Synthesis, crystal structures, spectral investigations, conformational analysis and DFT studies of N- heterocyclic carbene precursors

Article abstract of DOI:10.1016/j.molstruc.2019.127519

Three new 2-hydroxyethyl substituted N-heterocyclic carbene (NHC) precursors were synthesized in this study. These NHC precursors were prepared from 1-(alkyl/aryl)benzimidazole and alkyl halides. Their structural characterizations were performed by elemental analysis, ¹H NMR, ¹³C NMR, FT–IR and UV–Vis spectroscopy and single-crystal X-ray diffraction. The spectral features were also characterized by Density Functional Theory (DFT) at B3LYP/Lanl2dz//6-31G++(d,p) basis set. Two most stable conformers belonging to the compounds were found by potential energy surface (PES) scan, and the theoretical ground-state geometries were investigated. Among these conformers, the geometry of the conformer-I for all compounds matches almost well with the experimental results. ¹H and ¹³C NMR chemical shifts were calculated with GIAO approach and compared to the observed ones. Detailed vibrational assignments of the wavenumbers of the conformers were carried out based on the potential energy distribution (PED). Natural bond orbital (NBO) analysis was used to analyze the stability of the molecules arising from hyperconjugative interactions and charge delocalization. The HOMO–LUMO energy gap of the stable conformers was calculated for comparing their chemical reactivity behavior. Molecular electrostatic potential (MEP) diagrams were used to get information about ?the size, shape, charge density distribution and site of chemical reactivity of each stable conformer. The 3D Hirshfeld surfaces and the associated 2D fingerprint plots were also carried out to obtain an insight into the behavior of the interactions in the compounds.

Full text of DOI:10.1016/j.molstruc.2019.127519

Journal Pre-proof
Synthesis, crystal structures, spectral investigations, conformational analysis and DFT
studies of N- heterocyclic carbene precursors
Fatoş Erdemir, Duygu Barut Celepci, Aydın Aktaş, Yetkin Gök
PII:
S0022-2860(19)31628-X
DOI:
https://doi.org/10.1016/j.molstruc.2019.127519
MOLSTR 127519
Reference:
To appear in: Journal of Molecular Structure
Received Date: 22 August 2019
Revised Date: 12 November 2019
Accepted Date: 1 December 2019
Please cite this article as: Fatoş. Erdemir, D.B. Celepci, Aydı. Aktaş, Y. Gök, Synthesis, crystal
structures, spectral investigations, conformational analysis and DFT studies of N- heterocyclic carbene
precursors, Journal of Molecular Structure (2020), doi: https://doi.org/10.1016/j.molstruc.2019.127519.
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Synthesis, Crystal Structures, Spectral Investigations, Conformational Analysis and DFT
Studies of N- heterocyclic carbene precursors
Fatoş Erdemir, Duygu Barut Celepci2*, Aydın Aktaş1*, Yetkin Gök1
1 İnönü University, Faculty of Science, Department of Chemistry 44280, Malatya, Turkey
2 Dokuz Eylül University, Faculty of Science, Department of Physics, 35160, İzmir, Turkey
E-mail:aydinaktash@hotmail.com, duygu.barut@deu.edu.tr
Abstract
Three new 2-hydroxyethyl substituted N-heterocyclic carbene (NHC) precursors were
synthesized in this study. These NHC precursors were prepared from 1-(alkyl/aryl)benzimidazole
1
and alkyl halides. Their structural characterizations were performed by elemental analysis, H
NMR, 13C NMR, FT–IR and UV-Vis spectroscopy and single-crystal X-ray diffraction. The
spectral features were also characterized by Density Functional Theory (DFT) at
B3LYP/Lanl2dz//6-31G++(d,p) basis set. Two most stable conformers belonging to the
compounds were found by potential energy surface (PES) scan, and the theoretical ground-state
geometries were investigated. Among these conformers, the geometry of the conformer-I for all
1
13
compounds matches almost well with the experimental results. H and C NMR chemical shifts
were calculated with GIAO approach and compared to the observed ones. Detailed vibrational
assignments of the wavenumbers of the conformers were carried out based on the potential
energy distribution (PED). Natural bond orbital (NBO) analysis was used to analyze the stability
of the molecules arising from hyperconjugative interactions and charge delocalization. The
HOMO–LUMO energy gap of the stable conformers was calculated for comparing their chemical
reactivity behavior. Molecular electrostatic potential (MEP) diagrams were used to get
information about the size, shape, charge density distribution and site of chemical reactivity of
each stable conformer. The 3D Hirshfeld surfaces and the associated 2D fingerprint plots were
also carried out to obtain an insight into the behavior of the interactions in the compounds.
Keywords: N-heterocyclic carbene, Crystal structure, Spectral investigations, Conformational
analysis, DFT
1

1. Introduction
Carbene precursors such as benzimidazolium salts have attracted considerable interest in
organic chemistry due to its structural and unique electronic properties, in recent years [1,2].
Particularly, these NHC precursors, which can form complexes almost with all of the transition
metals [3-5], have shown strong activity in enzyme inhibition studies and have the focus of
interest in their biological activity studies [6,7].
One approach used for the synthesis of benzimidazolium salts is the cyclization of ortho
phenylenediamine with formic acid. Benzimidazolium salts are NHC precursors including two
alkyl/aryl substituents that could be adjusted as steric bulk on two nitrogen atoms. A large number
of different benzimidazolium salts have recently been described [8].
Our study on the single X-crystal structure of NHC precursors containing iodide ion has been
published recently [9]. In this study, we investigated the structural and electronic properties of
three new benzimidazolium salts by using single-crystal X-ray diffraction method and
1
spectroscopic techniques H NMR, 13C NMR, FT–IR, and UV-Vis. In the literature, very few
studies being important in terms of the biological activity and involving both experimental and
theoretical details on the NHC precursors have been conducted [10]. So, to support the obtained
experimental results with theoretical approaches, we performed comprehensive DFT studies. We
aim to report the most important intramolecular interactions, to know the chemical reactivity
behaviors of the compounds. Thus, frontier molecule orbitals (FMO), molecular electrostatic
potential (MEP) and natural bond orbital (NBO) analyses were carried out. Additionally, to
determine the most stable geometry of the compounds, a systematic quantum chemical study of
the possible conformations, their relative stabilities were performed by using potential energy
scan (PES) analysis. Vibrational modes of these stable conformers of the NHC salts were
1
assigned based on the potential energy distribution (PED) analysis. H and 13C NMR chemical
shifts of the conformers were determined with gauge independent atomic orbital (GIAO)
approach. To identify the intermolecular interactions, the 3D Hirshfeld surface analysis and the
associated 2D fingerprint plots.
2. Experimental Section
Syntheses of the 2-hydroxyethyl substituted NHC precursors 1a-c were prepared under an
inert atmosphere in flame-dried glassware using standard Schlenk techniques. Iodoethanol,
iodomethane,
2,4,6-trimethylbenzyl
chloride,
2,4,5,6-tetramethylbenzyl
chloride,
2

