The first copper(I)-olefin complexes bearing a 1,3,4-oxadiazole core: Alternating-current electrochemical crystallization, X-ray experiment and DFT study

Article abstract of DOI:10.1016/j.poly.2017.05.052

By means of alternating-current electrochemical technique, four new π-complexes, namely [Cu₂(C₁₁H₁₀N₂OS)₂Br_1.91Cl_0.09] (1), [Cu(C₁₁H₁₀N₂OS)NO

Full text of DOI:10.1016/j.poly.2017.05.052

Accepted Manuscript
The First Copper(I)-Olefin Complexes Bearing a 1,3,4-Oxadiazole Core: Al-
ternating-Current Electrochemical Crystallization, X-ray Experiment and DFT
Study
Yu. Slyvka, E. Goreshnik, G. Veryasov, D. Morozov, M. Luk'yanov, M. Mys'kiv
PII:
S0277-5387(17)30408-4
DOI:
http://dx.doi.org/10.1016/j.poly.2017.05.052
POLY 12671
Reference:
Polyhedron
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Revised Date:
Accepted Date:
16 March 2017
12 May 2017
14 May 2017
Please cite this article as: Yu. Slyvka, E. Goreshnik, G. Veryasov, D. Morozov, M. Luk'yanov, M. Mys'kiv, The
First Copper(I)-Olefin Complexes Bearing a 1,3,4-Oxadiazole Core: Alternating-Current Electrochemical
Crystallization, X-ray Experiment and DFT Study, Polyhedron (2017), doi: http://dx.doi.org/10.1016/j.poly.
2017.05.052
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The First Copper(I)-Olefin Complexes Bearing a 1,3,4-Oxadiazole Core: Alternating-Current
Electrochemical Crystallization, X-ray Experiment and DFT Study
Yu. Slyvka†, E. Goreshnik*,‡, G. Veryasov‡ D. Morozov§, M. Luk’yanov† and M. Mys’kiv†
,
†
Department of Inorganic Chemistry, Ivan Franko National University of Lviv, Kyryla i Mefodiya
Str., 6, 79005, Lviv, Ukraine
‡ Department of Inorganic Chemistry and Technology, Jožef Stefan Institute, Jamova 39, SI-1000
Ljubljana, Slovenia
§ Department of Chemistry, Nanoscience Center, Univeristy of Jyväskylä, P.O. Box 35, FI-40014
Jyväskylä, Finland
* Corresponding author. Department of Inorganic Chemistry and Technology, Jožef Stefan Institute,
Jamova 39, 1000 Ljubljana, Slovenia.Tel.: +386 1 477 36 45;
e-mail: evgeny.goreshnik@ijs.si
1

Abstract
Using the alternating-current electrochemical technique, four new π-complexes, namely
[Cu2(C11H10N2OS)2Br1.91Cl0.09] (1), [Cu(C11H10N2OS)NO3] (2), [Cu2(C11H10N2OS)2(H2O)2](BF4)2
(3) and [Cu2(C11H10N2OS)2(H2O)2](ClO4)2 (4), were obtained using copper(II) salts and the 2-
(allylthio)-5-phenyl-1,3,4-oxadiazole (C11H10N2OS) ligand. The metal and halogen centers in 1
form Cu2X2 dimers; the N-atom from the oxadiazole ring and the C=C bond of the allyl group from
the same ligand complete the copper coordination environment, giving [Cu(C11H10N2OS)X]2
isolated fragments. The ligand plays the same chelating role in 2, whereas the O (NO3) atom
occupies the third position in the copper atom’s equatorial plane. Two more elongated Cu–O(NO3)
contacts associate the Cu(C11H10N2OS)NO3 fragments into 1D chains. The geometries of the
2+
[Cu(C11H10N2OS)]2 cationic units in 3 and 4 are affected by the position of two water molecules
in the coordination spheres of the copper atoms with respect to the plane containing the oxadiazole
rings and the copper atoms. The molecular structures and Raman spectra of the compounds were
computed using the DFT/B3LYP/cc-pVDZ level of theory. The results are compared with the
experimental data obtained and used for vibrational band assignment.
Keywords: copper(I); olefin; π-complex; 1,3,4-oxadiazole derivatives; crystal structure; ac-
electrochemical technique, DFT, Raman spectroscopy
2

