Orthogonal hydrogen/halogen bonding in 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione-I2 adduct: An experimental and theoretical study

Article abstract of DOI:10.1016/j.saa.2015.02.043

The molecular complex between 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione (Hmim^OMe) and iodine (I₂) was investigated. Single crystal of [(Hmim^OMe)I₂] adduct was grown by slow evaporation technique from chloroform at room temperature. Spectroscopic techniques such as FT-IR and Raman techniques, as well as elemental and thermal analysis were used to characterize the complex. The crystal structure shows that the formed adduct stabilized by two noncovalent interactions, namely, hydrogen bond (HB) and halogen bond (XB). Orthogonal HB/XB associated with iodine atom (I) was observed and fully characterized. The ability of iodine to behave as hydrogen bond acceptor and halogen bond donor was held responsible for the orthogonal HB/XB presence. In addition, the structure of Hmim^OMeI₂ was investigated theoretically using MP2/aug-cc-pVDZ level of theory. Natural bond orbital analysis (NBO) was used to investigate the molecular orbitals interactions and orbitals stabilization energies.

Full text of DOI:10.1016/j.saa.2015.02.043

Accepted Manuscript
Orthogonal Hydrogen/Halogen bonding in 1-(2-methoxyphenyl)-1H-imida-
zole-2(3H)-thione-I2 adduct: An Experimental and Theoretical study
Hamdy S. El-Sheshtawy, Mohammed M. Ibrahim, Ibrahim El-Mehasseb,
Maged El-Kemary
PII:
S1386-1425(15)00195-X
http://dx.doi.org/10.1016/j.saa.2015.02.043
SAA 13333
DOI:
Reference:
Spectrochimica Acta Part A: Molecular and Biomo-
lecular Spectroscopy
To appear in:
Received Date:
Revised Date:
Accepted Date:
1 November 2014
3 February 2015
9 February 2015
Please cite this article as: H.S. El-Sheshtawy, M.M. Ibrahim, I. El-Mehasseb, M. El-Kemary, Orthogonal Hydrogen/
Halogen bonding in 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione-I2 adduct: An Experimental and Theoretical
study, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy (2015), doi: http://dx.doi.org/
10.1016/j.saa.2015.02.043
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Orthogonal Hydrogen/Halogen bonding in 1-(2-methoxyphenyl)-1H-imidazole-
2(3H)-thione-I2 adduct: An Experimental and Theoretical study
Hamdy S. El-Sheshtawy1,3*, Mohammed M. Ibrahim2,4, Ibrahim El-Mehasseb2,3, Maged El-Kemary2,3
1Biotechnology and Fish Processing Department, Faculty of Aquatic and Fisheries Sciences, Kafrelsheikh,
University, 33516 Kafr ElSheikh, Egypt
2Chemistry Department, Faculty of Science, Kafrelsheikh University, 33516 Kafr ElSheikh, Egypt.
3Nanochemistry Laboratory, Chemistry Department, Faculty of Science, Kafrelsheikh University, 33516
Kafr ElSheikh, Egypt
4Chemistry Department, Faculty of Science, Taif University, Taif, Saudi Arabia
Abstract
The molecular complex between 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione
(HmimOMe) and iodine (I2) was investigated. Single crystal of [(HmimOMe)•I2] adduct was
grown by slow evaporation technique from chloroform at room temperature.
Spectroscopic techniques such as FT-IR and Raman techniques, as well as elemental and
thermal analysis were used to characterize the complex. The crystal structure shows that
the formed adduct stabilized by two noncovalent interactions, namely, hydrogen bond
(HB) and halogen bond (XB). Orthogonal HB/XB associated with iodine atom (I) was
observed and fully characterized. The ability of iodine to behave as hydrogen bond
acceptor and halogen bond donor was held responsible for the orthogonal HB/XB
presence. In addition, the structure of HmimOMe⋅I2 was investigated theoretically using
MP2/aug-cc-pvdz level of theory. Natural bond orbital analysis (NBO) was used to
investigate the molecular orbitals interactions and orbitals stabilization energies.
1