dimethylformamide, ethanol and diethyl ether as solvents and all other commercial chemicals
were used without further purification. Melting points were identified in glass capillaries under air
with an Electrothermal-9200 melting point apparatus. FT-IR spectra were saved in the range 400-
1
4000 cm-1 on Perkin Elmer Spectrum 100 FT-IR spectrometer. H NMR and 13C NMR spectra
were recorded using a Bruker AS 400 spectrometer operating at 400 MHz (1H) and 100 MHz
(13C). Chemical shifts (δ) are given in ppm relative to TMS, and coupling constants (J) in Hz. The
UV spectrum was measured with the Shimadzu UV-1601 instrument. Elemental analyses were
performed by İnönü University Scientific and Technological Research Center (Malatya,
TURKEY).
2.1 Synthesis of bis(2-hydroxyethyl)benzimidazolium iodide, 1a
A mixture of 1-(2-hydroxyethyl)benzimidazole (162 mg, 10 mmol) and 2-hydroxyethyl iodide
(172 mg, 10 mmol) was added in dry DMF (4 mL). The reaction mixture was stirred for 22 h at
70°C and 2 h at 110 °C temperatures. The excess of DMF was evaporated in vacuum. Diethyl
ether was added to the reaction mixture and the white solid was filtered off. The crude product
was crystallized in a mixture of ethyl alcohol-diethyl ether (1/3).Yield: 80 % (267 mg); m,p,:
219-221 °C; ν(CN): 1561 cm-1; ν(O-H): 3301 and 3400 cm-1. Anal. Calc. for C11H15IN2O2: C: 39.54;
1
H: 4.52; N: 8.38. Found: C: 39.57; H: 4.49; N: 8.36. H NMR (400 MHz, DMSO), δ 3.85 (s, 2H,
-NCH2CH2OH); 4.60 (s, 2H, -NCH2CH2OH); 5.20 (s, 1H, -NCH2CH2OH); 7.69 and 8.09 (dd, m,
4H, J= 6.3, 3.1 Hz, Ar-H); 9.70 (s, 1H, 2-CH), 13C NMR (400 MHz, DMSO), δ 50.0 (-
NCH2CH2OH); 59.2 (-NCH2CH2OH); 114.4, 126.8 and 131.8 (Ar-C); 143.3 (2-CH).
2.2 Synthesis of 1-(2-hydroxyethyl)-3-(2,4,6-trimethylbenzyl)benzimidazolium iodide, 1b
According to the same procedure as salt 1a, salt 1b was prepared from 1-(2,4,6-
trimethylbenzyl)benzimidazole (150 mg, 6 mmol) and 2-hydroxyethyl iodide (103 mg, 6 mmol).
Yield: 79 % (200 mg), m,p,: 145-147 °C; ν(CN): 1556 cm-1; ν(O-H): 3324 cm-1. Anal. Calc. for
C19H23IN2O: C: 54.04; H: 5.49; N: 6.63. Found: C: 54.00; H: 5.51; N: 6.65. 1H NMR (400 MHz,
DMSO), δ 2.26 and 2.30 (s, 9H, -NCH2C6H2(CH3)3); 3.75 (dd, 2H, J= 9.8, 5.1 Hz, -
NCH2CH2OH); 4.54 (t, 2H, J= 4.7 Hz, -NCH2CH2OH); 5.06 (t, 1H, J= 5.4 Hz, -NCH2CH2OH);
5.65 (s, 2H, -NCH2C6H2(CH3)3); 7.04 (s, 2H, -NCH2C6H2(CH3)3); 7.73 and 8.09 (m, dd, 4H, J=
8.7, 4.2 Hz, Ar-H); 9.06 (s, 2-CH),13C NMR (400 MHz, DMSO), δ 19.6 and 21.1 (-
NCH2C6H2(CH3)3); 45.6 (-NCH2CH2OH); 49.7 (-NCH2C6H2(CH3)3); 58.9 (-NCH2CH2OH);
114.0, 114.4, 125.8, 127.2, 127.3, 130.0, 131.9, 132.0, 138.8 and 139.5 (Ar-C); 141.6 (2-CH).
3

