Structural and vibrational analysis of copper(II) 1,3-benzothiazol-2- yl[imino(phenyl)methyl]azanide

Article abstract of DOI:10.1016/j.molstruc.2013.01.056

A Cu(II) complex with in situ formed 1,3-benzothiazol-2-yl[imino(phenyl) methyl]azanide-anion was obtained and characterized by X-ray single crystal diffraction and Raman spectroscopy. The organic anion L acts as a chelate ligand, being connected to Cu²⁺ cation by the nitrogen atom of thiadiazole core and one another N center from imino-group. Two nearly planar L moieties, attached to the same metal cation, are mutually tilted by 50° because of sterical hindrances resulting in a formation of pseudo-tetrahedral surrounding of the Cu²⁺ ion. CuL₂ neutral units are bound into 3-D structure by weak interactions only. The molecular structure and Raman spectrum of the compound have been computed using the DFT B3LYP methodology and the cc-pVDZ basis set. The results are compared with the experimental data obtained. Bond distances and angles are in good agreement with the values obtained from X-ray diffraction. Spectrum calculation followed by normalization to the most intensive peak allowed providing detailed vibrational band assignment.

Full text of DOI:10.1016/j.molstruc.2013.01.056

Journal of Molecular Structure 1038 (2013) 200–205
Contents lists available at SciVerse ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Structural and vibrational analysis of copper(II)
1,3-benzothiazol-2-yl[imino(phenyl)methyl]azanide
c
b
E.A. Goreshnik a, G.S. Veryasov a, , D.I. Morozov , M.G. Mys’kiv
⇑
a
ˇ
Department of Inorganic Chemistry and Technology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
b Department of Chemistry, Ivan Franko National University of Lviv, Kyryla i Mefodiya St. 6, Lviv 79005, Ukraine
c Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russian Federation
h i g h l i g h t s
"
"
"
Cu(II) complex with in situ formed 1,3-benzothiazol-2-yl[imino(phenyl)methyl]azanide was obtained and characterized.
The optimized geometry of the molecule was found using DFT calculation.
The Raman spectrum was calculated using DFT calculations and band assignments were preformed.
a r t i c l e i n f o
a b s t r a c t
Article history:
A Cu(II) complex with in situ formed 1,3-benzothiazol-2-yl[imino(phenyl)methyl]azanide-anion was
obtained and characterized by X-ray single crystal diffraction and Raman spectroscopy. The organic anion
L acts as a chelate ligand, being connected to Cu2+ cation by the nitrogen atom of thiadiazole core and one
another N center from imino-group. Two nearly planar L moieties, attached to the same metal cation, are
mutually tilted by 50° because of sterical hindrances resulting in a formation of pseudo-tetrahedral sur-
rounding of the Cu2+ ion. CuL2 neutral units are bound into 3-D structure by weak interactions only. The
molecular structure and Raman spectrum of the compound have been computed using the DFT B3LYP
methodology and the cc-pVDZ basis set. The results are compared with the experimental data obtained.
Bond distances and angles are in good agreement with the values obtained from X-ray diffraction. Spec-
trum calculation followed by normalization to the most intensive peak allowed providing detailed vibra-
tional band assignment.
Received 31 October 2012
Received in revised form 7 January 2013
Accepted 24 January 2013
Available online 4 February 2013
Keywords:
Thiadiazole
Copper(II)
Crystal structure
Raman spectroscopy
DFT calculations
Ó 2013 Elsevier B.V. All rights reserved.
1. Introduction
ligands, as a typical Schiff bases, are of interest as the ligands in
coordination chemistry of transition metals [17,18].
Polyfunctional ligands based on benzazole derivatives are rele-
vant due to their newly discovered biological activity as fungicides,
antibiotics, pesticides and neuroprotectors [1–3]. Namely
2-aminobenzothiazole derivatives are broadly applied in drug
discovery and development of the treatments of diabetes [4],
epilepsy [5], inflammation [6], amyotrophic lateral sclerosis [7],
viral infection [8], etc. They are also used as efficient building
blocks for crystal engineering of metal–organic complexes
[9–11]. Recent investigations showed improvement of the activity
of drugs while inserted to coordination compounds as a ligands
[12,13], what is resulted in intensive work on investigations of
Cu(II), Zn(II), Co(II) and Ni(II) compounds behavior in interactions
with DNA molecules and antibacterial activity [14–16]. Benzazole
It was observed recently, that a mixture of 2-aminobenzothia-
zole and a product of its alkylation 2-imino-3-allylbenzothiazole
– selectively reacts with different copper salts depending on the
type of anion [19,20]. In this context, we have tried to synthesize
complexes with some other salts. Unexpectedly benzonitrile, used
as a solvent, condensed with 2-aminobenzothiazole and gave anio-
nic ligand 1,3-benzothiazol-2-yl-[imino(phenyl)methyl]azanide.
Obtained crystals of Cu2+ salt with the above ligand were investi-
gated by single crystal X-ray diffraction, Raman spectroscopy and
DFT calculations. The results are represented in this paper.
2. Experimental
2.1. Alkylation of 2-aminobenzothiazole
⇑
Mixture of 0.05 M (7.30 g) of 2-aminobenzothiazole, 0.05 m
(4.20 g) of NaHCO3 and 0.054 M (4.3 ml) of freshly distilled allyl
Corresponding author. Tel.: +386 64137034.
E-mail address: glebveryasov@gmail.com (G.S. Veryasov).
0022-2860/$ - see front matter Ó 2013 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.molstruc.2013.01.056