Keywords: 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione, Halogen bond, Hydrogen
bond, X-ray crystal structure, Theoretical calculations.
*Corresponding author:
Tel.: +201062668020,
E-mail: h.elsheshtawy@fsh.kfs.edu.eg
1. Introduction
The increasing role of noncovalent interactions in different fields such as crystal
engineering, molecular recognition, and drug design attracts the interest of researches [1,
2]. In particular, hydrogen bond (HB) and halogen bond (XB) were extensively
investigated [1, 3, 4]. Different types of Hydrogen bond (HB) were reported such as
conventional HB (Y-H…Z, where Y is electronegative atoms and Z encompass free
electron pairs) and unconventional HB (C–H···Y, Y–H···C, Y–H···ꢀ-electrons or even
C–H···C) [5]. In addition, short-strong hydrogen bond (SSHB) was reported as binding
motive in the unique tertiary structures of protein [6, 7]. In analogy, the specific
interaction (C–X···Y) between halogen atoms (X=I, Br, and Cl) in halogenated ligands
and the electron pairs of donor atoms (Y= S, N, O, π-electrons of organic systems) forms
the highly directional and linear halogen bond (XB). The charge distribution along the C-
X bond is not uniform but rather anisotropic where an increase of charge concentration is
found in the plane perpendicular to the C-X bond. On the other hand, the charge deficient
is centered on the same axis of the C-X bond, which forms the basis of σ-hole principal
[8, 9]. The strength of the XB increases linearly with the size of σ-hole, which manifests
the electrostatic nature of these bonds [10-13]. In addition, polarization and dispersion
2

forces plays a key role in the XB stabilization [11, 12]. The strength of the stabilization
energy of HB is frequently higher than that of XB [1], nevertheless, competition between
HB and XB was recently reported [14, 15].
The orthogonal molecular interaction between the HB and XB to develop the hX-
bond was reported by Voth et al [16]. In hX-bonds, both hydrogen and halogen atoms
share the same acceptor oxygen atom rather than competing to each other. The XB were
perpendicular to HB with a maximum bond angle of 88.2º and energetically independent
of the HB. The orthogonality principal was first reported in the interaction between
ligands and proteins [16] and subsequently confirmed for different systems [17, 18].
Similarly, halogen atom can possesses the dual nature as the HB acceptor and XB donor.
On one hand, halogen atom possesses loan pair of electrons, which could be the motive
for HB interaction; on the other hand the presence of σ-hole along the bond axis leads to
the XB donor nature of the halogen atom [19].
Herein, we synthesized a new 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione
(HmimOMe), which could have pharmaceutical importance. The molecular structure of
HmimOMe and its molecular adduct with I2 was investigated with different spectroscopic
techniques such as FT-IR, FT-Raman, elemental analysis and thermal analysis. Single
crystal of HmimOMe•I2 was grown and the structure was investigated both theoretically
and experimentally. Theoretical calculations using both MP2/aug-cc-pVDZ-PP and
B3LYP/6-311++G(d,p) level of theory were corroborated the experimental results to shed
more light on both HmimOMe and HmimOMe•I2 molecular structures.
3

2. Experimental
2.1. Materials and methods
Infrared spectral measurements (FT-IR) for the free thione and the molecular
adduct with iodine were recorded in KBR pellets using FT-IR Prestige-21 Shimadzu, in
the range of 400-4000 cm-1. Raman spectra were obtained as powder in glass capillaries
on a Nicolet FT Raman-950 spectrophotometer. The spectra were recorded at room
temperature with a germanium detector, maintained at liquid nitrogen temperature and
using 1064.0 nm radiation, generated by a Nd-YAG laser with a resolution of 2 cm-1.
Thermal analysis of the complex was recorded on Netzsch STA 449F3 with system
interface device in the atmosphere of nitrogen. The temperature scale of the instrument
was calibrated with high purity calcium oxalate. Accurately 5 mg of pure sample was
subjected for dynamic TG scans at heating rate of 10 °C min-1.
2.2 Computational details
All calculations were performed using Gaussian03 program [20]. In case of HmimOMe-I2,
Dunning's correlation-consistent polarized valence double-zeta basis set augmented with diffuse
functions and employing pseudo potentials to describe the inner core orbitals of the heavy-atom
elements, I, (aug-cc-pVDZ-PP) was employed in the abinito calculations. The energies were
obtained by using second order Møller–Plesset perturbation theory (MP2), with and without
counterpoise (CP) correction for basis set superposition errors (BSSE). The use of larger basis set
in addition to the CP corrections usually, for BSSE, results in overestimation of the binding
4

