å) in -scanning mode. The structure was solved
x
usability of these compounds and their derivatives in the field of
optical sensors, solar energy conversion systems, electronic devices,
etc. depends on the control of the features of compounds geometry,
photo-physical/-chemical and electrochemical properties [15,16].
Particularly, 2,6-bis(benzimidazol-2-yl)pyridine (bizimpy) and its
metal complexes are used in many applications such as biochemis-
try [17], electrochemistry [18,19] and catalysis [20–23]. 2,
6-Bis(benzimidazol-2-yl)pyridines like other benzimidazoles are
easily substituted with the reaction of alkyl halides in basic condi-
tions. However, in this work, we show that a new pyridinium salt
has been synthesized with the reaction of 2,6-bis(benzimidazol-2-
yl)pyridine and 2-mesitylenesulfonyl chloride in basic conditions.
We report here results of a detailed study of the synthesis and
characterization of bizimpy and title compound using IR, NMR (1H
and 13C NMR) and UV–vis. spectroscopies and quantum chemical
methods. The density functional theory at the B3LYP/6-311G(d,p)
level was employed for the theoretical characterization of the both
compounds. The crystal structure of the title compound was also
determined by single-crystal X-ray diffraction experiment.
by direct methods using SHELXS-97 [25] and refined through the
full-matrix least-squares method using SHELXL-97 [26] imple-
mented in the WinGX [27] program suite. Carbon bound hydrogen
atoms were positioned geometrically and treated using a riding
model, fixing the bond lengths at 0.93 and 0.96 Å for CH and CH3
atoms, respectively, while the nitrogen bound hydrogen atoms
were located in a difference Fourier map and refined isotropically
[NAH = 0.85(2)–0.90(2) Å]. Data collection: X-AREA [28], cell
refinement: X-AREA, data reduction: X-RED32 [28]. Details of the
data collection conditions and the parameters of refinement pro-
cess are given in Table 1. The general-purpose crystallographic tool
PLATON [29] was used for the structure analysis and presentation
of the results. The molecular graphics were done using ORTEP-3 for
Windows [30].
Computational technique
All geometries were fully optimized in the ground state using
the Berny algorithm [31,32] without symmetry restrictions and
using the default convergence criteria. The calculations were
performed by means of the Gauss-View molecular visualization
program [33] and Gaussian 03W program package [34] using the
density functional theory (DFT) [35] with the three-parameter
hybrid functional (B3) [36] for the exchange part and the
Lee–Yang–Parr (LYP) correlation function [37], denoted B3LYP, at
6-311G(d,p) [38,39] basis set. All the geometry optimizations were
followed by frequency calculations and no imaginary frequencies
were found, approving the stable nature of the optimized
structures. A scale factor of 0.9679 [40] was used to correct the cal-
culated vibrational frequencies. The 1H and 13C NMR chemical
shifts were calculated within the gauge-independent atomic orbi-
tal (GIAO) approach [41,42] applying the same method and the
basis set as used for geometry optimization. The 1H and 13C NMR
chemical shifts were converted to the TMS scale by subtracting
Materials and methods
General remarks
All reagents and solvents were obtained from commercial sup-
pliers and used without further purification. Melting points were
determined in open capillary tubes on a digital Stuart SMP10 melt-
ing point apparatus. NMR spectra were recorded at 297 K on a Var-
ian Mercury AS 400 NMR spectrometer at 400 MHz (1H),
100.56 MHz (13C) in DMSO-d6 with TMS as the internal standard.
Infrared spectra were measured with a Perkin Elmer SpectrumOne
FTIR system and recorded using a universal ATR sampling acces-
sory within the range 4000–650 cmꢂ1. UV–vis. spectra were
recorded with a Perkin Elmer Lambda 25 UV–vis. spectrometer.
the calculated absolute chemical shielding of TMS (d = R0
ꢂ
R,
where d is the chemical shift, is the absolute shielding and R0
R
Syntheses
is the absolute shielding of TMS), whose value are 31.99 and
185.06 ppm, respectively. The effect of solvent on the theoretical
NMR parameters was included using the default model IEF-PCM
(Integral-Equation-Formalism Polarizable Continuum Model) [43]
provided by Gaussian 03W. DMSO was used as solvent. The
electronic absorption spectra were calculated using the time-
dependent density functional theory (TD-DFT) method [44,45].