E.A. Goreshnik et al. / Journal of Molecular Structure 1038 (2013) 200–205
201
bromide in 75 ml of 95% ethanol was refluxed during 10 days (with
breaks for nights). After that a precipitate was filtered off and an
excess of alcohol was removed by distillation. Then 20 ml of ben-
zene was added to make a negligible solubility of NaBr in the rest
of C2H5OH. Amount of filtered NaBr was practically 0.05 m. This so-
lid did not react with concentrated HCl which has indicated an ab-
sence of NaHCO3 in the precipitate. The benzene solution (with a
small amount of C2H5OH) was used in a further experiment. One
can add that such the alkylation is accompanied by a tautomeric
transformation of 2-aminobenzothiazole core into 2-iminobenzo-
thiazole one.
detector, using graphite monochromatized Cu K
a
radiation. Data
were treated using the CrysAlisPro program package [28]. Struc-
tures was solved by direct methods using SIR-92 [29] and refined
with SHELXL-97 [30] software, implemented in program package
WinGX [31]. All atoms, including hydrogens, were found on Fourier
maps. Full-matrix least-squares refinements based on F2 were car-
ried out for the positional and thermal parameters for all non-
hydrogen atoms. Positions of H atoms were treated as riding atoms
and refined with C–H fixed distances and with Uiso(H) values of
1.2Ueq(C). The figures were prepared using DIAMOND 3.1 software
[32].
2.1.1. Preparation of Cu(C14H10N3S)2 compound
3. Results and discussion
Crystals were grown during 5 days after interaction of CuCN
with copper wire and 2-imino-3allylbenzothiazole in a presence
of 2 ml of C6H5CN as a solvent (with an addition of 0.5 ml benzene
and 0.5 ml ethanol). A 4.5 ml test-tube was closed, but there
was nearly 2 cm layer of air at the top of solution. The
1,3-benzothiazol-2yl[imino(phenyl)-methyl]azanide-anion was
formed in situ by a condensation of 2-imino-3allylbenzothiazole
and benzonitrile. Such a reaction is known: copper(I)-induced addi-
tion of amines to nitriles was already observed and studied [21].
3.1. Crystal structure
The structure comprises of isolated CuL2 units (Fig. 1). Location
of the copper center at the special position (axis 2) and the pres-
ence in the asymmetric part of the only one crystallographically
independent ligand anion confirm undoubtedly the +2 copper oxi-
dation state. The organic anion L acts as chelate ligand being at-
tached to the Cu2+ ion by the nitrogen atom of thiadiazole core
and one another N center from imino-group (Fig. 1). The Cu–Nimino
distances are slightly shorter than Cu–Ncore ones (1.926(2) and
1.951(2) Å respectively). Two L moieties, attached to the same me-
tal cation, because of sterical hindrances are mutually tilted by
51.69° (an angle between N1–Cu–N2 and N10–Cu–N20 planes) rep-
resenting a noticeable distortion from a square planar geometry
(0°) towards a tetrahedral geometry (90°) of the Cu2+ ion coordina-
tion polyhedron. Thus, this structure represents rather rare exam-
ple of X-ray structurally characterized pseudo-tetrahedral
surrounding of Cu2+ ion. In a row of copper(II) complexes with
chelate deprotonated form of 2-(20-hydroxy-30-methylphenyl)-
benzimidazole, N–R substituted salicylaldimine and N-tert-butyl-
pyridoxylideneimine (metal is bound to 2N + 2O atoms) the
smallest dihedral angle between two (LCuL0) planes vary from
9.4° to 59.6° [33]. In [Cu(bdpp)Cl2] (bdpp = 1,3-bis(30,50-dimethyl-
pyrazol-10-yl)propane), where the copper ion is four-coordinated
with two N and two Cl atoms, the smallest dihedral angle between
2.2. Raman spectroscopy
Raman spectrum was measured on crystal directly on air with a
Horiba Jobin–Yvon LabRAM HR spectrometer by using the
632.81 nm excitation line of a He–Ne laser with power 17 mW.
To exclude decomposition of the sample, the power of the laser
has been reduced to 1.7 mW using filter. An Olympus x50 long-dis-
tance objective has been used. Spectrum was obtained as a result
of 100 scans with an integration time of 30 s. These settings have
resulted in the best signal-to-noise ratio. Spectrometer was previ-
ously calibrated using Si plate as a standard with characteristic
band at 520.6 cmꢀ1
.
2.3. Computational details
All calculations were performed using DFT with B3LYP func-
tional [22,23] using GAMESS(US) program package [24]. The
cc-pVDZ basis set as well known for correlated methods and
effective core potential on Cu atom has been used. At first, initial
geometry of the complex was optimized. An experimental geome-
try has been used as a starting point for the geometry optimization.
Then Forces Constants Matrix (also known as Hessian matrix),
which is matrix of the second derivatives of energy by all coordi-
nates, were calculated. Normal modes frequencies were obtained
by diagonalization of this matrix, no imaginary frequencies were
observed. For Raman spectra intensities first polarizability tensor
was calculated and then resulting Raman activities (Si) were
converted to Raman intensities (Ii) using following relationship
from the intensity theory of Raman scattering [25–27]
Table 1
Crystal data and structure refinement for the compounds 1.
X-ray
Empirical formula
Formula weight
Temperature, K
Radiation
Crystal system, space group
Unit cell dimensions, Å
a, Å
C28H20CuN6S2
568.19
150
Cu Ka (1.5418 Å)
Orthorhombic, P b c n
19.5357(8)
12.5778(9)
10.0011(9)
2457.4(3)
b, Å
c, Å
4
V, Å3
fðm0
ꢀ
miÞ Si
ꢀ
ꢁ
Ii ¼
ð1Þ
À
Á
Z
4
ꢀꢀhc
m
i
Calculated density, g/cm3
Absorption coeff., mmꢀ1
F(000)
1.536
3.089
1164
kT
mi 1 ꢀ exp
where m0 is the exciting frequency (cmꢀ1) and mi is the vibrational
Crystal size, mm
Color
0.59 ꢁ 0.28 ꢁ 0.13
wave number of the ith normal mode (cmꢀ1).
Dark
Theta range for data collection
Limiting indices
Refinement method
Measured reflections
Independent used in refinement
Free parameters
Goodness-of-fit on F2
R indices
6.09–73.96
For the simulated spectra plots Doppler broadening was used
with a bandwidth at half height of peak 20 cmꢀ1
.
ꢀ24 to 19, ꢀ15 to 10, ꢀ12 to 8
Full-matrix on F2
7934
2.4. X-ray crystal structure determination
2412
172
1.058
0.0295
0.085
The crystallographic parameters and a summary of data collec-
tion are presented in Table 1. Single-crystal data were collected on
a SuperNova diffractometer equipped with an Atlas CCD area
Largest diff. peak and hole