energies. The parent compound (HmimOMe) was optimized at B3LYP/6-311++G(d,p) level of
theory, which gives satisfactory results compared to the experimental data [21]. Analytical
frequency calculations were done in order to verify the stationary points on the potential energy
surface. Natural population analysis (NPA) was used to calculate the natural bond orbital
interactions and their second-order perturbation stabilization energies (E2) at MP2/ aug-
cc-pVDZ-PP level of theory.
2.3. Syntheses
2.3.1. Synthesis of 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione (HmimOMe
)
The ligand 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione (HmimOMe) was prepared
according to a modified procedure reported in literature [22-24] (Scheme 1). In details, N-
(2,2-diethoxyethyl)-2-methoxyaniline (30.63 g, 0.128 mol)) in ethanol (130 mL) were mixed with
14.90 g (0.153 mol) of potassium thiothianate, to which 75 mL of HCl (2N) were added. The
reaction mixture was refluxed for 24 hrs and the solvent was removed by rotatory evaporator. A
hot water (500 ml) was added to the residue with continuous stirring. After cool down, a raw
product was obtained as pale yellow solid, which filtered, dried, and crystallized from ethanol by
using activated charcoal. Anal. For C10H10N2SO (206.26): Calcd. C, 58.32; H, 4.89; N,
13.58; S, 15.54; Found C, 58.02; H, 4.93; N, 13.64; S, 15.44. 1H NMR (DMSO), 298 K,
TMS): δ = 3.82 [s, 3H, CH3], 6.92 [d, 1H, H3-thioimidazole], 7.14 [d, 1H, H2-
thioimidazole], 7.29-7.43 [m, 4H, Ph] and 12.21 ppm [b, 1H, NH]. I R (KBr): ν (cm−1):
3088 [s, br, NH], 1567 [s, -C=C-], 1502 [s, C=N], 1446 [s, Thioamide I], 1278 [s,
5

Thioamide II], 1014 [m, thioamide III], 727 and 676 [s, Thioamide IV], 613 [m, δ
(C=S)], and 531 [s, π (C=S)].
O
O
NH
O
O
S
N
+
K
NH2
NH
S
C
N
Br
O
O
O
HCl (2N)
Ethanol/
one weak
Ethanol/
12 hrs
Scheme 1. The synthesis of 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione (HmimOMe
)
2.3.2. Synthesis of the CT complex 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione.
Iodine [HmimOMe•I2]
A chlorofrm solution (10 mL) containing iodine solution (1.0 mmol, 0.254 gm) was
added to a chlorofrm solution (10 mL) of the donor 1-(2-methoxyphenyl)-1H-imidazole-
2(3H)-thione (1.0 mmol, 0.206 gm). Immediately, a brown solution was obtained, which
was kept standing for 3 days. Single brown crystals were obtained of the HmimOMe•I2
adduct, which were washed and crystallized from cold chloroform. Anal. For
C10H10N2SOI2 (460.07): Calcd. C, 26.11; H, 2.19; N, 6.09; S, 6.97; Found C, 25.87; H,
1
2.08; N, 6.24; S, 6.73. H NMR (DMSO), 298 K, TMS): δ = 3.87 [s, 3H, CH3], 6.97 [d,
1H, H3-thioimidazole], 7.18 [d, 1H, H2-thioimidazole], and 7.34-7.55 ppm [m, 4H, Ph].
1
IR (KBr): ν (cm− ): 3116 [s, br, NH], 1553 [s, -C=C-], 1499 [s, C=N], 1424 [s, Thioamide
6