2.3 Synthesis of 1-(2-hydroxyethyl)-3-(2,3,5,6-tetramethylbenzyl)benzimidazolium iodide, 1c
According to the same procedure as salt 1a, salt 1c was prepared from 1-(2,3,5,6-
tetramethylbenzyl)benzimidazole (158 mg, 6 mmol) and 2-hydroxyethyl iodide (103 mg, 6
mmol). Yield: 72 % (188 mg), m,p,: 255-257 °C; ν(CN): 1560 cm-1; ν(O-H): 3287 cm-1. Anal. Calc.
1
for C20H25IN2O: C: 55.05; H: 5.78; N: 6.42. Found: C: 55.01; H: 5.80; N: 6.39. H NMR (400
MHz, DMSO), δ 2.17 and 2.26 (s, 12H, -NCH2C6H(CH3)4); 3.76 (s, 4H, -NCH2CH2OH); 4.54 (s,
4H, -NCH2CH2OH); 5.04 (s, 1H, -NCH2CH2OH); 5.72 (s, 2H, -NCH2C6H(CH3)4); 9.00 (2-CH);
7.16 (s, 1H, -NCH2C6H(CH3)4); 7.74 and 8.13 (m, dd, J= 20.9, 7.4 Hz, 4H, Ar-H), 13C NMR
(400 MHz, DMSO), δ 15.8 and 20.6 (-NCH2C6H(CH3)4); 46.3 (-NCH2CH2OH); 49.8 (-
NCH2C6H(CH3)4); 59.0 (-NCH2CH2OH); 114.2, 114.6, 127.0, 127.1, 128.6, 132.0, 132.1, 133.4,
134.7 and 134.9 (Ar-C); 141.9 (2-CH).
H
N
R
N K+
N
NH2
NH2
N
HCOOH
-H2O
R-X
EtOH
1 h, 25 0C
+ KOH
+ KX
24 h
reflux
N
N
OH
R-X:
I
Cl
Cl
Scheme 1. Synthesis of 1-(alkyl/aryl)benzimidazole
Scheme 2. Synthesis of 1-(2-hydroxyethyl)benzimidazolium salts 1a-c
2.4 Single-crystal X-ray diffraction
4

Single-crystal X-ray data of the compounds 1a-c were recorded at room temperature by ω-
scan technique, on a Rigaku-Oxford Xcalibur diffractometer with an EOS-CCD area detector
operated at 50 kV and 40 mA using graphite-monochromated MoKα radiation (λ= 0.71073 Å)
from an enhance X-ray source with CrysAlisPro software [11]. Data reduction and analytical
absorption corrections were performed by CrysAlisPro program [12]. The structural solution,
refinement, and analysis were performed using OLEX2 [13]. The crystal structure of the
compounds was solved using Intrinsic Phasing method with SHELXT and refined by full-matrix
least-squares on F2 in SHELXL [14,15]. Anisotropic thermal parameters were applied to all non-
hydrogen atoms. Except for the O–H hydrogen atoms in the compound 1a, all other hydrogen
atoms were placed using standard geometric models and with their thermal parameters riding on
those of their parent atoms (O–H = 0.82 Å; C–H = 0.93, 0.96 and 0.97 Å). In both hydroxyethyl
groups in 1a, O–H hydrogen atoms were located in difference Fourier map and freely
isotropically refined. DFIX 0.86 Å was also applied to fix the O1–H1 distance. To ensure
satisfactory refinement of disordered hydroxyethyl group in the structure, rigid-bond restraint
RIGU and isotropic restraint ISOR were applied to the hydroxyethyl group of the compound 1b.
Table 1. Crystallographic data and structure refinement for the compounds 1a-c.
1a
C11H15N2O2I
334.15
1b
C19H23N2OI
422.29
1c
C20H25N2OI
436.32
Empirical Formula
Formula weight
Temperature/K
Crystal system
Space group, Z
a/Å
293(2)
293(2)
293(2)
Monoclinic
P21/n, 4
Monoclinic
P21/c, 4
Monoclinic
P21/c, 4
8.9682(5)
10.6343(4)
13.8686(6)
93.754(4)
1319.82(11)
1.682
8.7386(4)
15.4147(8)
14.0661(6)
93.971(4)
1890.20(15)
1.484
9.7610(6)
13.1166(9)
15.7840(9)
102.110(6)
1975.9(2)
1.467
b/Å
c/Å
β/°
Volume/Å3
ρcalcg/cm3
ꢀ/mm-1
2.416
1.700
1.629
F(000)
656
848
880
Crystal size/mm3
Reflections collected
Independent reflections
Parameters
0.488 × 0.380 × 0.205
4669
0.428 × 0.348 × 0.207
5903
0.399 × 0.275 × 0.192
6355
2498 [Rint = 0.021]
153
3560 [Rint = 0.021]
212
3710 [Rint = 0.023]
222
5

Goodness-of-fit on F2
R, wR2 [I > 2σ(I)]
1.038
1.040
0.987
R1 = 0.0312, wR2 = 0.0622
R1 = 0.0526, wR2 = 0.1265
R1 = 0.0709, wR2 = 0.1384
R1 = 0.0447, wR2 = 0.0966
R1 = 0.0808, wR2 = 0.1170
R, wR2 (all data)
R1 = 0.0449, wR2 = 0.0689
2.5 Theoretical Studies
The quantum chemical calculations have been performed at DFT (B3LYP) methods with
Lanl2dz//6-31G++(d,p) basis set using Gauss–View6 molecular visualization and Gaussian 09W
program packages [16,17]. In order to determine the most stable conformers of the molecular
structures, the conformational analysis in the gas phase was carried out. Two stable structures
were found for each compound by PES (potential energy surface) scan. The vibrational frequency
calculations were performed at the same level of the theory, and the fundamental normal modes
of all the conformers were assigned based on the potential energy distribution (PED). The 1H and
13C NMR chemical shifts of each conformer of the 1a-c were obtained by using the gauge
1
invariant atomic orbital (GIAO) method in the gaseous phase [18]. Values for the H and 13C
chemical shifts were referenced to TMS. The natural bonding orbital (NBO) calculations were
performed using NBO 3.1 program as implemented in Gaussian 09W package to get detailed
insight about the intramolecular interactions and investigate charge transfer, delocalization or
hyperconjugative interactions in the molecular systems of 1a-c [19]. Frontier molecular orbitals
(FMO) and molecular electrostatic potential (MEP) surfaces were also generated to understand
the chemical reactivity tendencies. Molecular Hirshfeld surfaces are generated by
CrystalExplorer version 17.5 computer program [20].
3. Results and Discussions
3.1 Structural Determination of 1a-c
The molecular view of the compounds 1a-c is represented in Figs. 1, 2 and 3. All compounds
crystallize in the monoclinic crystal system. Each unit of the salts consists of a benzimidazolium
cation and an iodide anion. In the asymmetric unit of the 1a, the NHC cation contains two
hydroxyethyl groups, which are arranged into U–shaped, extend parallel to the a-axis. The twist
angles of hydroxyethyl around the benzimidazole ring system are very similar [N1–C8–C9–O1 =
65.3(4)°, N2–C10–C11–O2 = -66.4(4)°]. In 1b and 1c, NHC ligands connect to trimethylbenzyl
and tetramethylbenzyl fragments, respectively, besides the hydroxyethyl groups. N-
benzimidazole ring systems are almost coplanar with a mean deviation of 0.009 Å for 1a, 0.010
6