Bizimpy (1)
Bizimpy was synthesized according to published procedures
[24]. Pyridine-2,6-dicarboxylic acid (dipicolinic acid) (20 mmol,
3.35 g) was added to 1,2-phenylenediamine (44 mmol, 4.7 g) in
phosphoric acid (40 ml). The reaction mixture was stirred during
4 h under Ar atmosphere. The obtained green–blue melt was
poured into ice and after reaching room temperature, filtered off.
Then sodium carbonate (10%, 100 ml) solution was added to the fil-
trate. After recrystallization from methanol, white-beige crystals
were obtained. Yield: 68% melting point: 626 K.
Results and discussion
Description of crystal structure
The title compound (2), an ORTEP-3 view of which is shown in
Fig. 2, crystallizes as a salt in the monoclinic system P21/c with
Z = 4, and composed of
2,20-(Pyridine-2,6-diyl)bis(1H-benzo[d]imidazol-3-ium) 2,4,6-
trimethylbenzenesulfonate chloride (2)
a
2,20-(pyridine-2,6-diyl)bis(1H-benzo
Bizimpy (3.21 mmol, 1 g) was dissolved in THF (20 ml). Potas-
sium hydroxide (6.42 mmol, 0.36 g) was added to this solution
and refluxed for 2 h. 2-Mesitylenesulfonyl chloride (6.42 mmol,
1.40 g, in THF) was added to the reaction mixture and refluxed
for 12 h (Fig. 1). After removing solvent, the obtained solid was
washed with brine and extracted with CH2Cl2 (20 mlx3). X-ray
quality crystals were grown from dichloromethane/hexane (1:3).
Yield: 70% melting point: 562 K (dec.).
[d]imidazol-3-ium) cation,
a
2,4,6-trimethylbenzenesulfonate
anion and one chloride anion.
The
2,20-(pyridine-2,6-diyl)bis(1H-benzo[d]imidazol-3-ium)
cation is essentially planar with the largest individual deviation
from planarity of 0.0938(17) Å for atom N3, while the benzene ring
plane of the 2,4,6-trimethylbenzenesulfonate anion is almost per-
pendicular to this plane with an angle of 78.349(64)°. In the
2,4,6-trimethylbenzenesulfonate anion, the methyl group showing
the greatest deviation from the least-squares plane of the aromatic
ring in the anion is that para to the sulfonate group, with a value of
0.0348(32) Å, while atom S1 deviates from the plane of the aro-
matic ring by 0.0250(18) Å. The aromatic CAC and CAN distances
and bond angles in both the benzimidazole and pyridine rings
X-ray crystallography
The intensity data of the title compound were collected on a
STOE diffractometer with an IPDS II image plate detector at room

N. Özdemir et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 131 (2014) 145–152
147
Fig. 1. Formation of the title compound.
Table 1
the 2,4,6-trimethylbenzenesulfonate anion shows also good agree-
ment with those previously reported [50,51].
Crystal data and structure refinement parameters for the title compound.
In the molecular structure of the 2,4,6-trimethylbenzenesulfo-
nate anion, there is a C28AH28Aꢁ ꢁ ꢁO1 intramolecular interaction
leading to the formation of a six-membered ring with graph-set
descriptor S(6) [52]. In the crystal structure, there are extensive
cationꢁꢁꢁanion intermolecular interactions. Each 2,20-(pyridine-2,6-
diyl)bis(1H-benzo[d]imidazol-3-ium) cation is hydrogen bonded
to both the chloride anion via a pair of NAHꢁ ꢁ ꢁCl hydrogen bonds
in an R12ð10Þ motif, and the 2,4,6-trimethylbenzenesulfonate anion
via the N2AH2ꢁ ꢁ ꢁO3 and C4AH4Aꢁ ꢁ ꢁO3 hydrogen bonds in an
CCDC deposition no.