I], 1244 [s, Thioamide II], 1012 [m, thioamide III], 742 and 679 [s, Thioamide IV], 620
[m, δ (C=S)], and 515 [s, π (C=S)].
2.4. X-Ray Crystallography
Crystallographic data of HmimOMe•I2 were collected on a Smart CCD diffractometer of Bruker
AXS using Mo Ka radiation. The crystal does not show significant intensity loss through data
collection. Lorentz-Polarization corrections were performed by SAINT [25]. Absorption
corrections were made by using SADABS [26]. The structure was solved by direct or Patter- son
methods using SHELXS-97 [27] to find the position of heavy atoms. Other non-hydrogen atoms
were located by Fourier syn- theses and refined using SHELXS-97. The least-squares refinements
were performed using all independent reflections by the full matrix on F2. All non-hydrogen
atoms were refined anisotropically. X-ray diffraction study was carried out using XRD-6000
(SHIMADZU). The X-ray was detected using a fast counting detector based on silicon strip
technology. The crystal structure and lattice parameter were analyzed by Bragg’s law, 2dsinθ =
nλ and particle size is calculated by Debye Scherer’s formula, t = 0.9 λ/B cos θ [28, 29].
3. Results and discussions
3.1.Molecular structures and X-Ray investigation
The structure of 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione (HmimOMe) [22-
24] was synthesized via the ring closure of N-(2,2-diethoxyethyl)-2-methoxyaniline and
potassium thiocyanate in ethanol and HCl (2N). The obtained thioimidazole was
crystallized from ethanol to form colourless crystals (Scheme 1). Crystals of HmimOMe•I2
7

adduct were produced by co-crystallising HmimOMe with the appropriate
concentration of iodine in chloroform to give the 1:1 stoichiometric ratio.
Table 1: crystallographic data of HmimOMe•I2
Compound
Thione
Empirical formula
Formula weight, g/mol
C10H9I2N2OS
459.06
Crystal system
Space group
Triclinic
P -1
a/Å
b/Å
c/Å
α/°
β/°
γ/°
Volume/Å3
Z
7.2897 (3)
9.0456 (4)
11.6315 (6)
69.181 (2)°
76.782 (2)°
80.439 (3)°
694.87 (6)
2
Dcalc/(g/cm3)
Absorption coefficient
F(000)
2.199
426.0
Crystal size/mm
8,10,13
→ range for data collection/° 2.910—32.032 °
Reflections collected
Independent reflections
R(int)
4952
4731
0.029
Observed (I > 2↔(I))
Goodness-of-fit on F2
R[I > 2↔(I)]b
1.0
wR (all data)c
0.0756
The crystallographic data of HmimOMe•I2 are collected in Table 1. Careful
examination of the HmimOMe•I2 crystal structure indicates the presence of two XB bonds
associated with the S atom, but has different strength due to the orthogonal HB, which
1

linked two successive layers (Fig.1). In addition, the crystal structure sheets are
connected with a short contact between the C⋅⋅⋅C bond (3.38 Å, 0.6 % less than vdW
radii).
Fig. 1: Halogen bond and hydrogen bond motif of HmimOMe•I2.
Fig. 2: Intermolecular interactions, and bond lengths (Å) in crystalline structure of
HmimOMe•I2 adduct
9

