Crystal structure of tetra-μ-acetato-bis­[(5-amino-2-methyl­sulfanyl-1,3,4-thia­diazole-κN1)copper(II)]

Torambetov, B.; Kadirova, S.; Toshmurodov, T.; Ashurov, J.M.; Parpiev, N.A.; Ziyaev, A.

doi:10.1107/S2056989019010272

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Volume 75| Part 8| August 2019| Pages 1239-1242

https://doi.org/10.1107/S2056989019010272

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Crystal structure of tetra-μ-acetato-bis[(5-amino-2-methylsulfanyl-1,3,4-thiadiazole-κN¹)copper(II)]

Batirbay Torambetov,^a Shaxnoza Kadirova,^a Turdibek Toshmurodov,^b Jamshid Mengnorovich Ashurov,^c ^* Nusrat Agzamovich Parpiev ^a and Abdukhakim Ziyaev ^b

^aNational University of Uzbekistan named after Mirzo Ulugbek, 100174, Tashkent, Uzbekistan, ^bInstitute of the Chemistry of Plant Substances, Academy of Sciences of Uzbekistan, Mirzo-Ulugbek str. 77, 100170, Uzbekistan, and ^cInstitute of Bioorganic Chemistry, Academy of Sciences of Uzbekistan, M. Ulugbek Str, 83, Tashkent, 700125, Uzbekistan
^*Correspondence e-mail: atom.uz@mail.ru

Edited by A. M. Chippindale, University of Reading, England (Received 10 July 2019; accepted 18 July 2019; online 23 July 2019)

The reaction of 2-methylthio-5-amino-1,3,4-thiadiazole (Me-SNTD; C₃H₅N₃S₂) with copper(II) acetate monohydrate [Cu(OAc)₂·H₂O; C₄H₈CuO₅] resulted in the formation of the title binuclear compound, [Cu₂(C₂H₃O₂)₄(C₃H₅N₃S₂)₂] or [Cu₂(OAc)₄(Me-SNTD)₂]. The structure has triclinic (P $[\overline{1}]$ ) symmetry with a crystallographic inversion centre located at the midpoint of the line connecting the Cu atoms in the dimer. These two Cu atoms of the dimer [Cu⋯Cu = 2.6727 (6) Å] are held together by four carboxylate groups. Each Cu atom is further coordinated to the N atom of an Me-SNTD molecule and exhibits a Jahn–Teller-distorted octahedral geometry. The dimers are connected into infinite chains by hydrogen bonds between the NH (Me-SNTD) and the carboxylate groups of neighbouring molecules, generating an R²₂(12) ring motif. The molecules are further linked by C—H⋯π interactions between the thiadiazole rings and the methyl groups of the acetate units.

Keywords: copper(II); thiadiazole; crystal structure; hydrogen bonding..

CCDC reference: 1941461

1. Chemical context

1,3,4-Thiadazoles are an important class of heterocycles and are of great interest because of their broad spectrum of biological activity. 1,3,4-Thiadiazole derivatives and their metal complexes have been shown to display antimicrobial (Önkol et al., 2008 ; Abdel-Wahab et al., 2009 ; Kadi et al., 2010 ), antituberculosis (Karakuşs et al., 2002 ; Foroumadi et al., 2004 ), antioxidant (Chitale et al., 2011 ; Sunil et al., 2010 ; Khan et al., 2010 ), anticancer (Padmavathi et al., 2009 ; Kumar et al., 2010 ;) and antifungal (Matysiak et al., 2007 ; Klip et al., 2010 ; Verma et al., 2011 ; Zoumpoulakis et al., 2012 ) activities. In addition, some of the 1,3,4-thiadiazole-ring-containing ligands can be efficient uptake agents of toxic metal ions (Mincione et al., 1997 ). 1,3,4-Thiadiazoles also exhibit great potential as pesticides in the fields of herbicides, fungicides, insecticides and even as plant-growth regulators. Their diverse biological activity possibly arises from the presence of the =NCS moiety in the molecule (Oruç et al., 2004 ). An interesting feature of the metal–ligand chemistry of these compounds is that the complexes can be either mononuclear (Tzeng et al., 2004 ; Varna et al., 2018 ; Qiu et al., 2014 ) or binuclear (Deckert et al., 2016 ; Ardan et al., 2017 ). A search of the Cambridge Structural Database (CSD Version 5.4, update of February 2019; Groom et al., 2016 ) revealed that although crystal structures have been reported for complexes of either 1,3,4-thiadiazole derivatives or OAc with a number of metal ions, including zinc, copper, nickel, manganese, cadmium, cobalt and palladium, no examples are known of mixed-ligand metal complexes containing both 1,3,4-thiadiazole derivatives and OAc. Herein, we report on the synthesis and crystal structure of a new binuclear complex, [Cu₂(OAc)₄L₂], with L = 2-methylthio-5-amino-1,3,4-thiadiazole (Me-SNTD).