Color/shape
802607
Colorless/prism
Chemical formula
Formula weight
Temperature (K)
Wavelength (Å)
Crystal system
Space group
C
19H15N25+ꢁC9H11O3SꢂꢁClꢂ
548.05
296
0.71073 Mo K
Monoclinic
P21/c (No. 14)
a
Unit cell parameters
a, b, c (Å)
18.5426(12), 8.2193(4), 20.5076(12)
a
, b,
c
(°)
90, 118.047(5), 90
2758.5(3)
4
1.320
0.253
Integration
0.9704, 0.8849
1144
R12ð7Þ motif [52]. There is also a CAHꢁ ꢁ ꢁ
p(arene) interaction between
Volume (Å3)
Z
the 2,20-(pyridine-2,6-diyl)bis(1H-benzo[d]imidazol-3-ium) cation
and 2,4,6-trimethylbenzenesulfonate anion. In addition, atoms N4
and C2 in the molecule at (x, y, z) act as hydrogen-bond donors,
respectively, to atoms O1 and O3 in the molecule at (ꢂx, y ꢂ 1/2,
ꢂz + 3/2), so forming an R22ð9Þ ring (see Fig. S1 in Supplementary
materials). Finally, atom C17 in the molecule at (x, y, z) acts as
hydrogen-bond donor to atom O2 in the molecule at (ꢂx, ꢂy,
ꢂz + 1). The full geometry of these interactions is given in Table 2.
Dcalc (g/cm3)
l
(mmꢂ1
)
Absorption correction
Tmin, Tmax
F000
Crystal size (mm3)
Diffractometer/measurement
method
0.80 ꢃ 0.39 ꢃ 0.14
STOE IPDS II/
x scan
Index ranges
ꢂ23 6 h 6 23, ꢂ10 6 k 6 10,
ꢂ24 6 l 6 25
h range for data collection (°)
Reflections collected
Independent/observed reflections
Rint
1.99 6 h 6 26.61
14635
Theoretical structure
5698/3242
0.0484
The optimized parameters (bond lengths, bond angles, and
dihedral angles) of the title compound have been obtained using
the B3LYP/6-311G(d,p) method. Some selected geometrical param-
eters experimentally obtained and theoretically calculated are
listed in Table 3.
From Table 3, one can easily say that agreement between the
calculated and experimental structures is sufficient. The largest
deviations in the bond distances are observed in SAO3 bonds of
the 2,4,6-trimethylbenzenesulfonate anion probably due to hydro-
gen bonding interactions. Similarly, the largest deviation of bond
angles appears to be 1.69° at O1AS1AC20. Although the 2,20-(pyri-
dine-2,6-diyl)bis(1H-benzo[d]imidazol-3-ium) cation is planar in
its solid state, this is not observed in the obtained theoretical
structure. The benzimidazole ring planes are tilted with respect to
Refinement method
Full-matrix least-squares on F2
5698/0/366
Data/restraints/parameters
Goodness-of-fit on F2
1.004
Final R indices [I > 2
R indices (all data)
D
r
(I)]
R1 = 0.0440, wR2 = 0.0713
R1 = 0.0951, wR2 = 0.0786
0.164, ꢂ0.229
qmax, D
qmin (e/Å3)
are within the usual ranges [46–49], confirming the aromatic char-
acter of the pyridine and benzimidazole moieties. The positions of
N2 and N4 atoms are trans–trans with respect to pyridine N1 atom,
and the protonation of these atoms has no effect on the aromatic
character of the two benzimidazole moieties. The geometry of

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N. Özdemir et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 131 (2014) 145–152
not observe the NAH out-of-plane bending vibration in the FT-IR
spectra of compound 1. However, this band is observed at 960
and 881 cmꢂ1 for compound
2 and appeared at 993 and
883 cmꢂ1, respectively, in the theoretical spectra.