Å for 1b and 0.019 Å for 1c. Bond parameters such as bond lengths, bond angles, and torsion
angles are comparable with similar compounds in our previous study and related studies in the
literature [9, 21-23]. In the crystal structure of the 1a, the cation molecule connects to iodide
anion by hydroxyethyl groups (Table 2). Also, there is a C–H···O type intermolecular weak
ꢅ
ꢁꢂ
ꢃ
interaction, forming ꢀꢁ 12 ꢀꢄꢂ20ꢃ dimer graph-set motif together with the hydrogen bonds, is
responsible for the stabilization of the structure (Fig. 1b-c). In the crystal structure of 1b and 1c,
there is only a hydrogen bonding interaction which occurs between the hydroxyethyl oxygen
atom of the cation molecule and iodide anion [21, 24]. For both compounds, the iodide anions
play role on the stabilization of the crystal structures. The crystal packing views are illustrated in
Fig. 2b and 3b.
(a)
(b)
(c)
ꢅ
ꢁꢂ
ꢃ
Fig. 1. Single crystal X-ray structure of 1a showing (a) Ellipsoid plot (30% probability level) (b) ꢀꢁ 12 ꢀꢄꢂ20ꢃ
dimeric motif through the O–H···I hydrogen bonds and C–H···O intermolecular interactions (c) 1D ladder-like motif
of the iodide anions along the b axis. All hydrogen atoms except those participating in the interactions were omitted
for clarity.
7

(a)
(b)
Fig. 2. Single crystal X-ray structure of 1b showing (a) Ellipsoid plot (30% probability level) (b) Packing of the
crystal structure viewed along the c-axis.
(a)
(b)
Fig. 3. Single crystal X-ray structure of 1c showing (a) Ellipsoid plot (30% probability level) (b) Packing of the
crystal structure viewed along the c-axis.
8

Table 2. Hydrogen-bonding and weak intermolecular interactions [Å,°] for the title compounds.
Compound
1a
D–HꢀꢀꢀA
D–H
0.85
0.85
0.93
0.82
0.82
HꢀꢀꢀA
2.77
2.60
2.16
2.57
2.60
DꢀꢀꢀA
D–HꢀꢀꢀA
165
O1–H1ꢁꢁꢁI1
O2–H2ꢁꢁꢁI1
C1–H1AꢁꢁꢁO2i
O1–H1ꢁꢁꢁI1
O1–H1AꢁꢁꢁI1
3.594(4)
3.427(3)
3.046(4)
3.383(8)
3.423(4)
165
160
170
1b
1c
176
Symmetry code: (i) 2-x, 1-y, 1-z
3.2 Molecular Geometry and Conformational Analysis
Optimized structural parameters of three NHC salts were calculated in the gaseous phase via
density functional theory [DFT/B3LYP/LanL2DZ//6-31G++(d,p)]. In order to find the
conformational stabilities of the NHC complexes, 1D relaxed potential energy surface (PES)
scans were performed around torsion angles (τ) of two sides of the benzimidazole fragments
[τ1(C1–N1–C8–C9), τ2(N1–C8–C9–O1), τ3(N2–C10–C11–O2), τ4(C1–N2–C10–C11), τ5(N2–
C10–C11–C16) and τ6(N2–C10–C11–C12)]. On account of the same torsion angle, we selected
only τ2(N1–C8–C9–O1) for the conformational analysis in here. Investigation results for the
other stable conformers were given in the supplementary information file. Scanning was started
from 60° to 280° by taking 4° intervals (i.e., 50 steps) and a total of 51 scan steps. Fig. 4 indicates
the potential energy surface curve of the NHC salt 1a, while the other stable conformers are in
supplementary data (Fig. S1 and S2). The values reveal that global minimum structures are the
most stable conformers, and they match well with the experimental one. The selected geometric
parameters such as bond distances, bond angles and torsion angles of the two most stable
conformers for the selected scan coordinate angle τ2(N1–C8–C9–O1) of the 1a-c were computed
and compared with the experimental X-ray data in Table 3. It is clear from the table, the
calculated bond lengths are slightly higher than the experimental ones, which is well known that
the experimental molecular structure was in solid-state form, while the theoretical computations
of the isolated structure were carried out in the gaseous phase of the molecule. The calculated
total energies and the energy differences between the most stable two conformers Conf-I and
Conf-II for the structures are listed in Table 4. Given that its energy is lower than Conf-II, Conf-I
is the most stable conformer for the selected scan coordinate angle τ2(N1–C8–C9–O1).
9