202
E.A. Goreshnik et al. / Journal of Molecular Structure 1038 (2013) 200–205
Fig. 1. Molecular structure of CuL2.
Table 2
Selected bond length (in Å) and angle (in °) values in the structure 1.
Fig. 2. Experimental geometry of the CuL2.
Cu1–N2
Cu1–N2i
Cu1–N1
Cu1–N1i
S1–C3
S1–C1
N–C1
N–C8
1.926(2)
1.926(2)
1.951(2)
1.951(2)
1.743(2)
1.758(2)
1.334(2)
1.354(2)
1.335(2)
1.405(2)
1.316(2)
N1–Cu1–N1i
N1–Cu1–N2i
N1–Cu1–N2
N2–Cu1–N2i
N–C1–N1
99.03(9)
143.88(6)
90.51(6)
102.04(9)
131.03(16)
125.03(16)
120.80(16)
121.41(12)
126.72(12)
121.31(14)
N2–C8–N
N2–C8–C9
C1–N1–Cu1
C2–N1–Cu1
C1–N–C8
N1–C1
N1–C2
N2–C8
Symmetry codes: (i) 1 ꢀ x, y, 1/2 ꢀ z.
two (ClCuN) planes is 65.7(2)° [34]. One may conclude that such
50° distortion of the copper2+ environment towards tetrahedral
appears one of the biggest from all observed examples. The
N1L1–Cu1–N2L1 angles within one L moiety are close to 90°,
whereas the
NL1–Cu1–NL2 angles vary from 102.04(9)° to
143.88(6)° (Table 2). Possibly because of mentioned sterical
hindrances the 6-membered CuN3C2 cycle is not planar with the
maximal deviation of Cu1 and N2 atoms on 0.1351(7) and
ꢀ0.139(1) Å respectively. Also above mentioned plane is tilted by
9.62(3)° from the plane of benzothiazole core. Isolated CuL2 neutral
units are bound into 3-D structure by weak interactions only. CIF
file is available at supplementary materials.
Fig. 3. Optimized geometry of the CuL2.
3.2. Optimized geometry
Optimized molecular structure in comparison to the experimental
geometry is represented at Figs. 2 and 3. At the energy minimum the
molecule was found to have Cu–N bond values 1.949 Å and 1.948 Å
for nitrogen atom occurring from imino-group and 1.996 Å and
1.997 Å for nitrogen from thiadiazole cycle; experimental values
are 1.926(2) Å and 1.951(2) Å for Nimino and Ncore, respectively. Such
a difference in bond lengths values of optimized and experimentally
– in phenyl rings the same bonds were found to have equal to a devi-
ation values, bonds Ph–C have values 1.494(2) Å and 1.501 Å (0.007 Å
difference) for experimental and optimized geometry, moreover, C–S
bonds with carbon from aromatic ring have values of 1.743(2) Å for
the crystal structure and 1.748 Å in calculation, 0.005 Å difference
which is much less than in case of Cu–N bonds. Nimino–Cu–Nimino an-
gle is found to have values 102.04(9)° and 100.60° in experimental
and optimized structures and Ncore–Cu–Ncore 99.04° and 103.48°,
respectively, that is much closer to tetrahedral environment in com-
parison to similar complexes with nitrogen and oxygen atoms in cop-
per surrounding with distortion towards tetrahedral geometry
[23,35–41]. It should be noted that such a significant elongation of
Cu–N bonds resulted in incurving of the ligand – C–N–C angle in-
creased from 121.31° to 122.81° (angles are marked in Figs. 2 and 3).
obtained bong lengths (0.07 Å for Cu–Nimino and 0.046 Å for Cu–Ncore
)
are probably occurred from cooling down of the crystal while mea-
surement. One should note that all hydrogen atoms were refined
with geometrical restrictions. The same situation observed with C–
S bonds but with lesser lengths difference: 1.758(2) Å and 1.776 Å
(0.018 Å difference) for the experimental and optimized geometries.
However, such bond lengths ratio is nearly offset in case of C–C bonds