It is stated the CAH stretching, CAH in-plane bending and CAH
out-of-plane bending vibrations of the aromatic compounds
appear in 2900–3150, 1100–1500 and 750–1000 cmꢂ1 frequency
ranges, respectively [54]. The CAH aromatic stretching modes
were recorded at 3111 and 3064 cmꢂ1 for compound 1 and at
3058 and 3034 cmꢂ1 for compound 2 experimentally and were
computed at 3095 and 3073 cmꢂ1 for compound 1 and at 3052
and 3048 cmꢂ1 for compound 2, respectively. The CAH in-plane
bending vibrations predicted at 1427, 1413 and 1132 cmꢂ1 for
compound 1 and at 1415 cmꢂ1 for compound 2 by B3LYP/6-
311G(d,p) method show good agreement with FT-IR bands at
1457, 1434 and 1150 cmꢂ1 for compound 1 and at 1411 cmꢂ1 for
compound 2. The CAH out-of-plane bending vibrations are identi-
fied at 925, 815 and 738 cmꢂ1 for compound 1 and at 850, 739 and
719 cmꢂ1 for compound 2, and these frequencies are found to be
well within their characteristic regions.
The CAH stretching vibrations of methyl groups occurs at lower
frequencies than those of aromatic ring. Moreover, the asymmetric
mode is usually at higher wavenumber than the symmetric mode.
In this work, the CAH3 symmetric stretching frequencies of com-
pound 2 are assigned at 2929 and 2853 cmꢂ1, whereas the CAH3
asymmetric frequency is assigned at 2969 cmꢂ1. These bands are
calculated as 2947, 2924 and 2973 cmꢂ1. The peak at 1454 cmꢂ1
is assigned to the CAH3 scissoring vibration whereas the peaks at
1031 and 1001 cmꢂ1 are assigned to the CAH3 wagging and twist-
ing vibrations, respectively, in FT-IR.
Fig. 2. A view of the title compound showing the atom-numbering scheme.
Displacement ellipsoids are drawn at the 30% probability level and H atoms are
shown as small spheres of arbitrary radii. Hydrogen bonds are shown as dashed
lines. For the sake of clarity, only hydrogen atoms involved in hydrogen bonding
have been included.
Table 2
Hydrogen bonding geometry for the title compound.
DAHꢁ ꢁ ꢁA
DAH (Å)
Hꢁ ꢁ ꢁA (Å)
Dꢁ ꢁ ꢁA (Å)
DAHꢁ ꢁ ꢁA (°)
C28AH28AꢁꢁꢁO1
N2AH2ꢁꢁꢁO3
0.96
2.46
3.162(3)
2.699(2)
3.164(2)
3.0816(19)
3.625(3)
3.337(3)
3.314(3)
2.668(2)
3.358(3)
129
0.90(2)
0.88(2)
0.88(2)
0.93
0.93
0.93
1.80(2)
2.30(2)
2.22(2)
2.72
2.44
2.45
179(2)
168.8(18)
166(2)
165
161
155
N3AH3ꢁꢁꢁCl1
N5AH5ꢁꢁꢁCl1
C8AH8ꢁꢁꢁCg
C2AH2AꢁꢁꢁO3a
C4AH4AꢁꢁꢁO3
N4AH4ꢁꢁꢁO1a
C17AH17ꢁꢁꢁO2b
0.85(2)
0.93
1.88(2)
2.51
153(2)
152
Cg: the centroid of the C20AC25 ring.
a
ꢂx, y ꢂ 1/2, ꢂz + 3/2,
b
ꢂx, ꢂy, ꢂz + 1.