Table 3. The selected geometric parameters of two conformers (for the scan coordinate angle N1–C8–C9–O1) of
each compound.
1a
1b
1c
Exp.
ConfI
ConfII
Exp.
ConfI
ConfII
Exp.
ConfI
ConfII
Bond Lengths
O1–C9
1.408(5) 1.442
1.417(4) 1.442
1.474(4) 1.478
1.472(4) 1.478
1.510(5) 1.530
1.512(5) 1.530
1.440
1.446
1.478
1.481
1.550
1.530
1.311(3) 1.444
1.438
-
1.424(7) 1.444
1.446
-
O2–C11
-
-
-
-
N1–C8
1.463(6) 1.477
1.475(6) 1.488
1.518(8) 1.532
1.509(7) 1.518
1.479
1.496
1.546
1.511
1.468(6) 1.477
1.478(6) 1.487
1.495(8) 1.532
1.513(6) 1.522
1.474
1.487
1.534
1.520
N2–C10
C8–C9
C10–C11
Bond Angles
O1–C9–C8
O2–C11–C10
C1–N1–C8
C1–N2–C10
111.6(3) 107.96
110.9(3) 107.97
125.3(3) 124.71
125.2(3) 124.71
109.47
108.44
123.82
125.02
106.1(6) 109.03
108.95
-
107.3(5) 108.97
114.11
-
-
-
-
-
124.9(4) 124.70
127.2(4) 124.31
124.27
126.21
125.3(4) 124.67
128.0(4) 124.56
124.78
124.54
N1–C8–C9
111.6(3) 111.89
111.8(3) 111.91
112.13
112.30
109.5(4) 112.21
112.6(4) 113.04
112.21
113.46
110.7(4) 112.10
111.1(4) 112.85
114.05
113.29
N2–C10–C11
Torsion Angles
C1–N1–C8–C9
-86.7(4) -62.44
-105.89
-82.6(6) -58.29
-96.34
79.0(6)
59.10
-40.44
N1–C8–C9–O1
65.3(4)
92.6(4)
64.00
62.38
-152.00
43.05
63.4(9)
-5.0(9)
65.02
161.02
-26.80
-63.8(6) -64.56
56.20
46.80
C1–N2–C10–C11
-51.49
-9.3(7)
-
46.46
-
N2–C10–C11–O2
N2–C10–C11–C12
N2–C10–C11–C16
-66.4(4) -63.99
69.39
-
-
-
-
-
-
-
-
-
-
83.7(6)
116.26
99.17
-81.56
-81.6(5) -119.03
97.2(5) 62.02
-114.02
66.94
-98.4(6) -65.37
10

Fig. 4. Representation of potential energy surface (PES) scan of the compound 1a with torsion angles τ1-4
3.3 Global reactivity descriptors, FMO (frontier molecular orbital) analysis, MEP (molecular
electrostatic potential)
Frontier Molecular Orbital (FMO) analysis provides important information about the
electronic properties and molecular reactivity of a compound. The highest occupied molecular
orbital (HOMO), as an electron donor, represents the distribution and energy of the least tightly
held electrons in the molecule, while the lowest unoccupied molecular orbital (LUMO) as an
electron acceptor, shows the ability to obtain an electron. The HOMO-LUMO analysis is used to
explain the charge transfer within a molecule. If in a molecule, HOMO is not doubly occupied or
the molecules do not have a large HOMO-LUMO energy gap, it is chemically reactive. The
higher energy values of HOMO, the more tendency to donate electrons to an appropriate
acceptor. Similarly, the lower values of LUMO energy show more probability to accept electrons.
In fact, the energy of the HOMO is a good approximation to the lowest ionization potential of the
molecule but the energy of the LUMO generally is a poor approximation to the molecule's
electron affinity [25]. Molecular electrostatic potential (MEP) is related to the electronic density
and is a very useful descriptor to predict the possible reactive sites for electrophilic and
nucleophilic attack reactions as well as hydrogen bonding interactions [26,27]. In the present
study, in order to investigate the chemical reactivity of these three NHC salts, the frontier
molecular orbital energies were calculated at DFT/B3LYP/LanL2DZ//6-31G++(d,p) level for
11

each stable conformer of selected torsion angle τ2. Table 5 displays some quantum chemical
quantities belonging these conformers such as electronegativity (χ), chemical hardness (η),
softness(S), chemical potential (ꢀ), charge transfer capability (ꢁNmax) and electrophilicity index
(ω). In addition to the ionization energy (I) [28] and electron affinity (A) [29] provided by the
Koopmans Theorem [30], these quantum chemical identifiers proposed by Parr and co-worker
[31,32] also provide theoretical insights into the chemical reactivity of a molecule. According to
the table, it can be said that Conf-II of 1b is the soft conformer with the lowest hardness value,
the best electrophile with the biggest electrophilicity index and has the most charge transfer
capability. Table 6 shows the HOMO-LUMO amplitudes and MEP diagrams of the stable
conformers. For all structures, HOMO for the Conf-I is localized on the iodide anion, whereas
LUMO is expanded on the benzimidazole moiety of the cation molecules.
MEP diagrams of the complexes reveal that the iodide anion center of the Conf-II of 1b has
the red color which means this region is the electron-rich region of the compound and therefore
the nucleophilic attack center of this molecule. NBO analysis also proves this result. The iodide
atom of Conf-II of 1b has the most maximum negative charge value [-0.85973] comparing to all
other molecules, which may due to the unfavorable geometry of Conf-II. Also, the resonance
energy of the electronic transition from LP(1)I1 to the O1-H1 has the lowest E(2) energy (see
Table 7). Therefore, the lone pair electrons of the iodide anion do not have as much
delocalization energy as the iodide atoms of other conformers and this makes this region is the
electron-rich region.
12

Table 4. Theoretically computed relative energies and the energy differences between the most stable two
conformers Conf-I and Conf-II for structures 1a-c.
Torsion angle
Compound 1a
Total Energy (kcal/mol)
ꢁE (kcal/mol)
Conf –I
Conf–II
τ1(C1–N1–C8–C9)
τ2(N1–C8–C9–O1)
τ3(N2–C10–C11–O2)
τ4(C1–N2–C10–C11)
Compound 1b
-438850.5613
-438850.5613
-438850.5613
-438850.5613
-438847.6183
-438845.7775
-438850.1828
-438845.5465
2.94
4.78
0.38
5.01
τ1(C1–N1–C8–C9)
τ2(N1–C8–C9–O1)
τ5(N2–C10–C11–C16)
τ6(N2–C10–C11–C12)
Compound 1c
-585953.3426
-585953.3426
-585953.3426
-585953.3426
-585953.4168
-585949.0091
-585952.6999
-585952.6973
-0.17
4.33
0.64
0.64
τ1(C1–N1–C8–C9)
τ2(N1–C8–C9–O1)
τ5(N2–C10–C11–C16)
τ6(N2–C10–C11–C12)
-610614.7007
-610615.6848
-610611.8593
-610611.7914
-610610.7694
-610615.1329
-610614.9651
-610614.973
3.93
0.44
-3.11
-3.18
Table 5. The calculated quantum chemical parameters (eV) for each conformer (for the scan coordinate angle N1–
C8–C9–O1) of NHC salts 1a-c.
1a
1b
1c
Conf-I
-4.79
-2.09
2.7
Conf-II
-5.03
-2.15
2.88
Conf-I
-4.69
-1.79
2.9
Conf-II
-4.56
-2.12
2.44
Conf-I
-4.64
-1.78
2.86
Conf-II
-4.80
-1.63
3.17
HOMO (-I)
LUMO (-A)
Egap
3.44
3.59
3.24
3.34
3.21
3.22
χ
1.35
-3.44
4.38
0.37
2.55
1.44
-3.59
4.48
0.35
2.49
1.45
-3.24
3.62
0.35
2.23
1.22
-3.34
4.57
0.41
2.74
1.43
-3.21
3.60
0.35
2.24
1.59
-3.22
3.27
0.31
2.03
η
ꢀ
ω
S
ꢁNmax
13