2. Structural commentary

The title binuclear Cu^II complex, (I) (Fig. 1), is arranged about a crystallographic inversion centre located at the midpoint of the Cu⋯Cu-connecting line. The asymmetric unit comprises one half of the complex molecule, namely, one Cu atom, two acetate groups and one 2-methylthio-5-amino-1,3,4-thiadiazole molecule. The two Cu atoms in the dimer are held together by the four carboxylate groups. Each Cu atom is bound in a square-pyramidal configuration to four carboxylate O atoms and to the N atom of an Me-SNTD molecule.

Figure 1
The molecular structure of [Cu₂(OAc)₄(Me-SNTD)₂] with the atom-numbering scheme. Displacement ellipsoids are drawn at the 25% probability level. Intramolecular hydrogen bonds are shown as dashed lines. Atoms labelled with the suffix A are generated by the symmetry operation 2 − x, 1 − y, 1 − z.

Each copper atom is displaced by 0.754 (3) Å from the plane defined by basal-plane atoms O1, O2, O3 and O4 towards the nitrogen atom, N2. The Cu1A —Cu1—N2 angle is 177.95 (7)° [symmetry code: (A) 2 − x, 1 − y, 1 - z]. The Cu—O bond lengths range from 1.962 (2) to 2.001 (2) Å and the Cu—N distance is 2.180 (3) Å. The Cu⋯Cu distance is 2.6727 (6) Å and each metal atom exhibits a Jahn–Teller-distorted octahedral geometry. The observed Cu—O2 bond length of 1.983 (2) Å is longer than the Cu—O1 distance of 1.962 (2) Å. The elongation of this Cu—O distance may be due to the intramolecular N3—H⋯O2 hydrogen bond (Table 1). The conformation of the ligand is approximately planar, with a maximum deviation from the least-squares plane of 0.066 (2) Å for atom N3. The thiadiazole ring is planar (r.m.s. deviation 0.0063 Å). The dihedral angle between the planes of the two independent acetate groups is 82.646 (14)°. The thiadiazole ring is twisted by 18.37 (2)° with respect to the acetate (C4/C5/O1/O2) ligand mean plane.

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the S1/N1/N2/C1/C2 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3A⋯O4ⁱ	0.86 (1)	2.16 (2)	2.963 (4)	156 (4)
N3—H3B⋯O2ⁱⁱ	0.86 (1)	2.11 (3)	2.884 (4)	150 (4)
Symmetry codes: (i) x, y, z+1; (ii) -x+2, -y+1, -z+1.

3. Supramolecular features

The packing of (I) is shown in Fig. 2. The acetate group containing oxygen atoms O1 and O3 does not form any hydrogen bonds. However, the acetate group containing oxygen atoms O2 and O4 forms both intra- and intermolecular hydrogen bonds. Each binuclear complex molecule exhibits one intramolecular N3—H3⋯O2ⁱ hydrogen bond, forming a six-membered ring. The dimers are connected through an intermolecular N3—H3⋯O4ⁱⁱ hydrogen bond between the NH (Me-SNTD) and the carboxylate groups, forming chains propagating parallel to [001]. The above-mentioned hydrogen bonds give rise to R₂²(12), C₂²(14) and S₁¹(6) graph-set motifs (Table 1 and Fig. 2). Additional C—H⋯π interactions between the thiadiazole rings and the acetate methyl groups generate a three-dimensional supramolecular framework (Fig. 3).

Figure 2
Part of the crystal structure with hydrogen bonds shown as dashed lines. For clarity, H atoms not involved in hydrogen bonding are omitted.

Figure 3
Packing of the structural units in (I)

. Hydrogen bonds are indicated by blue dashed lines and C—H⋯π interactions by black dashed lines.

4. Database survey

A survey of the Cambridge Structural Database (CSD Version 5.4, update of February 2019; Groom et al., 2016) revealed that crystal structures have been reported for complexes of 1,3,4-thiadiazole derivatives and OAc with a number of metal ions, including zinc, copper, nickel, manganese, cadmium, cobalt and palladium. Copper(II) acetate complexes of the general formula [Cu₂(OAc)₄L₂], where L is a ligand with an oxygen or nitrogen ligator atom, have been well explored. The structures of 2-methylthio-5-amino-1,3,4-thiadiazole and a complex of this molecule with cadmium have been deposited in the CSD [XUVPEK (Lynch, 2010 ) and JIZKEK (Soudani et al., 2014 ), respectively]. However, no mixed-ligand metal complexes containing both 1,3,4-thiadiazole derivatives and OAc have been documented in the CSD.