Azomethine (C@N) bond stretching vibration was observed at
1490 cmꢂ1 for compound 1 and at 1621 cmꢂ1 for compound 2
experimentally, while these were calculated at 1521 and
1615 cmꢂ1, respectively. The band at 1576 cmꢂ1 in the FT-IR
spectra of compound 1 and the bands at 1564 and 1522 cmꢂ1 in
the FT-IR spectra of compound 2, which can be attributed to the
ring C@C stretching vibrations, were calculated at 1571, 1580
and 1555 cmꢂ1 for B3LYP, respectively.
the central pyridine ring by angles of 13.04° and 9.76° for N2/N3/C6-
C12 and N4/N5/C13-C19, respectively, while the dihedral angle
between the 2,20-(pyridine-2,6-diyl)bis(1H-benzo[d]imidazol-3-
ium) cation and 2,4,6-trimethylbenzenesulfonate anion is 72.16°.
To globally compare the experimental and theoretical struc-
tures, these structures are overlapped with each other, giving
RMSE’s of 0.155 and 0.603 Å for the 2,20-(pyridine-2,6-diyl)b-
is(1H-benzo[d]imidazol-3-ium) cation and 2,4,6-trimethylben-
zenesulfonate anion, respectively (see Fig. S2 in Supplementary
materials). The large RMSE value obtained for the anion can be
explained by the intermolecular interactions in the crystal
structure.
Asymmetric vibrations of SO3ꢂ group of sulfonic acid salts usu-
ally occur in the FT-IR at 1250–1140 cmꢂ1. The band due to the
symmetric stretching vibration is sharper and occurs at 1130–
1080 cmꢂ1 [53]. We calculated the asymmetric and symmetric
SAO3 stretching vibrations at 1181 and 1061 cmꢂ1 for compound
2, while these bands were obtained at 1153 and 1119 cmꢂ1 in
the FT-IR spectra, respectively. In addition, the band at 653 cmꢂ1
in the FT-IR spectra of compound 2, which is assigned to the CAS
stretching vibration, was calculated at 641 cmꢂ1. The other exper-
imental and theoretical vibrational frequencies can be seen in
Table 4.
Vibrational spectra
The experimental FT-IR spectra of compounds 1 and 2 are shown
in Fig. 3. Harmonic vibrational frequencies of the compounds were
computed at the B3LYP/6-311G(d,p) level and the vibrational band
assignments were done by means of the Gauss-View molecular
visualization program. Comparison of the observed and calculated
vibrational frequencies is given in Table 4. From the table, it is seen
that there exists an acceptable agreement between the experimen-
tal and theoretical vibrational frequencies.
It is reported that the NAH stretching band is usually observed
in the region 3300–3500 cmꢂ1 [53]. In the IR spectra of compound
1, the peak at 3181 cmꢂ1 represents to secondary amine NAH
stretching vibration that has been calculated at 3539 cmꢂ1. The
corresponding stretching frequency for compound 2 is seen as
two bands at 3242 and 2733 cmꢂ1 while these were calculated at
3535 and 2905 cmꢂ1, respectively. The NAH in-plane bending
vibration is assigned to the wavenumber at 1385 and 1230 cmꢂ1
for compound 1 and at 1352 cmꢂ1 for compound 2, that have been
calculated at 1378, 1193 and 1363 cmꢂ1, respectively. We could
NMR spectra
The characterization of the compounds was further enhanced
by the use of NMR spectroscopy. The NMR spectra of the
compounds were recorded on a Varian Mercury AS 400 NMR spec-
trometer and shown in Figs. S3 and S4 in Supplementary materials.
Theoretical 1H and 13C NMR chemical shift values of the com-
pounds have been computed using the same method and the basis
set for the optimized geometry. The results of these calculations
are collected in Table 5 together with the experimental values.
Since experimental 1H chemical shift values were not available
for the individual hydrogen atoms of the methyl groups in com-
pound 2, the average of the computed values is given for these
hydrogen atoms.
All NMR data are consistent with the structural formula of the
compounds. In the 1H NMR spectra of compound 1, the chemical

N. Özdemir et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 131 (2014) 145–152
149
Table 3
Optimized and experimental geometries of the title compound.