E.A. Goreshnik et al. / Journal of Molecular Structure 1038 (2013) 200–205
203
Fig. 4. Experimental and simulated Raman spectra.
Fig. 5. Normal modes of the most intensive peaks in Raman spectrum with frequencies in simulated spectrum, shown on fragment of molecule (we have hidden the second
ligand not to overload images, the same vibrations appear in the second ligand as well) 1215 cmꢀ1, 1457 cmꢀ1 and 1507 cmꢀ1 and in experimental spectrum 1215 cmꢀ1
1448 cmꢀ1 and 1517 cmꢀ1, respectively.
,
Table 3
Simulated and experimental Raman frequencies (all frequencies are given in cmꢀ1) and
intensities for CuL2 with tentative band assignments.
Experimental
Calculated
Tentative assignments
129
149
185
220
253
286
343
370
427
441
459
503
m
m
w
w
w
115
162
181
215
260
280
337
372
409
435
466
500
554
579
620
670
720
s
m
m
w
vw
w
w
vw
vw
vw
vw
w
vw
vw
vw
w
Ligand torsion
Ligand torsion
Ligand torsion
Ligand torsion
Ligand torsion
w
Cu–Ncore stretching
Thiasole ring torsion
Thiasole ring torsion
Ph ring torsion
Ph ring torsion
Ph ring torsion
Ph ring deformation
Ph ring torsion
Cu–Nimine stretching
Ring deformation
Cu–Ncore stretching
C–H wagging
Ph ring deformation
C–H wagging
C–S bending
C–H wagging
C–H wagging
vw
vw
w
w
w
vw
584
vw
671
713
747
w
w
vw
m
770
792
845
874
933
vw
vw
vw
vw
vw
m
m
vw
m
793
vw
C–H wagging
1002
1023
1089
1131
1159
m
m
m
s
993
C–C stretching in ring
C–C stretching in ring
C–C stretching
C–C stretching
C–S stretching
1030
1090
1137
1171
w
w