Table 2: Selected bond lengths, bond angles and torsional angles of HmimOMe•I2
molecular adduct.
bond distance /Å
bond angle/º
torsional angle/º
2.579(1)
2.9966(4)
1.718(4)
1.348(5)
1.331(5)
1.371(9)
1.395(5)
0.88(6)
174.87(3)
-163.6(3)
I1−S5
S5−I1−I16
I16−I1−S5−C2
128.0(3)
126.2(4)
105.7(4)
120.7(5)
122(3)
70.1(4)
-111.6(4)
-2.0(6)
179.9(4)
179.5(4)
1.4(5)
I1−I16
S5−C2−N8
N8−C2−S5−I1
C2−S5
S5−C2−N10
N8−C2−N10
C7−C3−C12
C7−C3−H25
C12−C3−H25
C9−O4−C12
I1−S5−C2
N10−C2−S5−I1
C2−N8
S5−C2−N8−C11
S5−C2−N8−C14
N10−C2−N8−C11
N10−C2−N8−C14
S5−C2−N7−C15
S5−C2−N10−H21
N8−C2−N10−C9
N8−C2−N10−H21
C12−C3−C7−C13
C12−C3−C7−H21
H25−C3−C7−C13
C7−C3−C12−O4
C7−C3−C12−C11
C9−O4−C12−C3
C9−O4−C12−C11
C13−C6−C11−N8
C13−C6−C11−C12
C11−C6−C13−C7
C3−C7−C13−C6
C2−N8−C11−C6
C2−N8−C11−C12
C14−N8−C11−C6
C14−N8−C11−C12
C2−N8−C14−C15
C2−N10
C3−C7
118(3)
C3−C12
C3−H25
O4−C9
117.7(4)
101.1(2)
119.4(5)
110(3)
-179.4(4)
-10(6)
1.430(8)
1.341(6)
1.379(8)
1.378(7)
0.89(5)
-0.8(5)
169(6)
O4−C12
C6−C3
C11−C6−C13
C11−C6−H23
C13−C6−H23
C3−C7−C13
C3−C7−H19
C13−C7−H19
C2−N8−C11
C2−N8−C14
C11−N8−C14
O4−C9−H24
O4−C9−H18
O4−C9−H17
C2−N10−C15
C2−N10−H21
C15−N7−H21
C6−C11−N8
C6−C11−C12
N8−C11−C12
130(3)
-0.3(8)
-179(3)
179(4)
C6−C13
C6−H23
C7−C13
C7−H19
N8−C11
N8−C14
C9−H24
C9−H18
C9−H17
N10−C15
N10−H21
C11−C12
C13−H22
C14−C15
C14−H20
C15−H26
121.4(5)
123(3)
1.37(1)
0.99(4)
115(3)
179.6(5)
-1.4(7)
-6.9(6)
174.1(4)
179.9(5)
-2.2(7)
0.4(8)
1.442(5)
1.387(6)
0.93(5)
125.7(3)
109.7(4)
124.5(4)
111(4)
1.15(7)
1.01(4)
104(3)
1.366(7)
0.77(5)
107(3)
110.6(4)
128(5)
0.8(9)
1.402(7)
0.82(7)
-105.8(5)
76.2(5)
72.0(6)
-105.9(5)
-1.5(5)
121(5)
1.332(6)
0.92(4)
119.5(4)
121.9(4)
118.6(4)
0.81(4)
In details, the crystal structure of HmimOMe•I2 shows a short and linear C=S2⋅⋅⋅I2
interaction (Fig. 2). The S2⋅⋅⋅I2 bond distance is 2.579 Å, which is 31.8 % shorter than
10

the sum of vdW radii of both S (1.80 Å) and I (1.98 Å) atoms. The S2⋅⋅⋅I2-I1 bond angle
is 174.87º, which is matching the linearity of the XB [30]. On the other hand, the S2⋅⋅⋅I3
bond distance is 3.697 Å, which is 2.2 % shorter than the sum of vdW radii for both I and
S atoms, and the bond angle (I3⋅⋅⋅S2-I1) is 152.11º. The weakness and deviation from
linearity of I3⋅⋅⋅S2 than the S2⋅⋅⋅I2 XB can be explained by the interference of the strong
I1⋅⋅⋅H2-N1 HB, the I1⋅⋅⋅H2 bond distance is 2.80 Å (12 % less than vdW radii) and
I1⋅⋅⋅H2-N1 bond angle is 171.93º [31]. Selected geometry parameters according to the
single crystal structure (Fig. 3) are in Table 2.
Fig. 3: Structure of HmimOMe•I2 from the crystal structure.
Theoretical calculations using both B3LYP/6-311++G(d,p) and MP2/aug-cc-
pVDZ-PP level of theory were corroborated to further investigate the structure of both
11