Parameters
Experimental
Calculated
Parameters
Experimental
Calculated
Bond lengths (Å)
S1AO1
S1AO2
S1AO3
S1AC20
N1AC1
1.4543(15)
1.4318(17)
1.4638(17)
1.780(2)
1.338(2)
1.324(3)
1.485
1.469
1.523
1.823
1.331
1.333
1.338
N2AC7
N3AC6
1.390(3)
1.333(3)
1.388(3)
1.332(3)
1.373(3)
1.337(3)
1.377(3)
1.383
1.346
1.380
1.356
1.392
1.329
1.384
N3AC12
N4AC13
N4AC14
N5AC13
N5AC19
N1AC5
N2AC6
1.332(3)
Bond angles (°)
O1AS1AO2
O1AS1AO3
O2AS1AO3
O1AS1AC20
O2AS1AC20
O3AS1AC20
N2AC6AN3
N4AC13AN5
C1AN1AC5
113.15(11)
110.13(10)
112.77(11)
105.57(10)
109.58(10)
105.08(10)
109.61(19)
108.5(2)
114.80
109.17
112.37
107.26
108.81
103.78
110.16
108.96
118.88
C6AN2AC7
C6AN3AC12
C13AN4AC14
C13AN5AC19
N2AC6AC5
N3AC6AC5
N4AC13AC1
N5AC13AC1
108.68(18)
108.48(19)
109.46(18)
109.21(19)
126.8(2)
123.5(2)
128.12(19)
123.4(2)
108.01
108.50
109.18
109.19
127.17
122.68
126.77
124.26
117.70(18)
Torsion angles (°)
N1AC5AC6AN2
N1AC5AC6AN3
N1AC1AC13AN4
N1AC1AC13AN5
ꢂ175.9(2)
1.6(3)
167.58
ꢂ12.59
ꢂ171.16
9.20
C4AC5AC6AN2
C4AC5AC6AN3
C2AC1AC13AN4
C2AC1AC13AN5
3.3(3)
ꢂ13.50
166.33
9.84
ꢂ169.80
ꢂ179.3(2)
ꢂ174.3(2)
5.5(4)
3.8(3)
ꢂ176.5(2)
Table 4
Comparison of the observed and calculated vibrational frequencies (cmꢂ1
)
for
compounds 1 and 2.
Assignments
1
2
Experimental
Calculated
Experimental
Calculated
m
NAH
3181
3111
3064
–
–
–
–
–
1576
–
1490
–
1457
1434
1385
1317
1277
1230
–
–
1150
–
3539
3095
3073
–
–
–
–
–
1571
–
1521
–
1427
1413
1378
1334
1255
1193
–
–
1132
–
3242
3058
3034
2969
2929
2853
2733
1621
1564
1522
–
3535
3052
3048
2973
2947
2924
2905
1615
1580
1555
–
ms CAH
mas CAH
mas CAH3
ms CAH3
ms CAH3
m
m
m
m
m
a
c
c
c
m
m
c
NAH
C@N
C@C
C@C
C@N
CAH3
CAH
CAH
NAH
CAN
CAN
NAH
1454
–
1452
–
1411
1352
1275
1219
–
1153
1119
–
1415
1363
1275
1216
–
1181
1061
–
mas SAO3
ms SAO3
c
x
d CAH3
CAH
CAH3
1031
1001
960
1037
1019
993
–
–
–
–
–
–
x
x
NAH
NAH
881
883
d CAH
h
h
925
844
–
915
824
–
850
811
759
849
830
793
x CAH
x CAH
m CAS
815
738
–
809
732
–
739
719
653
744
736
641
Vibrational modes: m, stretching; a, scissoring; c, rocking; x, wagging; d, twisting; h,
ring breathing. Abbreviations: as, asymmetric; s, symmetric.
shifts of AHbenzimidazole peaks were appeared as two multiplets
around 7.23–7.41 and 7.66–7.86 ppm, which have been calculated
at 7.62–7.69 and 7.90–8.09 ppm, respectively. Pyridine backbone
hydrogen’s were observed as triplet at 8.17 ppm for AH3A and as
doublets at 8.34 ppm for AH2A,4A. These signals have been obtained
Fig. 3. FT-IR spectra of compounds 1 (a) and 2 (b).