5. Synthesis and crystallization

Cu(OAc)₂·H₂O (0.218 g, 1 mmol) and 2-methylthio-5-amino-1,3,4-thiadiazole (0.147 g, 1 mmol) were dissolved separately in a mixture of methanol-dichloromethane (10 mL, 1:1 v/v), mixed together and stirred for 1.5 h. The green solid that precipitated was dissolved in methanol to form a green solution. Single crystals of the complex suitable for X-ray analysis were obtained by slow evaporation of the solution over a period of 10 d.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The restraint N—H = 0.86 ± (1) Å was applied. Methyl H atoms were positioned geometrically C—H = 0.96) and refined as riding with U_iso(H) = 1.5Ueq(C).

Table 2
Experimental details

Crystal data
Chemical formula	[Cu₂(C₂H₃O₂)₄(C₃H₅N₃S₂)₂]
M_r	657.69
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	571
a, b, c (Å)	8.1069 (4), 8.8955 (4), 9.0421 (5)
α, β, γ (°)	100.656 (4), 98.966 (4), 97.643 (4)
V (Å³)	624.14 (5)
Z	1
Radiation type	Cu Kα
μ (mm⁻¹)	5.70
Crystal size (mm)	0.44 × 0.38 × 0.28

Data collection
Diffractometer	Rigaku Oxford Diffraction Xcalibur, Ruby
Absorption correction	Multi-scan (CrysAlis PRO; Rigaku OD, 2018 $[Rigaku OD (2018). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ )
T_min, T_max	0.083, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	11239, 2582, 2244
R_int	0.052
(sin θ/λ)_max (Å⁻¹)	0.630

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.040, 0.118, 1.07
No. of reflections	2582
No. of parameters	165
No. of restraints	2
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.47, −0.44
Computer programs: CrysAlis PRO (Rigaku OD, 2018 $[Rigaku OD (2018). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ ), SHELXL (Sheldrick, 2015 ) and OLEX2 (Dolomanov et al., 2009 ).

Supporting information

CCDC reference: 1941461

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989019010272/cq2032sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989019010272/cq2032Isup2.hkl

checkCIF report

Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2018); cell refinement: CrysAlis PRO (Rigaku OD, 2018); data reduction: CrysAlis PRO (Rigaku OD, 2018); program(s) used to refine structure: SHELXL (Sheldrick, 2015); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

Tetra-µ-acetato-bis[(5-amino-2-methylsulfanyl-1,3,4-thiadiazole-κN¹)copper(II)] top

Crystal data top

[Cu₂(C₂H₃O₂)₄(C₃H₅N₃S₂)₂]	Z = 1
M_r = 657.69	F(000) = 334
Triclinic, P1	D_x = 1.750 Mg m⁻³
a = 8.1069 (4) Å	Cu Kα radiation, λ = 1.54184 Å
b = 8.8955 (4) Å	Cell parameters from 5762 reflections
c = 9.0421 (5) Å	θ = 5.0–75.8°
α = 100.656 (4)°	µ = 5.70 mm⁻¹
β = 98.966 (4)°	T = 571 K
γ = 97.643 (4)°	Block, blue
V = 624.14 (5) Å³	0.44 × 0.38 × 0.28 mm

Data collection top

Rigaku Oxford Diffraction Xcalibur, Ruby diffractometer	2582 independent reflections
Radiation source: fine-focus sealed X-ray tube, Enhance (Cu) X-ray Source	2244 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.052
Detector resolution: 10.2576 pixels mm^-1	θ_max = 76.2°, θ_min = 5.1°
ω scans	h = −10→10
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2018)	k = −11→11
T_min = 0.083, T_max = 1.000	l = −10→11
11239 measured reflections

Refinement top

Refinement on F²	2 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.040	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.118	w = 1/[σ²(F_o²) + (0.0726P)² + 0.1915P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max = 0.001
2582 reflections	Δρ_max = 0.47 e Å⁻³
165 parameters	Δρ_min = −0.44 e Å⁻³