HmimOMe and HmimOMe•I2. The relative calculated energies (B3LYP/6-311++G(d,p)
shows that thione form (HmimOMe-I) was more stable by 4.5 kcal mol−1 than thiol form
(HmimOMe-II). Electrostatic potential V(r) that electrons and nuclei of a molecule create at
any point (r) is an effective method for interpreting and quantifying noncovalent
interactions [32]. Here, we compute the electrostatic potential surface (EPS) of both
HmimOMe-I and HmimOMe-II to investigate the electron density distribution. Fig. 4
displays the positions of the concentrated and deficient electron densities located on the
two isomers as well as the I2 molecule. EPS shows the presence of a strong negative
potential (−37.65 kcal mol−1) situated around the S atom in HmimOMe-I isomer. The
symmetrically high negative potential distributed over the S atom facilitates the contacts
with two Lewis acid atoms (two I atoms in crystal structure). In contrast, a weak negative
electrostatic potential (− 9.05 kcal mol−1) were observed on the S in the HmimOMe-II
structure and increases at the two N atoms of the imidazole moiety. Interestingly,
relatively high positive potential (+25.2 kcal mol−1) were centered on the H atom of N-H
bond, which is the motif forces for the HB formation. On the other hand, ESP of the I2
molecule nicely visualizes the σ-hole principal, where a strong positive electrostatic
potential (+40.45 kcal mol−1) is formed along the I-I bond axes. Such electron deficient
region was found in the covalently chlorinated, brominated, and iodinated organic
molecules [33, 34]. Perhaps, the most interesting region in I2 ESP is the negative
electrostatic potential (− 29.15 kcal mol−1) belt perpendicular to the I-I bond axes. The
propensity of the negative electrostatic potential (− 29.15 kcal mol−1) belt on I2 molecule
12

and the positive electrostatic potential (+25.2 kcal mol−1) found on the H atom of N-H
bond forms HB, I1⋅⋅⋅H2 bond distance is 2.80 and 171.93º bond angle (I1⋅⋅⋅H2-N1).
Fig. 4: a) calculated structure of HmimOMe-I and HmimOMe-II using B3LYP/6-
311++G(d,p), b) the ESP of the optimized structure, c) ESP of I2 optimized at MP2/aug-
ccp-pvdz, d) ESP of HmimOMe•I2 (single energy calculation at MP2/aug-ccp-pvdz) color
codes, blue (positive), red (negative).
13

In order to give more insights to the complex, natural bond orbital analysis (NBO) were
performed at MP2/aug-cc-PVDZ level of theory. Table 3 shows selected bonding, antibonding,
and lone pair interaction orbitals as well as the second-order perturbation stabilization
energies (E2). NBO analysis reveals the strong stabilization from the lone pair electrons
of the S atom to the σ* of the I2 molecule (LP(3) S5 → BD*(1) I1 - I16) with E(2) =
163.58 kcal/mol. This result confirms the n-σ* nature of the transition similar to
compounds incorporate thion (C=S) group. Strong stabilization energy manifests the role
of the charge transfer for the HmimOMe•I2 complex [35]. In fact, the charge transfer to the
antibonding orbital of I1 - I16 bond weaken and consequently lengthen [36, 37] the I1 -
I16 bond length: the I1 - I16 bond length in crystal structure is 2.9966 Å, which is 0.2766
Å longer than the I−I bond in crystalline I2 (2.72 Å) [38]. Interestingly, a strong
intramolecular interaction was observed from the LP (1) N8 → LP*(1) C2 and LP (1)
N10 → LP*(1) C2 with strong stabilization energy of 206.82 and 179.87 kcal/mol
respectively, which manifests the role of the intramolecular charge transfer in the
stabilization of adduct [35, 39].
Table 3: Some significant donor-acceptor (D →A) natural bond orbital interactions and
14