150
N. Özdemir et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 131 (2014) 145–152
Table 5
Experimental and theoretical 13C and 1H NMR chemical shifts d(ppm) from TMS for compounds 1 and 2.
Atom
1
2
Experimental
Calculated
Experimental
Calculated
C1
C2
C3
C4
C5
C6
C7
C8
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
9.01
–
9.01
–
141.86
123.30
145.34
123.30
141.86
148.64
115.29
130.13
130.13
130.13
130.13
115.29
148.64
115.29
130.13
130.13
130.13
130.13
115.29
136.05
137.02
124.65
139.92
124.65
137.02
22.71
20.27
22.71
10.28 (br, 4H)
10.28 (br, 4H)
10.28 (br, 4H)
10.28 (br, 4H)
8.52 (d, 2H, J = 9 Hz)
8.39 (t, 1H, J = 8.5 Hz)
8.52 (d, 2H, J = 9 Hz)
7.83–7.86 (m, 4H)
7.46–7.49 (m, 4H)
7.46–7.49 (m, 4H)
7.83–7.86 (m, 4H)
7.83–7.86 (m, 4H)
7.46–7.49 (m, 4H)
7.46–7.49 (m, 4H)
7.83–7.86 (m, 4H)
6.81 (s, 2H)
6.81 (s, 2H)
2.57 (s, 6H)
2.19 (s, 3H)
2.57 (s, 6H)
147.16
131.20
148.83
138.92
150.86
153.31
141.50
121.48
133.12
133.72
120.20
139.33
152.66
138.61
119.71
135.31
134.17
121.88
139.67
151.01
144.00
136.50
148.58
136.71
146.68
27.10
23.68
24.69
19.34
15.57
9.64
18.89
8.44
8.69
11.42
8.02
7.79
7.88
8.28
8.13
8.02
8.00
8.51
7.12
7.36
2.70
2.36
2.92
C9
C10
C11
C12
C13
C14
C15
C16
C17
C18
C19
C20
C21
C22
C23
C24
C25
C26
C27
C28
H2 (N2)
H3 (N3)
H4 (N4)
H5 (N5)
H2A
H3A
H4A
H8
13.01 (br, 2H)
–
13.01 (br, 2H)
–
8.34 (d, 2H, J = 9 Hz)
8.17 (t, 1H, J = 9 Hz)
8.34 (d, 2H, J = 9 Hz)
7.66–7.86 (m, 4H)
7.23–7.41 (m, 4H)
7.23–7.41 (m, 4H)
7.66–7.86 (m, 4H)
7.66–7.86 (m, 4H)
7.23–7.41 (m, 4H)
7.23–7.41 (m, 4H)
7.66–7.86 (m, 4H)
–
8.03
8.37
8.03
7.90
7.69
7.62
8.09
7.90
7.69
7.62
8.09
–
H9
H10
H11
H15
H16
H17
H18
H22
H24
H26a
H27a
H28a
–
–
–
–
–
–
–
–
Note: the atom numbering according to Fig. 2 used in the assignment of chemical shifts.
a
Average.
at 8.37 and 8.03 ppm theoretically. A broad peak at 13.01 ppm may
be assigned to the ANH protons, which has been calculated at
9.01 ppm.
mesitylene backbone carbons were observed at 124.65, 136.05,
137.02 and 139.92 ppm, while the carbon peaks belonging to the
benzimidazole backbone were observed at 115.29, 130.13 and
148.64 ppm. The pyridine backbone carbons were appeared in
the region 123.30–145.34 ppm. These signals have been calculated
in the range of 131.20–150.86 ppm, respectively. The individual
experimental and theoretical chemical shift values can be seen in
Table 5.