204
E.A. Goreshnik et al. / Journal of Molecular Structure 1038 (2013) 200–205
Table 3 (continued)
Experimental
Calculated
1215
Tentative assignments
1215
1239
1263
1289
1310
1392
1426
1448
1463
1517
1567
1585
1598
3058
3066
3080
3351
vs
s
vs
Ph–C stretching
C–C stretching
C–H bending
C–N stretching
C–C stretching
C–C stretching
C–H bending
vs
vs
m
vw
m
vs
s
vs
m
m
s
1262
1296
1337
s
vs
vw
1457
vs
C–N stretching
C–H bending
1507
1582
1617
vs
m
vs
C–Nimino stretching
C–C stretching
C–C stretching
C–C stretching
C–H stretching
C–H stretching
C–H stretching
N–H stretching
m
vw
w
w
3128
3464
s
w
The most important difference between two structures lies in
Appendix A. Supplementary material
mutual orientation of ligand planes: angles between planes of li-
gands are 51.69° in experimental structure and 55.56° (3.87° more)
in the calculated structure, which can be explained by Van-der-
Waals repulsion of atoms. MOL file with optimized geometry is
available at supplementary materials.
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.molstruc.2013.01.
056.
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3.3. Raman spectra
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0.9775 which is widely used and this approach was found to give
a good correlation between experimental and calculated spectra
[42]). Experimental Raman spectrum is comprised of 39 bands.
Most intensive bands appear at 1215 cmꢀ1
,
1448 cmꢀ1 and
1517 cmꢀ1 in experimental spectrum and 1215 cmꢀ1, 1457 cmꢀ1
and 1507 cmꢀ1 in simulated one belong to C–C stretching and
two modes of C–N stretching vibrations, respectively, normal
modes of these vibrations are represented Fig. 5. Difference in
intensities of the bands can be explained as an influence of the
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orientation of crystal in
a laser beam. Bands appeared at
3350 cmꢀ1 in experimental and at 3464 cmꢀ1 in simulated spec-
trum belong to N–H stretching vibrations; frequencies at
3058 cmꢀ1, 3066 cmꢀ1 and 3080 cmꢀ1, appeared as a single band
with Raman shift 3128 cmꢀ1 refer to C–H stretching. The only
band observed in the calculated spectrum can be explained by
offset effect of the Doppler band broadening applied. Such shift
of peaks at low frequencies can be explained as an influence of
different normal modes to vibrations with a high energy; in
simulation we were not taken into account anharmonism.
More detailed summary on vibrational bands appeared in
experimental and simulated spectra are represented in Table 3.
We listed all bands with non-zero activity. DFT calculation of
the Raman spectrum with following shifting of the scale allowed
making a complete band assignment by comparison of normal
modes.
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Work was financially supported by Slovenian Research Agency
(ARRS).

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