their second-order perturbation stabilization energies (E2), in kcal/mol) at the MP2/aug-
a
cc-pVTZ level
D → A interaction
E(2)
E(j)-E(i) a.u. F(i,j) a.u.
BD (1) I1 - I16
BD*(1) I1 - I16
BD*(1) I1 - I16
BD*(1) I1 - I16
BD*(1) I1 - I16
RY*(1) S5
BD*(1) C2 - S5
BD*(1) I1 - I16
BD*(1) I1 - I16
BD*(1) I1 - I16
BD*(1) I1 - I16
BD*(1) C2 - S5
BD*(1) C2 - N8
BD*(1) C2 - N10
LP*(1) C2
2.77
3.80
0.51
0.78
2.72
1.88
1.18
11.93
2.86
163.58
5.46
0.39
0.90
0.37
0.38
1.39
0.84
0.90
0.83
0.34
0.32
1.49
1.55
1.08
0.23
1.07
0.27
0.31
0.033
0.058
0.013
0.017
0.055
0.036
0.032
0.098
0.030
0.212
0.080
0.102
0.114
0.134
0.050
0.236
0.236
LP (1) I1
LP (2) I1
LP (3) I1
BD (1) I1 - I16
LP (3) I1
BD (1) C2 - S5
LP (1) S5
LP (2) S5
LP (3) S5
BD (1) N8 - C14
LP (1) S5
8.38
LP (2) S5
LP (3) S5
LP (3) S5
LP (1) N8
LP (1) N10
14.68
82.77
2.29
206.82
179.87
BD*(1) C2 - N10
LP*(1) C2
LP*(1) C2
aLP denotes the occupied lone pair. BD* denotes the formally empty antibonding orbital. RY*
denotes Rydberg orbital.
3.2.Characterization of the CT complex
The reaction of 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione with iodine in 1:1
molar ratio in chloroform readily produced the crystalline CT complex HmimOMe•I2. The
elemental analysis of the complex confirmed the 1:1 stoichiometry and physical
properties is in accordance with the proposed structure. In order to investigate the
molecular interactions, different spectroscopic techniques such as FT-IR, FT-Raman, and
thermal analysis were used.
15

3.2.1 FT-IR and Raman Spectra
The FT-IR spectrum of HmimOMe•I2 adduct (Fig. 5) shows the absence of ν(SH)
band at 2500 cm−1 and the presence of ν(NH) band at 3116 cm−1, which clearly reveals
the dominance of HmimOMe-I (thione) structure in solid. Upon complexation of HmimOMe
with I2, the ν(C=S) absorption was shifted from 759 cm−1 to 742 cm−1. The shift of ν(C=S)
absorption to 742 cm−1 ascribed to the change of C=S electronic state; loses some of the
double bond character and lengthen the C−S bond distance (Table 2). The thioamide
bands are shifted, however the most significant change was that observed in the
thioamide IV bands, which have the largest shift to lower frequency [40, 41]. The
thioamide IV band is affected with the bands in the free ligand (759 and 730 cm−1),
which are replaced by a sharp band at 741 and 673 cm−1 for the complex. Besides, the
electron charge-transfer between the S atom of a thioamide and iodine will result in
stabilization of the lone pair of electrons on the S atom by overlapping of the S donor
orbital with the ꢁ*-orbital of iodine [42]. This situation will lead to a lengthening of the
thione double bond in the thioamide and subsequent bond formation between the S atom
and diiodine, together with a concomitant lengthening of the I−I bond.
1
The FT-Raman spectra of HmimOMe•I2 in the 90 – 4000 cm− region was
1
investigated (Fig. 6. Shows selected region from 0 - 600 cm− ). The spectra show an
1
intense peak at 177 cm− , which attributed to the uncomplexed I2. As expected, the ν(I−I)
value in the molecular adduct was shifted to lower frequency value from the ν(I−I) of the
1
solid I2 (180 cm− ). The lower frequency value is associated with the increase of the I – I
bond length (2.99 nm) compared of the free I – I bond length in the solid state. Further,
16