Table 6. HOMO and LUMO amplitudes (isovalue:0.02) and MEP diagrams (isovalue:0.0004) of each stable
conformers (for the scan coordinate angle N1–C8–C9–O1) for the compounds at B3LYP/Lanl2dz//6-31G++(d,p).
1a
HOMO
LUMO
MEP
Conf-I
Conf-II
1b
Conf-I
Conf-II
1c
Conf-I
14

Conf-II
3.4 Natural Bond Orbital (NBO) Analysis
The natural bond orbital (NBO) calculations provide an efficient method in order to
understand the intramolecular interactions between the bonds and the charge transfer within the
molecular systems. In the present work, the second-order perturbation theory analysis of Fock-
matrix for the stable conformers of the structures 1a-c was carried out to evaluate the donor-
acceptor interactions on the NBO basis. The larger the E(2) value, the more intense is the
interaction between electron donors and acceptors, i.e. more donating tendency from electron
donors to electron acceptors and greater the extent of conjugation of the whole system [33]. Table
7 indicates the stabilization energy, orbitals' occupancies and Fock matrix element for the
conformers of selected torsion angle τ2(N1-C8-C9-O1) for three NHC salts. As it is expected, the
strongest donations occur in the aromatic rings, especially in the benzimidazolium ring for all
structures, which give rise to the stabilization of the molecules. The stabilization energy for LP(1)
N1→π*(N2–C1) charge transfer for all conformers is similar to each other and calculated in the
range of 79.49–86.62 kJ/mol. In the structure 1b, the Conf-II, the donation from the antibonding
orbital of π*(C11–C12) to the π*(C13–C14) has the strongest energy of 232.50 kJ/mol. The
important second-order perturbative energies belonging to the stable conformers of the torsion
angles τ1,3,4 are tabulated in supporting information file (Table S1).
Table 7. The Second Order Perturbation Theory Analysis Results of the Fock Matrix in NBO Basis for the stable
conformers of selected torsion angle τ2(N1-C8-C9-O1) at B3LYP/Lanl2dz//6-31G++(d,p) level of the theory. The
greatest three stabilization energy is shown.
Donor(i)
Acceptor(j)
EDi(e)
EDj(e)
E(2)
Ej–Ei (a.u)
Fi,j
kJ/mol
(a.u)
Compound 1a
Conf-I
π* C2–C7
π* C2–C7
LP(1) N1
π* C3–C4
π* C5–C6
π* N2–C1
0.47354
0.47354
1.52488
0.30052
141.84
141.82
84.07
0.02
0.02
0.21
0.081
0.081
0.120
0.30051
0.49419
15

LP(1) I1
σ* O1–H1
1.99928
0.07044
0.64
0.89
0.022
Conf-II
π* C2–C7
π* C2–C7
LP(1) N1
LP(1) I1
π* C3–C4
π* C5–C6
π* N2–C1
σ* O1–H1
0.47709
0.47709
1.52127
1.99689
0.30238
0.30729
0.50757
0.02600
133.24
144.06
85.82
0.43
0.02
0.02
0.21
0.92
0.081
0.081
0.121
0.018
Compound 1b
Conf-I
π* C2–C7
π* C2–C7
LP(1) N1
LP(1) I1
π* C3–C4
π* C5–C6
π* N2–C1
σ* O1–H1
0.47375
0.47375
1.53659
1.99891
0.30978
160.64
150.76
81.17
0.69
0.02
0.02
0.21
0.90
0.081
0.081
0.119
0.023
0.30622
0.50806
0.07015
Conf-II
π*C11– C12 π*C13–C14
0.38724
0.47707
0.47707
1.51560
1.99873
0.32525
0.29925
0.30590
0.49369
0.03471
232.50
136.96
150.66
86.25
0.33
0.01
0.02
0.02
0.21
0.92
0.082
0.081
0.080
0.120
0.016
π* C2–C7
π* C2–C7
LP(1) N1
LP(1) I1
π* C3–C4
π* C5–C6
π* N2–C1
σ* O1–H1
Compound 1c
Conf-I
π* C2–C7
π* C2–C7
LP(1) N2
LP(1) I1
π* C3–C4
π* C5–C6
π* N1–C1
σ* O1–H1
0.47318
0.47318
1.52008
1.99895
0.30904
163.55
153.73
86.62
0.70
0.02
0.02
0.21
0.89
0.081
0.081
0.121
0.023
0.30619
0.51898
0.07257
Conf-II
π* C2–C7
π* C2–C7
LP(1) N1
LP(1) I1
π* C3–C4
π* C5–C6
π* N2–C1
σ* O1–H1
0.47386
0.47386
1.54688
1.99895
0.31707
0.31892
0.51776
0.05469
172.10
176.36
79.49
0.44
0.02
0.02
0.21
0.91
0.081
0.081
0.118
0.018
3.5 Vibrational Analysis
The FT-IR spectra of the 2-hydroxyethyl substituted NHC precursors 1a-c were compared
with the corresponding simulated ones. The vibrational spectral assignments of the stable
conformers were carried out with the help of potential energy distribution (PED) analysis. The
PED contributions corresponding to each of the observed frequencies are listed in Table 8.
Also, the recorded and calculated FT-IR spectra of the NHC salts can be seen from Fig. S3-S4
(suppl. data).
16