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Cu1	0.94133 (5)	0.41682 (4)	0.59528 (5)	0.03080 (16)
S1	0.77895 (10)	0.21114 (9)	1.00281 (9)	0.0416 (2)
S2	0.42143 (12)	0.08505 (14)	0.83586 (12)	0.0659 (3)
O4	1.0956 (3)	0.3780 (2)	0.2926 (2)	0.0403 (5)
O2	0.8200 (3)	0.5370 (3)	0.2953 (3)	0.0409 (5)
O1	0.7249 (3)	0.3994 (3)	0.4563 (3)	0.0458 (5)
O3	1.0032 (3)	0.2430 (2)	0.4575 (3)	0.0438 (5)
N3	1.0840 (4)	0.3406 (3)	0.9585 (3)	0.0442 (6)
N2	0.8489 (3)	0.2883 (3)	0.7575 (3)	0.0354 (5)
N1	0.6790 (3)	0.2193 (3)	0.7215 (3)	0.0385 (6)
C1	0.9196 (4)	0.2903 (3)	0.8988 (3)	0.0327 (6)
C6	1.0679 (4)	0.2556 (3)	0.3428 (3)	0.0363 (6)
C4	0.7032 (4)	0.4586 (3)	0.3410 (4)	0.0367 (6)
C2	0.6271 (4)	0.1756 (3)	0.8362 (4)	0.0383 (6)
C7	1.1194 (5)	0.1119 (4)	0.2574 (5)	0.0567 (9)
H7A	1.106850	0.114281	0.150585	0.085*
H7B	1.048657	0.021473	0.270116	0.085*
H7C	1.235495	0.108716	0.297339	0.085*
C5	0.5263 (4)	0.4374 (5)	0.2518 (5)	0.0565 (9)
H5A	0.459075	0.495634	0.311649	0.085*
H5B	0.477358	0.329410	0.228270	0.085*
H5C	0.529261	0.473477	0.158389	0.085*
C3	0.3241 (6)	0.0719 (6)	0.6412 (5)	0.0740 (13)
H3C	0.373741	0.001172	0.574724	0.111*
H3D	0.341504	0.172515	0.616365	0.111*
H3E	0.204871	0.034989	0.627943	0.111*
H3A	1.119 (5)	0.357 (4)	1.0554 (14)	0.048 (10)*
H3B	1.149 (5)	0.377 (5)	0.903 (5)	0.070 (13)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cu1	0.0315 (2)	0.0301 (2)	0.0309 (3)	0.00161 (15)	0.00874 (17)	0.00645 (16)
S1	0.0421 (4)	0.0494 (4)	0.0336 (4)	−0.0010 (3)	0.0112 (3)	0.0114 (3)
S2	0.0408 (5)	0.0941 (7)	0.0623 (6)	−0.0141 (5)	0.0082 (4)	0.0347 (6)
O4	0.0516 (13)	0.0353 (10)	0.0367 (12)	0.0105 (9)	0.0164 (10)	0.0054 (9)
O2	0.0312 (10)	0.0497 (11)	0.0409 (12)	0.0015 (9)	0.0043 (9)	0.0130 (10)
O1	0.0333 (11)	0.0572 (13)	0.0450 (13)	−0.0018 (9)	0.0039 (9)	0.0154 (11)
O3	0.0599 (14)	0.0309 (9)	0.0423 (13)	0.0072 (9)	0.0171 (11)	0.0056 (9)
N3	0.0374 (14)	0.0580 (16)	0.0353 (16)	−0.0021 (11)	0.0051 (12)	0.0132 (13)
N2	0.0371 (13)	0.0357 (11)	0.0334 (13)	−0.0002 (9)	0.0077 (10)	0.0106 (10)
N1	0.0375 (13)	0.0409 (12)	0.0373 (14)	−0.0007 (10)	0.0072 (11)	0.0138 (10)
C1	0.0377 (14)	0.0286 (11)	0.0339 (15)	0.0037 (10)	0.0127 (12)	0.0081 (11)
C6	0.0389 (15)	0.0318 (13)	0.0352 (16)	0.0085 (11)	0.0027 (12)	0.0006 (11)
C4	0.0294 (13)	0.0399 (14)	0.0369 (17)	0.0024 (11)	0.0060 (12)	0.0004 (12)
C2	0.0365 (15)	0.0382 (14)	0.0408 (17)	0.0001 (11)	0.0084 (13)	0.0130 (12)
C7	0.077 (3)	0.0424 (17)	0.056 (2)	0.0278 (17)	0.0212 (19)	0.0030 (15)
C5	0.0329 (16)	0.075 (2)	0.059 (2)	0.0039 (15)	0.0028 (16)	0.0144 (19)
C3	0.053 (2)	0.093 (3)	0.067 (3)	−0.015 (2)	−0.004 (2)	0.024 (2)