1. Introduction
Complexes involving transition metals and olefins have received considerable theoretical
and practical interest because of remarkable advances in the development of various catalytic
processes. This means they have also played an important role in organometallic chemistry in recent
decades [1-4]. Among them, considerable attention has been paid to the investigation of Cu(I) π-
complexes with allyl derivatives of heterocyclic organic compounds, since the combination of the
allyl radical and heterocyclic cores (both of which, according to hard soft acid base (HSAB) theory,
act as soft bases) efficiently contributes to the stabilization of inorganic fragments that occur only
extremely rarely [5]. This is caused by a certain deficiency in the electron density in the dx2-y2 orbital
→C=C)
(due to the π-dative (Cu
π component of the Cu(I)-olefin bond) and the difference in electron
donation from the atoms of the competing heterocylic molecule and the present inorganic (or
2-
organic) anions. For example, despite the “hard character” of the SiF6 anion, its fluorine atoms in
the presence of π,σ-coordinated 1-allylbenzotriazole were first observed to be bound with a “soft”
Cu(I) center in the corresponding crystalline compound [6]. A specific contribution of the allyl
radical attached to the 2-amino-5-phenyl-1,3,4-thiadiazole fragment through an amino group was
also observed in an acetonitrile solution, where the organic ligand, while reacting with CuNO3,
undergoes deprotonation and gives a new, tetra-nuclear [CuI(L)]4 (L = ligand) complex of the
azanide type [7].
Among a number of nitrogen-containing, five-membered aromatic heterocycles with an
electron-deficient nature, 1,3,4-oxadiazole derivatives have been intensively studied in the fields of
organic light-emitting diodes, biological activity, as well as crystal engineering [8-11]. Despite the
huge advances in the synthesis and the possible applications of 1,3,4-oxadiazole derivatives, the
data concerning their use as co-ligands in metal-olefine π-coordination is still limited: only 16
corresponding entries have been found in the Cambridge Crystallographic Database (CCD) [12],
while the analogous Cu(I) π-compounds appear to be structurally unstudied. Moreover, the
coordination of CuCl, CuNO3 and CuClO4 with a 1,3,4-oxadiazole core has not been observed in
the CCD references. To reveal the main features of copper-olefin π-coordination in the presence of
a 1,3,4-oxadiazole core we present the synthesis and structural characterization of four new π-
complexes, [Cu2(Atphod)2Br1.91Cl0.09] (1), [Cu(Atphod)NO3] (2), [Cu2(Atphod)2(H2O)2](BF4)2 (3)
and [Cu2(Atphod)2(H2O)2](ClO4)2 (4), with 2-(allylthio)-5-phenyl-1,3,4-oxadiazole (Atphod),
emphasizing the influence of the inorganic anions on the diverse 1,3,4-oxadiazole π,σ-coordination
mode with the Cu+ ion, in particular enabling the first observation of CuNO3 and CuClO4 binding
with a 1,3,4-oxadiazole ring. The compounds were studied by means of single-crystal XRD and
Raman spectroscopy.
3