When the FT-IR spectra were investigated, the bands were observed in the range 3024-3146
cm-1 in the high-frequency region correspond to C-H stretching vibrations of the aromatic rings.
These vibration modes were calculated in the range of 3226-3246 cm-1 for three stable
conformers. The band at 1064, 1083 and 1073ꢂcm−1 corresponds to the symmetric C-O stretching
for 1a-c, respectively. The corresponding modes for the stable conformers were assigned at 1056-
1060 cm-1 for 1a, 1090-1065 cm-1 for 1b, 1073-1078 cm-1 for 1c. The O-H stretching on the
hydroxyethyl groups was observed at 3301-3400, 3324 and 3287 cm-1 for 1a-c, respectively. We
calculated them in the range of 3267-3511 cm-1. The FT-IR data clearly indicated the presence of
the C-N stretching at 1561, 1556 and 1560 cm-1 for 1a-c, respectively. Theoretically, they were
found very close to the experimental values [1573-1575 cm-1 for the conformations of 1a, 1571-
1568 cm-1 for 1b and 1577-1575 cm-1 for 1c]. It is worth noting that the vibration modes
assignments of the three conformers have differed at somewhere depending on the
conformational structure.
Table 8. The selected vibrational assignments (in cm_1) of the stable conformers of selected torsion angle τ2(N1-C8-C9-O1) of 1a-c,
with the percentage of potential energy distribution.
1a - Calculated wavenumber (unscaled)
1b - Calculated wavenumber (unscaled)
1c - Calculated wavenumber (unscaled)
Exp. ConfI PED(%)
3362 3355 νC1(65)
3301 3288 νO1(18)
3400 3288 νO2(18)
ConfII PED(%) Exp. ConfI PED(%) ConfII PED(%) Exp. ConfI PED(%) ConfII PED(%)
3332
3511
3333
νC1(17)
νO1(32)
νO2(16)
3352 3366
3324 3280
νC1(64)
νO1(32)
3153
3437
νC1(24)
νO1(33)
3284 3366 νC1(65)
3287 3267 νO1(32)
3344
3344
νC1(16)
νO1(16)
3131 3246 νsC6+C3(21) 3246
νsC5+C4(21)
νsC3(28) 3131 3246
+C4(22)
νsC3(28) 3245
+C4(22)
νsC3(26) 3146 3246 νsC3(13) 3244
νsC3(25)
+C4(20)
+C5(18)
+C6(20)
νaC3(18)
+C4(20)
+C5(21)
+C6(20)
νaC8(14)
νaC10(24)
νaC9(13)
+C4(21)
+C5(18)
+C6(18)
+C4(15)
+C5(21)
+C6(33)
+C5(17)
+C5(17)
+C6(15)
+C6(15)
3024 3228 νaC6+C3(19) 3228
νaC5+C4(20)
νaC3(17) 3082 3227
+C4(18)
νaC3(23) 3227
+C4(23)
νaC3(18) 3089 3226 νaC3(23) 3225
+C4(19)
+C5(21)
+C6(21)
+C4(23)
+C5(17)
+C6(15)
+C5(22)
+C5(18)
+C6(22)
+C6(15)
2956 3157 νaC8+C10(19) 3172
νaC8(17) 2968 3151
νaC8(26) 3165
νaC10(14) 3143
νaC8(15) 2937 3152 νaC8(25) 3121
3149
3130
3100
νaC10(29)
νaC9(18)
νaC11(16)
3136
νaC10(20)
3147 νaC10(13) 3160
3110 νaC9(15) 3121
-
-
-
-
-
-
-
-
-
-
3190 3192
3185
νC13(55) 3204
νC15(54) 3190
νaC19(16) 3118
νaC18(30) 3119
νaC17(22) 3111
νC14(61) 3021 3185 νC14(60) 3184
νC17(61)
νC14(60)
2958 3121
3116
νaC19(13) 2915 3128 νaC20(16) 3128
νaC20(19)
νaC19(21)
νaC18(22)
νaC18(25)
νaC17(21)
3114 νaC19(23) 3107
3108 νaC18(22) 3114
3120
17

3108 νaC17(23) 3128
νaC17(16)
νsC17(17)
νsC18(27)
νsC19(25)
νsC20(24)
νC1N(2)
νCO(3)
opb
-
-
-
-
-
2907 3041
3039
νsC17(25) 3031
νsC18(25) 3043
νsC19(19) 3034
νsC17(25) 2873 3034 νsC17(21) 3030
νsC18(28)
νsC19(17)
3033 νsC18(21) 3042
3042 νsC19(27) 3032
3032 νsC20(17) 3037
3035
1561 1573 νC1N(3)
1064 1056 νCO(2)
1013 1027 opb
C4HC5H
1575
1060
1028
νC1N(3) 1556 1571
νC1N(2) 1568
νC1N(2) 1560 1577 ν1N(2)
1575
1078
1020
νCO(2)
opb
1083 1090
1015 1023
νCO(1)
opb
1065
1028
νCO(1)
opb
1073 1073 νCO(3)
1033 1023 opb
C4HC5H
C4HC5H
(14)
C4HC5H
(14)
C4HC5H
(12)
C4HC5H
(14)
(14)
(14)
3.6 13C and 1H NMR studies
1
13
The data of the H NMR and C NMR spectra obtained for 2-hydroxyethyl substituted NHC
precursors 1a-c in DMSO-d6 are given in the experimental section. The plots of spectra are given
in supporting data (Fig. S5-7). The theoretical GIAO 1H and 13C chemical shift calculations (with
respect to TMS) were carried out using the DFT/B3LYP/6–31G++(d,p) basis set and compared
with experimental ones. The results of the calculations regarding the conformations of torsion
angle τ2(N1–C8–C9–O1), which is common to all compounds, are listed in supporting data
(Table S4) together with the experimental values. The 1H and 13C NMR chemical shifts are
converted to the TMS scale by subtracting the calculated absolute chemical shielding of
TMS (δ=Σ0−Σ) where δ is the chemical shift, Σ is the absolute shielding and Σ0 is the absolute
shielding of TMS, whose values are 32.33 and 194.58 ppm for B3LYP/6-31G++(d,p),
respectively. When the NMR spectra were examined, the -CH2 protons of hydroxyethyl group of
the NHC precursors (1a and 1c) appeared downfield shifted singled at 3.85-4.60 and 3.76-4.54
ppm for 1a and 1c, respectively. However, the -CH2 protons of hydroxyethyl group of the NHC
precursor 1b appeared downfield shifted double-doubled at 3.75 and tripled at 4.54 ppm. These
signals were calculated for the conformers as 3.56-4.20 and 3.80-4.27 ppm for 1a, 3.34-3.57 and
3.39-5.35 ppm for 1b, 3.30-4.34 and 3.23-4.64 ppm for 1c.
13
The carbon resonances of the NHC precursors (1a-c) for hydroxyethyl group in the C NMR
spectrum appeared downfield at 50.0-59.2, 45.6-58.9 and 46.3-59.0 ppm for 1a-c, respectively. As
expected, the chemical shifts of the Conf-I of all the compounds are more consistent with these
values, which are 49.62-57.64, 49.26-58.47 and 49.19-58.11 ppm, respectively. The characteristic
proton peak on the hydroxyl groups (-OH) of the NHC precursors 1a-c appeared highly downfield
shifted singled at 5.20, 5.06 and 5.04 ppm for 1a-c, respectively. These signals were found quite
low [in the range of 2.49-3.62 ppm] theoretically. The NCHN carbon resonances of the
18