In the 1H NMR spectra of compound 2, the mesitylene backbone
hydrogen’s were appeared as three singlets at 2.19 ppm for AH27
,
at 2.57 ppm for AH26,28 and at 6.81 for AH22,24 that have been
observed at 2.36 ppm AH27, at 2.70 ppm for AH26, at 2.92 ppm
for AH28, at 7.12 ppm for AH22 and at 7.36 ppm for AH24 in the the-
oretical spectra. The AHbenzimidazole peaks give two multiples around
7.46–7.49 ppm and 7.83–7.86 ppm while the pyridine backbone
hydrogen’s were observed as triplet at 8.39 ppm for AH3A and as
doublets at 8.52 ppm for AH2A,4A. The ANH protons were identified
at 10.28 ppm as broad peak, which have been computed in the
region 9.64–19.34 ppm.
Electronic absorption spectra
The UV–vis. absorption spectra of the two compounds in meth-
anol were recorded at room temperature within the 200–500 nm
range and shown in Fig. 4. The two compounds have absorption
in the range of 200–360 nm. In the spectra of compounds, four
transitions (at 310, 301, 240 and 223 nm) for compound 1 and
two transitions (at 311 and 206 nm) for compound 2 were
In the 13C NMR spectra of compound 2, there are two aliphatic
peaks at 20.27 and 22.71 ppm for C27 and C26,28, respectively. These
signals have been calculated as 23.68 ppm for C27, 27.10 ppm for
C26 and 24.69 ppm for C28. The peaks belonging to the rest of the
observed, which can be assigned to
p ?
pꢄ transitions. There is

N. Özdemir et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 131 (2014) 145–152
151
Conclusions
In this study, a novel benzimidazole salt compound (2) have
been synthesized unexpectedly by the reaction of 2,6-bis(ben-
zimidazol-2-yl)pyridine (1) with 2-mesitylenesulfonyl chloride in
basic conditions while we plan to synthesize 2,6-bis{1-(mes-
itylsulfonyl)-1H-benzo[d]imidazol-2-yl}pyridine compound. Com-
pounds 1 and 2 have been characterized by spectroscopic (FT-IR,
NMR and UV–vis.) technique and single-crystal X-ray diffraction
technique has been employed for the structural characterization
of compound 2. In addition, computational studies have been per-
formed employing B3LYP hybrid density functional method with
the 6-311G(d,p) basis set. When the experimental and theoretical
results are compared, good correlations are found between them.
The major discrepancies can mainly attributed to the solid state
interactions in the crystal structure which are absent in the
quantum mechanical modeling of the compounds.
Acknowledgements
This research has been supported by The Scientific and Techni-
_
cal Research Council of Turkey (TUBITAK) (Project No: 107T808).
We wish to thank Prof. Dr. Orhan Büyükgüngör for his help with
the data collection and acknowledge the Faculty of Arts and Sci-
ences, Ondokuz Mayıs University, Turkey, for the use of the STOE
IPDS II diffractometer (purchased under Grant No. F-279 of the
University Research Fund).
Appendix A. Supplementary material
CCDC 802607 contains supplementary crystallographic data
(excluding structure factors) for the compound reported in this
article. These data can be obtained free of charge at http://
www.ccdc.cam.ac.uk/cgi-bin/catreq.cgi [or from the Cambridge
Crystallographic Data Centre (CCDC), 12 Union Road, Cambridge
CB2 1EZ, UK; fax: +44 (0)1223 336033; e-mail: deposit@ccdc.ca-
m.ac.uk]. Supplementary data associated with this article can be
found, in the online version, at http://dx.doi.org/10.1016/
j.saa.2014.04.148.
Fig. 4. UV–vis. spectra of compounds 1 (a) and 2 (b) in methanol.
one extra peak observed at 327 nm for compound 2, which proba-
bly arises from charge transfer.
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