1
−
two peaks were observed at 80, 109 cm− , which ascribed to the ν(I3 ), and ν (I−I)
s
respectively.
(b)
(a)
Fig. 5: FT-IR spectra of a) HmimOMe, and b) HmimOMe•I2 adduct.
17

Fig. 6: Selected Raman spectra of the HmimOMe•I2 molecular adduct.
3.3.Thermal analysis
The structure of HmimOMe and it’s adduct with I2, HmimOMe•I2, were also
characterized by thermal analysis. Fig. 7a displays the collected TGA, DTG, and DSC
curves for the thermal decomposition of HmimOMe. The TGA curve exhibits one weight
loss step with a mass loss of 93.09% (calcl. 91.27%), which is mainly due to the
decomposition of HmimOMe forming 1.5 mole of solid carbon. The DSC curve shows
o
o
o
three main events at 238.1 C (exo), 318.6 C (exo), and 591.8 C (endo). The first
exothermic peak is accompanied by no weight loss, which suggests a physical process
(possibly ligand melting). The second exothermic peak is attributed to the decomposition
of HmimOMe. The third endothermic peak with no weight loss change attributed to the
recrystallization of the final carbon product.
18

Table 4: Kinetic and thermodynamic parameters of the HmimOMe and HmimOMe•I2
Sample
Step
1st
T
A
ꢂE*
ꢂH*
ꢂS*
ꢂG*
HmimOMe
533
16.6557
107.71
104.795 -0.1113 164.107
HmimOMe•I2
1st
588
8.9093
69.444
1.9124
66.5262 -0.1766 170.314
2nd
1038
10.2909
1.0058
-0.1698 177.206
Fig. 7b displays the collected TGA, DTG, and DSC curves for the thermal
decomposition of the HmimOMe•I2 adduct. The TGA curve exhibits three weight loss
steps with a total mass loss of 85.01% (calc. 84.35%), due to the decomposition of
HmimOMe•I2 forming 6.0 mole of carbon. The DSC curve shows three main events, which
are maximized at 149.4 oC (exo), 289.1 oC (exo) and 628.2 oC (exo). The first exothermic
peak is accompanied by no weight loss, which suggests a physical process (possible
melting of the complex). The second and third exothermic peaks are attributed to the
decomposition of the complex. The kinetic (∆E#) and thermodynamic parameters (∆S#,
∆H#, and ∆G#) for the decomposition of HmimOMe and HmimOMe•I2 were calculated by
Coats–Redfern equation [43]. The negative values (Table 4) of more entropies in
HmimOMe•I2 indicate that the activated complex has more ordered structure than the
reactants [44]. In addition, thermal analysis reveled the stabilization of the iodinated
adduct than the reactant (HmimOMe).
19

Fig. 7: TGA (black), DTG (red), and DSC (blue) curves of the HmimOMe (a) and
HmimOMe•I2 (b).
Conclusion
The new compound, 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione (HmimOMe), was
synthesized and structurally investigated. The molecular interaction between HmimOMe and
molecular iodine (I2) were discussed. The crystal structure reveals the presence of orthogonal
hydrogen and halogen bonding associated with iodine atom (I). The reason for such orthogonality
was ascribed to the presence of negatively charged belt perpendicular to the I-I bond in addition
to the positively charged region (σ-hole) in the same plane with the I-I bond. Theoretical
calculations, using NBO analysis, confirms the n-σ* nature of the charge transition from the
S atom to I atom in the molecular adduct. In addition, spectroscopic techniques such as
FT-IR and Raman techniques were used to further investigate the adduct formation.
20

Acknowledgment
H. S. El-Sheshtawy thanks the Computational Laboratory for Analysis, Modeling, and
Visualization (CLAMV) at the Jacobs University Bremen (Germany) for computation time.
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23

Highlights
•
Synthesis of 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione (HmimOMe).
•
•
•
Orthogonal Hydrogen bond (HB) and halogen bond (XB) in HmimOMe•I2 crystal structure.
Spectroscopic and thermal investigation of HmimOMe•I2 adduct.
Theoretical investigation of the HmimOMe and HmimOMe•I2 structures.
24