compounds in the 13C NMR spectrum appeared highly downfield at 143.3, 141.6 and 141.9 ppm,
respectively. We found these signals for the conformers I-II at 139.97-136.67 ppm, 136.95-136.04
ppm, 137.52-138.27 ppm, for 1a-c, respectively.
3.7 UV-Vis spectral analysis
When the 2-hydroxyethyl substituted NHC precursors 1a-c were dissolved in chloroform at 25
°C and, the UV-Vis spectra of them, which were depicted in Fig. 5, were observed in the range of
200–500 nm. The UV-Vis spectra of the NHC precursors 1a-c were observed as three absorption
bands from 210 to 270 nm in the CHCl3. The iodides in all NHC precursors 1a-c have peak
absorbances at 210 nm.[11] That the absorption bands were at 230 and 270 nm for 1a, at 230 and
260 nm for 1b and, at 230 and 270 nm for 1c are practically identical and can be attributed to π
→ π* transitions in the benzene and benzimidazole ring [34].
Fig. 5. UV-Vis spectra of the compounds 1a-c.
3.8 Hirshfeld Surface (HS) Analysis
Hirshfeld surface analysis method was carried out to quantify the intermolecular interactions
of the investigated compounds. The Hirshfeld surfaces of 1a-c are displayed in Fig. S8-10,
showing surfaces that have been mapped over a dnorm. The surfaces are shown as transparent to
allow visualization of the molecules. The larger red circular regions on dnorm surfaces represent
the strong hydrogen bonding interactions. As can be seen from the dnorm map of compound 1a,
19

the H⋯O reciprocal contacts have a pair of adjacent deep-red regions, which is attributed to C1–
ꢁꢂ
ꢃ
H1AꢁꢁꢁO2 hydrogen bonds (Table 2) forming ꢀꢁ 12 dimers as described in Fig 1b. The strong
hydrogen bond interactions O1–H1ꢁꢁꢁI1 and O2–H2ꢁꢁꢁI1 also appear as bright red areas in the
Hirshfeld surfaces. Similarly in 1b and 1c, the red points, which represent closer contacts and
negative dnorm values on the surface, correspond to the O–HꢁꢁꢁI hydrogen bonding contacts, are
also proven in Table 2. The 2D fingerprint plots of the intermolecular contacts are also shown in
Fig. S8-10. For all compounds, the O–HꢁꢁꢁI hydrogen bonding intermolecular interactions appear
as small spikes. In the plot of the structure 1a, there are also two sharp spikes, which are
identified as a result of C1–H1AꢁꢁꢁO2 hydrogen bonds. The broad regions at the middle of plots
are reflected as HꢁꢁꢁH interactions comprising 50.3%, 68.0% and 61.6% of the total Hirshfeld
surfaces, respectively.
4. Conclusion
In this study, three new 2-hydroxyethyl substituted NHC precursors 1a-c were synthesized,
characterized by FT-IR, 1H, 13C NMR and UV-Vis spectroscopy. Crystal and molecular structure
of the compounds were determined by single-crystal X-ray diffraction method. Structural
determination showed that the crystal structure of the compounds is stabilized by O–H···I type
hydrogen bonds. Potential energy surface (PES) scans, around the torsion angles (τ) of two sides
of the NHC fragments, reveal that global minimum structures are the most stable conformers, and
they match well with the experimental one. MEP of the compounds shows that the iodide ion
around of the Conf-II of 1b seems to be the most electron-rich region with the red color for the
nucleophilic attack reactions when comparing to all other molecules. This is probably due to the
unfavorable geometry of Conf-II. The intercontacts in the crystal structures of the molecules were
also analyzed using the Hirshfeld surface analysis method. For all compounds, all the interaction
calculations were found to be in good agreement with the experimental XRD structural
parameters.
Acknowledgment
The authors acknowledge İnönü University Scientific and Technology Center for the
elemental analyses of the compounds and Dokuz Eylül University for the use of the Rigaku
Oxford Xcalibur Eos Diffractometer (purchased under University Research Grant No: 2010
KB.FEN.13). The authors also thank to Muhittin Aygün for the use of Gaussian 09W/Gauss
View package programs.
20

Supplementary
Crystallographic data as .cif files for the structures reported in this paper have been deposited
at the Cambridge Crystallographic Data Center with CCDC 1948427 for 1a, 1948440 for 1b and
1948441 for 1c. Copies of the data can be obtained free of charge at
http://www.ccdc.cam.ac.uk/conts/retrieving.html or from the Cambridge Crystallographic Data
Center, 12, Union Road, Cambridge CB2 1EZ, UK, fax: (+44) 1223-336-033. email:
deposit@ccdc.cam.ac.uk.
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