2. Experimental
2.1. Materials and instrumentation
Unless mentioned otherwise, all the chemicals were obtained from commercial sources and
1
used without further purification. The NMR experiments, i.e. H NMR (500 MHz) and 13C[1H]
NMR (125 MHz), were recorded on a Bruker Advance 500-MHz NMR spectrometer. The chemical
1
shifts are reported in ppm relative to the residual peak of deuterated CDCl3 for the H and 13C[1H]
NMR spectra. Diffraction data were collected on an Agilent Gemini A four-circle diffractometer
equipped with an Atlas CCD detector.
2.1. Preparation of 2-(allylthio)-5-phenyl-1,3,4-oxadiazole (Atphod)
5-Phenyl-1,3,4-oxadiazole-2-thiol was synthesized from benzhydrazide and carbon disulfide, in
accordance with the reported method [13]. The reaction of 5-phenyl-1,3,4-oxadiazole-2-thiol with
3-chloroprop-1-ene in the presence of KOH yields the corresponding 2-(prop-2-en-1-ylsulfanyl)-5-
phenyl-1,3,4-oxadiazole (Atphod) as a yellow liquid (at room temperature). The yield was about
1
93%. Atphod: H NMR (500 MHz, CDCl3) δ, ppm: 7.91 (dd, J = 6.3, 1.3 Hz, 2H, HPh-2,6), 7.49-
7.33 (m, 3H, HPh-3-5), 6.04-5.83 (m, 1H, =CH), 5.33 (dd, J = 16.9, 1.2 Hz, 1H, CH2=), 5.15 (dd, J =
10.0, 0.8 Hz, 1H, CH2=), 3.85 (d, J = 7.0 Hz, 2H, CH2). 13C NMR (126 MHz, CDCl3) δ, ppm:
165.69 (C-h-ring), 163.53 (C-h-ring), 131.58 (=CH), 128.91 (C-Ph), 126.48 (C-Ph), 123.46 (C-Ph),
119.62 (CH2=), 35.11 (CH2).
2.2 Synthesis of the copper(I) π-complexes
Crystals of the complexes were obtained under the conditions of alternating-current electrochemical
synthesis [5,7,14-21], starting from an alcohol solution of the Atphod ligand and the corresponding
copper(II) salt.
2.2.1 Preparation of [Cu2(Atphod)2Br1.91Cl0.09] (1)
To 4.3 mL of an ethanol solution of CuBr2 (1.1 mmol, 0.246 g), 0.218 g (1.0 mmol) of Atphod and
0.034 g (0.2 mmol) of NaCl were added. The mixture was carefully stirred, the resulting solution
was placed into a 5 mL test tube and then copper-wire electrodes in cork were inserted. With the
application of an alternating-current tension (frequency 50 Hz) of 0.55 V for 3 days the solution
was discolored and good-quality colorless crystals of 1 appeared on the copper electrodes. The yield
was about 20%. M.p.: 156 ºC.
2.2.1 Preparation of [Cu(Atphod)NO3] (2)
4

To 4.3 mL of an ethanol solution of Cu(NO3)2·3H2O (1.2 mmol, 0.290 g), 0.218 g (1.0 mmol) of
Atphod was added. The resulting green-colored mixture, after careful stirring, was subjected to an
alternating-current tension (frequency 50 Hz) of 0.60 V for 2 days. Good-quality colorless crystals
of 2 appeared on the copper electrodes. The yield was about 20%. M.p.: 137 ºC.
2.2.3 Preparation of [Cu2(Atphod)2(H2O)2](BF4)2 (3)
To 4.3 mL of an ethanol solution of Cu(BF4)2·6H2O (1.1 mmol, 0.380 g), 0.218 g (1.0 mmol) of
Atphod was added. With the application of an alternating-current tension (frequency 50 Hz) of 0.6
V for 1 day, crystals of 3 appeared on the copper electrodes. The yield was about 15%. M.p.: 173 ºC
(dec.).
2.2.4 Preparation of [Cu2(Atphod)2(H2O)2](ClO4)2 (4)
To 4.3 mL of an ethanol solution of Cu(ClO4)2·6H2O (1.1 mmol, 0.408 g), 0.218 g (1.0 mmol) of
Atphod was added. With the application of an alternating-current tension (frequency 50 Hz) of 0.6
V for 2 days, the green solution was discolored and good-quality colorless crystals of 4 appeared on
the copper electrodes. The yield was about 15%, M.p.: 165 ºC.
2.3. Single crystal X-ray diffraction studies.
Single-crystal data were collected on a Gemini A diffractometer equipped with an Atlas CCD
detector, using graphite monochromated CuKa radiation for crystals 1 and 2 or graphite
monochromated MoKa radiation for compounds 3 and 4. The collected diffraction data for 1-4
were processed with the CrysAlis PRO program [22]. The structures were solved using direct
methods with SHELXS-97 and refined using the least-squares method on F2 with SHELXL-2013
and using the graphical interface of OLEX2 [23-25]. The atomic displacements for the non-
hydrogen atoms were refined using an anisotropic model. The hydrogen atoms (except the water
molecules) were placed in ideal positions and refined as riding atoms with relative isotropic
displacement parameters. In 2 and 3, the one allylsulfanyl group (C3 and C4 atoms) is disordered
over two sites with an occupancy ratio of 0.886(6):0.114(6) and 0.874(4):0.126(4) respectively.
–
Similar behaviour of the allylsulfanyl group was observed in 4. Also, the ClO4 anion (O3, O4 and
O6 atoms) is disordered in 4 over two sites with an occupancy ratio of 0.798(6):0.202(6). The
crystal parameters, data collection and the refinement are summarized in Table 1.
5