Geometric parameters (Å, º) top

Cu1—Cu1ⁱ	2.6728 (8)	N3—H3B	0.856 (10)
Cu1—O4ⁱ	2.0007 (19)	N2—N1	1.394 (3)
Cu1—O2ⁱ	1.983 (2)	N2—C1	1.313 (4)
Cu1—O1	1.962 (2)	N1—C2	1.282 (4)
Cu1—O3	1.970 (2)	C6—C7	1.510 (4)
Cu1—N2	2.180 (2)	C4—C5	1.502 (4)
S1—C1	1.745 (3)	C7—H7A	0.9600
S1—C2	1.740 (3)	C7—H7B	0.9600
S2—C2	1.752 (3)	C7—H7C	0.9600
S2—C3	1.789 (5)	C5—H5A	0.9600
O4—C6	1.262 (4)	C5—H5B	0.9600
O2—C4	1.267 (4)	C5—H5C	0.9600
O1—C4	1.251 (4)	C3—H3C	0.9600
O3—C6	1.249 (4)	C3—H3D	0.9600
N3—C1	1.339 (4)	C3—H3E	0.9600
N3—H3A	0.857 (10)

O4ⁱ—Cu1—Cu1ⁱ	83.88 (6)	N2—C1—S1	113.1 (2)
O4ⁱ—Cu1—N2	94.39 (9)	N2—C1—N3	124.8 (3)
O2ⁱ—Cu1—Cu1ⁱ	84.10 (7)	O4—C6—C7	117.0 (3)
O2ⁱ—Cu1—O4ⁱ	89.30 (9)	O3—C6—O4	125.8 (3)
O2ⁱ—Cu1—N2	94.80 (9)	O3—C6—C7	117.2 (3)
O1—Cu1—Cu1ⁱ	82.97 (7)	O2—C4—C5	117.6 (3)
O1—Cu1—O4ⁱ	89.12 (10)	O1—C4—O2	124.5 (3)
O1—Cu1—O2ⁱ	167.07 (9)	O1—C4—C5	117.8 (3)
O1—Cu1—O3	90.92 (10)	S1—C2—S2	119.34 (18)
O1—Cu1—N2	98.11 (10)	N1—C2—S1	115.2 (2)
O3—Cu1—Cu1ⁱ	83.44 (7)	N1—C2—S2	125.5 (3)
O3—Cu1—O4ⁱ	167.22 (9)	C6—C7—H7A	109.5
O3—Cu1—O2ⁱ	87.81 (10)	C6—C7—H7B	109.5
O3—Cu1—N2	98.26 (9)	C6—C7—H7C	109.5
N2—Cu1—Cu1ⁱ	177.95 (7)	H7A—C7—H7B	109.5
C2—S1—C1	86.58 (14)	H7A—C7—H7C	109.5
C2—S2—C3	100.75 (18)	H7B—C7—H7C	109.5
C6—O4—Cu1ⁱ	122.12 (19)	C4—C5—H5A	109.5
C4—O2—Cu1ⁱ	122.8 (2)	C4—C5—H5B	109.5
C4—O1—Cu1	125.6 (2)	C4—C5—H5C	109.5
C6—O3—Cu1	124.56 (19)	H5A—C5—H5B	109.5
C1—N3—H3A	121 (3)	H5A—C5—H5C	109.5
C1—N3—H3B	119 (3)	H5B—C5—H5C	109.5
H3A—N3—H3B	119 (4)	S2—C3—H3C	109.5
N1—N2—Cu1	116.61 (18)	S2—C3—H3D	109.5
C1—N2—Cu1	128.89 (19)	S2—C3—H3E	109.5
C1—N2—N1	113.1 (2)	H3C—C3—H3D	109.5
C2—N1—N2	112.1 (3)	H3C—C3—H3E	109.5
N3—C1—S1	122.1 (2)	H3D—C3—H3E	109.5

Symmetry code: (i) −x+2, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the S1/N1/N2/C1/C2 ring.

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···O4ⁱⁱ	0.86 (1)	2.16 (2)	2.963 (4)	156 (4)
N3—H3B···O2ⁱ	0.86 (1)	2.11 (3)	2.884 (4)	150 (4)
C7—H7B···Cgⁱⁱⁱ	0.96	3.00	3.346 (4)	103

Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) x, y, z+1; (iii) −x+2, −y, −z+1.

Funding information

This work was supported by a Grant for Fundamental Research of the Center of Science and Technology, Uzbekistan (No. BA-FA– F7–004).

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