Table 1. Selected crystal data and structure refinement parameters of 1-4.[a]
Crystal data
1
2
3
4
CCDC number
(Appendix A)
1531990
1531991
1531992
1531993
Empirical formula C22H20Br1.91Cl0.09Cu2N4O2S2 C11H10CuN3O4S C22H24Cu2N4O4S2B2F8 C22H24Cu2N4O12S2Cl2
F. w. (g mol-1)
Crystal system,
space group
a (Å)
b (Å)
c (Å)
719.35
Triclinic,
P1
7.737(2)
8.470(3)
10.182(7)
96.87(4)
343.82
Monoclinic,
C2/c
773.27
Monoclinic,
P21/c
798.55
Monoclinic,
P21/n
23.6143(9)
7.5312(4)
15.9270(8)
-
10.7140(5)
8.1394(4)
33.3579(14)
-
10.2776(3)
10.5321(3)
13.4213(4)
-
α (º)
β (º)
94.43(4)
113.493(4)
91.771(4)
98.415(3)
γ (º)
110.63(3)
614.9(5)
1
7.687
354.3
-
-
-
V (Å3)
2597.7(2)
8
4.056
1392
2907.6(2)
4
1.695
1552
1437.14(7)
2
1.881
808
Z
µ (mm-1)
F(000)
Crystal size (mm)
0.41× 0.18 × 0.10
0.21× 0.20 ×
0.15
0.37× 0.30 × 0.06
0.55× 0.27 × 0.07
Crystal color
colorless
colorless
colorless
1.766
colorless
1.845
Calculated density, 1.943
(g/cm3)
Data collection
1.758
Radiation type,
wavelength, λ (Å)
Temperature (K)
R[F2 > 2σ(F2 )]
Cu Ka, 1.5418
Cu Ka, 1.5418
Mo Ka, 0.71073
Mo Ka, 0.71073
150(2)
0.034
0.093
1.040
150(2)
0.050
0.141
1.043
150(2)
0.033
0.079
1.067
150(2)
0.032
0.080
1.052
wR(F2 )
GooF = S
2.4. Raman spectroscopy
Raman spectra were measured in the air on crystals of 1-4 and the ligand powder with a
Horiba Jobin–Yvon LabRAM HR spectrometer using the 632.81-nm excitation line of a He-Ne
laser with a power of 17 mW. The spectrometer was calibrated using a Si polycrystalline plate as a
standard with a characteristic band at 520.6 cm-1.
2.5. Computational details
All the calculations were performed at the DFT/B3LYP/cc-PVDZ level [26,27] using the
GAMESS(US) program package [28]. A basis set with effective core potentials (ECPs) was
applied for the copper atoms. The initial geometries, derived from the crystal structure, were
assumed to have C1 symmetry and were utilized for the geometry optimization. The equilibrium
geometries obtained were used for the Forces Constants matrix calculation. A polarizability tensor
was then calculated and the resulting Raman activities (Si) were converted to Raman intensities (Ii)
using the following relationship from the intensity theory of Raman scattering [29,30].
6

3. Results and discussion
3.1 Crystal structures.
The structures 1-4 demonstrate the first examples of copper(I)-olefin π-complexes with an
active 1,3,4-oxadiazole core bonded to Cu(I) ion. The atphod molecule in compounds 1 and 2 acts
as a bidentate chelating π,σ-ligand, being attached to the Cu(I) ion by means of the C=C bond of the
allyl group and one the most nucleophilic N1 atoms of the oxadiazole ring (Figs. 1 and 2). The
copper(I) atom in 1 adopts close to a trigonal pyramidal geometry (τ4=0.85, τ4 – four-coordinate
geometry index), including the N atom, the C=C bond and one of the halogen X atoms in the basal
plane of the metal polyhedron. The second halogen atom, that is apically bonded to the Cu(I) ion, is
at a distance of 2.836(2) Å from the metal center, which is significantly shorter than the sum of the
VdW radii of the Cu and Cl (3.15 Å) or the Cu and Br (3.23 Å) atoms, reported by Bondi, [31,32]
and very much shorter than the corresponding sum of 4.20 Å for the Cu and Cl atoms, recently
discovered by Alvarez [33]. As a result, in 1 the bridging halogen atoms connect the organometallic
[Cu(Atphod)] fragments into a centrosymmetric [Cu2(Atphod)2Br1.91Cl0.09] dimer. A similar [-
N,(C=C)Cl2-]2 coordination topology for CuX (X = Cl or Br) was previously found in the structure
of seven copper(I) chloride and three copper(I) bromide complexes with olefin-containing ligands,
among
which
are
diallylamine
[34],
1-allyl-3,5-dimethylpyrazole
[35],
(dimethyl(vinyl)silyl)pyridine [36], allylacetone oxime [37], and 2-(allylthio)benzimidazole [15].
Figure 1. Fragment of the crystal structure of 1. Thermal ellipsoids are shown at 50 % probability.
Symmetry codes: (i) 1−x, 2−y, 2−z. X = Br, Cl. Selected bond length (in Å) and angle (in deg)
values: Cu1–X 2.3673(9), Cu1–Xi 2.836(2), Cu1–N1 1.986(3), Cu1–m 1.946(4) (m – middle point
of C4=C5 bond), C4–C5 1.365(5), N1–N2 1.411(4), C2–C6 1.458(5), C1–N1 1.300(5), C2–N2
1.291(5), N1–Cu1–X 110.8(1), N1–Cu1–Xi 103.3(1), N1–Cu1–m 116.1(1), m–Cu1–X 124.7(1), m–
Cu1–Xi 91.0(1).
7

A phenyl group of the Atphod ligand in complex 1 is tilted by 10.34° with respect to the 1,3,4-
oxadiazole ring, and the distance of 1.458(5) Å for C2–C6 between the carbon atoms of the
oxadiazole and phenyl rings indicates a significant contribution of the π-component to the bond.
Due to the π-dative Cu(I)→(C=C)π part of the Cu(I)–olefine interaction, the C=C bond of the ligand
allyl group in 1 is elongated to 1.365(5) Å, in comparison with the free C=C distance in ethylene of
1.338(1) Å (gas phase, [38]), 1.3142(3) Å (at 85 K [39])
Taking into account that according to Pearson`s HSAB theory, a soft base, such as a C=C
bond, should readily react with a soft acid Cu(I) ion. The contributions of heterocyclic N atoms
(possessing borderline basicity) to the metal coordination have a considerable effect on the Cu(I)
ion’s interaction with inorganic anions, thus stabilizing unknown (or less-stable), in the free state,
copper(I) salts [5]. This conclusion is largely confirmed by the existence of the [Cu(Atphod)NO3] π-
complex (2) in the crystalline form. To the best of our knowledge, 2 is the first known crystalline
example of a CuNO3 compound containing a 1,3,4-oxadiazole ligand. Previously, the coordination
behavior of 1,3,4-oxadiazole derivatives was studied exclusively with respect to copper(II) nitrate
[40,41].
Figure 2. Fragment of the crystal structure 2. Thermal ellipsoids are shown at 50 % probability.
−
−
Symmetry codes: (i) 1.5−x, y−0.5, 1.5 z; (ii) 1.5−x, 0.5+y, 1.5 z. Selected bond length (in Å) and
angle (in deg) values: Cu1–O2 1.990(2), Cu1–O3i 2.598(2), Cu1–N1 1.968(3), Cu1–m 1.910(4)
(m – middle point of C4A=C5 bond), C4A–C5 1.383(5), N1–N2 1.411(4), C2–C6 1.458(5), C1–N1
1.292(4), C2–N2 1.289(4), N1–Cu1–O2 111.7(1), N1–Cu1–O3i 89.2(1), N1–Cu1–m 117.1(1), m–
Cu1–O2 131.2(1), m–Cu1–O3i 98.5(1), O3i-Cu1-O2ii 167.3(1), O3i-Cu1-O3 129.7(1).
The Cu(I) atom in the structure of 2 adopts close to a trigonal-pyramidal geometry (τ4 =
0.79) [42], with one oxadiazole N atom, the allylic C=C bond and two O atoms of two symmetry-
–
related NO3 anions. The coordination of the apically bonded O3i atom is intriguing, since the Cu–
O3i distance value of 2.598(2) Å is very close to the limiting distance of 2.63 Å for a Cu–Oap
8

interaction in the structures of Cu(I) π-complexes with allyl derivatives of heterocycles [5,12]. On
the other hand, the fact that the copper atom is located in the plane of the equatorial ligands was
never reported in the analogous compounds and indicates a significant deficiency of the electron
density in the dx2-y2 copper orbital due to an effective π-dative Cu(I)→(C=C)π component of the π-
bond. The appearance of one more elongated Cu–O3 contact with a distance of 2.729(2) Å, shorter
than the corresponding rvdW sum (2.92 Å), is mostly the result of geometrical factors, typically
–
observed for a coordinated NO3 anion. It is worth noting that the Cu(I) anisotropic displacement
parameter U22 (0.0449(4) Å2), with a larger value than U11 (0.0188(3) Å2) or U33 (0.0278(3) Å2),
indicates a greater metal anisotropy in two opposite directions, one of which is directed to the O3i
–
atom and the other one to the O2ii atom of another NO3 moiety (Cu-O2ii) 3.469(3) Å. The above
statement might suggest that the Cu atom in structure 2 is five-coordinated and adopts a geometry
–
that occurs for the Ag(I) ion in its π-coordination with olefins [43,44]. Thus, bridging NO3 anions,
by means of weak Cu–O3i bonds in 2, connect [Cu(Atphod)] units into infinite chains in the 010
direction.
Figure 3. Coordination polymer in the structure of 2. Thermal ellipsoids are shown at 50 %
probability.
In contrast to 1 and 2, in complexes 3 and 4 the coordination behavior of the Atphod ligand,
with regard to the Cu(I) ion, is reminiscent of 2-allylamino-5-methyl-1,3,4-thiadiazole [19] and 5-
allylthio-1-phenyl-tetrazoles [17, 45] in terms of dimer formation. The Atphod molecule in 3 and 4
acts as a tridentate chelate-bridging ligand, being attached to the metal centers by both oxadiazole N
atoms (Figs. 4 and 5). A close to trigonal pyramidal Cu(I) environment in both structures (for 3 τ4 =
0.83 and 0.85; for 4 τ4 = 0.80) involves an allylic C=C bond in an equatorial position and two
different N atoms of two neighboring oxadiazole rings, while the apical position of the metal
polyhedron is occupied by a water molecule. Thus, a pair of copper atoms connects two Atphod
9

molecules into cationic [Cu2(Atphod)2]2+ dimers, characterized in 3 and 4 by different symmetries
–
and modes of coordination of the water molecules. A common tendency for the BF4 anion to be
bound with a copper(I) center through a water bridge by means of hydrogen bonding leads to the
appearance of the acentric [Cu2(Atphod)(H2O)2]2+ dimer, within which both H2O molecules are
–
located on one side of the [Cu2(Atphod)2]2+ tecton (Fig. 4a). One of the BF4 anions in 3 is involved
in an H-bridge between the water molecule of the same dimer, while the other one assembles the
[[Cu2(Atphod)2(H2O)2]·BF4] synthons into an infinite chain (Fig. 5a). The dihedral angle between
the 1,3,4-oxadiazole rings within the dimer is 20.9(1)º.
In contrast to 3, the structure of [Cu2(Atphod)2(H2O)2](ClO4)2 (4) is organized in another
-
manner. Due to the aspiration of the ClO4 anion to form O-H···O bonds in a more symmetrical
array, the [Cu2(Atphod)]2+ tecton transforms into a centrosymmetrical dimer, allowing the H2O
molecule to coordinate the Cu(I) ion from different sides of the [Cu2(Atphod)2]2+ tecton. Thus, it
–
provides an organization of [Cu2(Atphod)2(H2O)2]2+ cations and ClO4 anions into hydrogen-bonded
2D layers (Fig. 5b). It should be noted that the CuClO4 coordination to the 1,3,4-oxadiazole ring
was previously studied only for copper(II) salts [40,46].
Figure 4. Part of the structure of 3 (a) and centrosymmetric fragment of 4 (b). Thermal ellipsoids
–
are shown at 50 % probability. The disorders of the allyl group (attached to Cu2, in 3) and the ClO4
anion (in 4) are omitted for clarity. Selected bond length (in Å) and angle (in deg) values: 3: Cu1–
N1 2.030(2), Cu1–N4 1.994(2), Cu1–O3 2.191(2), Cu2–N2 2.002(2), Cu2–N3 2.036(2), Cu2–O4
2.191(2), Cu1–m1 1.964(3), Cu2–m2 1.962(2) (m1 and m2 – middle point of the C4A=C5 and
C14=C15 bonds), C4A–C5 1.359(4), C14–C15 1.354(3), N1–Cu1–O3 100.31(8), N4–Cu1–O3
96.11(8), N1–Cu1–m1 113.4(1), m1–Cu1–O3 100.1(1), m1–Cu1–N4 129.5(1), N2–Cu2–N3
109.76(7), N2–Cu2–O4 101.33(8), N2–Cu2–m2 127.0(1), m2–Cu2–O4 107.0(1), m2–Cu2–N3
113.2(1). Symmetry codes in 3: (i) -x, 2-y, 1-z; (ii) x, 1+y, z;
4: Cu1–N1 2.004(2), Cu1–N2i 1.992(2), Cu1–O2 2.310(2), Cu1–m 1.941(2) (m – middle point of te
C4=C5 bond), C4A–C5 1.347(4), N1–N2 1.413(3), C2–C6 1.463(3), C1–N1 1.300(3), C2–N2
10

1.294(3), N1–Cu1–O2 92.08(8), N1–Cu1–N2i 111.34(7), N2i–Cu1–O2 86.93(8), N1–Cu1–m
112.9(1), N2–Cu1–m 135.0(1), m–Cu1–O2 98.9(1). Symmetry code in 4: (i) 1-x, 1-y, -z.
Figure 5. H-bonded arrays in the structures of 3 (a) and 4 (b). Thermal ellipsoids are shown at 50 %
probability.
−H···A interactions in
Table 2. Geometry of selected D
the crystal structures of 3 and 4.
Atoms involved
−H···A
Symmetry
Distances, Å
Angle, deg
−H···A
D
D···H
H···A
D···A
D
3
−H3B···F7
O3
x, 1+y, z
x, 1+y, z
-x, 2-y, 1-z
x, 1+y, z
x, 1+y, z
1-x, 2-y, 1-z
0.75(2)
0.75(2)
0.75(2)
0.74(2)
0.74(2)
0.75(2)
2.23(2)
2.34(2)
2.04(2)
2.42(2)
2.28(2)
2.06(2)
2.890(3)
3.011(3)
2.779(3)
3.052(3)
2.977(3)
2.803(3)
148(3)
150(3)
172(3)
143(3)
157(3)
175(4)
O3−H3B···F8
−H3A···F4
O3
O4−H4B···F6
−H4B···F8
O4
O4−H4A···F2
4
O2−H2A···O3A
−H2B···O5
O2
0.85(4)
0.84(4)
1.92(4)
2.04(4)
2.692(4)
2.847(3)
151(3)
160(4)
1.5-x, 0.5+y, 0.5-z
11

Figure 6. Packing mode of 3 (a) and 4 (b) along the [100] direction. A plain stick model is used for
clarity.
3.1 Computed geometries
The optimized structures are shown in Figures S1-S3, Supplementary Material. Selected
geometrical parameters for every compound in comparison to the experimental ones are provided
below each figure.
All the compounds were computed with C1 symmetry. For compound 1 both halogen atoms were
set to be Br, since the fraction of C1 is low in the experimental structure. The geometrical
parameters at the equilibrium point appeared to be close to the experimental values.
−
For compound 2 the calculation was on an anion with two NO3 groups to keep the coordination
−
surrounding the Cu atom. As expected, a slight distortion of the NO3 group’s position appeared
due to the absence of lattice influence, i.e., the O3 atom is pushed back and the Cu atom has only
−O distances
two oxygen atoms within the coordination sphere. This change affected the Cu
, and the
Cu–O3i bond at the equilibrium point has a length of 2.0539 Å, while the same bond in the
experimental structure was significantly longer at 2.598(2) Å.
For compounds 3 and 4 the geometry optimization faced some difficulties: in both cases the oxygen
atom from the water molecules in the coordination sphere of the Cu atom tends to be equidistant
from both metal centers. This leads to the exclusion of a second water molecule in the case of
compound 3, so it was decided to use the dimer structure without water molecules. The optimized
geometry appeared to be close to the experimental geometry. All the optimized structures are
available in the Supplementary Material in XYZ format.
The equilibrium geometries were applied for Raman spectra calculations. In the computed spectra
no imaginary frequencies appeared.
3.2 Raman spectra
The Raman spectra of compounds 1-4 are shown in Figure 7. The band assignments were made on
the basis of the computed Raman spectra, see Tables S1-S3. The spectrum of the pure ligand is
given in Figure S4.
The most intensive band in all the spectra appeared at 1604–1610 cm−1 and is due to ν(CC) from the
ring of the Atphod ligand. The most interesting peculiarity of the spectra is related to the bands from
the allyl group. The ν(C=C) band from the allyl group is a commonly used “fingerprint” for such
compounds; it appeared at 1639 cm-1 in the spectrum of the pure ligand and was observed in the
spectra of compounds 1-4 at 1561, 1565, 1562 and 1566 cm-1, respectively. The computed spectrum
for the cationic unit [Cu2(Atphod)2]2+ appearing in the structures of 3 and 4 indicated that this band
is of zero intensity and is expected to appear at approximately 1570 cm-1. Presumably, the
12

suppression of the ν(C=C)allyl band is caused by the contribution of the Cu coordination
surroundings to the resulting polarizability tensor, whereas the presence of water molecules in the
structures of 3 and 4 indicated distortions, so that the band becomes Raman active.
Figure 7. Raman spectra recorded on single crystals of 1, 2, 3 and 4. The region 1700–2700 cm-1 is
removed due to the absence of bands.
4. Conclusions
We have synthesized and determined the crystal structures of four new π-compounds with 2-
(allylthio)-5-phenyl-1,3,4-oxadiazole
(Atphod),
namely
[Cu2(Atphod)2Br1.91Cl0.09
]
(1),
[Cu(Atphod)NO3] (2), [Cu2(Atphod)2(H2O)2](BF4)2 (3) and [Cu2(Atphod)2(H2O)2](ClO4)2 (4). These
compounds are the first-known π-complexes bearing the 1,3,4-oxadiazole core bound to a Cu(I) ion.
The Atphod ligand in 1-4 acts as a chelate π,σ-ligand, being attached to the Cu(I) ion by means of
–
–
an allylic C=C bond and one or two oxadiazole N atoms. In the presence of BF4 and ClO4 anions,
the copper(I) ion acts as a bridge, connecting two neighboring Atphod molecules into a
[Cu2(Atphod)2(H2O)2]2+ dimeric tecton, each of which is bound with H2O molecules in various
13

ways, most likely due to the different H-bonded arrays in the structure. Two bridging halogen atoms
in 1 connect the [Cu(Atphod )]+ units into a centrosymmetric fragment with a [-N,(C=C)Cl2-]
coordination topology of CuX (X =Cl or Br), previously observed for 7 copper-olefine compounds.
The structures of 2 and 4 were found to be the first-known examples of CuNO3 and CuClO4
coordination with a 1,3,4-oxadiazole ring. Taking into account one more weakly coordinated nitrate
–
O atom (Cu-O 2.598(3) Å) in 2, the [Cu(Atphod)]+ fragments are bound by means of bringing NO3
anions into a 1D-polymer. To analyze the interactions between the molecules in 3 and 4, Raman
spectroscopy accompanied by computational modelling at the DFT/B3LYP/cc-pVDZ level was
used for the vibrational spectral analyses and band assignments.
Appendix A. Supplementary data
CCDC 1531990, 1531991, 1531992 and 1531993 contain the supplementary crystallographic data
for compounds 1, 2, 3 and 4, respectively. These data can be obtained free of charge via
http://www.ccdc.cam.ac.uk/conts/retrieving.html, or from the Cambridge Crystallographic Data
Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: (+44) 1223-336-033; or e-mail:
deposit@ccdc.cam.ac.uk.
A comparison of the experimental and calculated geometries and details of the experimental and
computed Raman spectra are also available in the Supplementary data.
5. Acknowledgments
E.G would like to acknowledge the financial support by Slovenian Research Agency
(ARRS), program P1-0045.
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16

17

Using the alternating-current electrochemical technique and starting from copper(II) salts and the 2-
(allylthio)-5-phenyl-1,3,4-oxadiazole ligand, four new π-complexes were obtained. All the
compounds were characterized by single crystal X-ray diffraction and Raman spectroscopy. The
molecular structures and Raman spectra of the compounds were computed using the
DFT/B3LYP/cc-pVDZ level of theory.
18