The molecular and crystal structure of a zinc coordination polymer with 5-phenyl-1,3,4-oxadiazole-2-thiolate were studied and Hirshfeld surfaces and fingerprint plots were generated to investigate various intermolecular interactions.
Keywords: crystal structure; zinc complex; 5-phenyl-1,3,4-oxadiazole-2-thiol; coordination polymer; Hirshfeld surface analysis
Abstract
A new zinc coordination polymer with 5-phenyl-1,3,4-oxadiazole-2-thiolate, namely, catena-poly[zinc(II)-bis(μ2-5-phenyl-1,3,4-oxadiazole-2-thiolato)-κ2 N 3:S;κ2 S:N 3], [Zn(C8H5N2OS)2] n , was synthesized. The single-crystal X-ray diffraction analysis shows that the polymeric structure crystallizes in the centrosymmetric monoclinic C2/c space group. The ZnII atom is coordinated to two S and two N atoms from four crystallographically independent (L) ligands, forming zigzag chains along the [001] direction. This polymer complex forms an eight-membered [Zn–S–C–N–Zn–S–C–N] chair-like ring with two ZnII atoms and two ligand molecules. On the Hirshfeld surface, the largest contributions come from the short contacts such as van der Waals forces, including H⋯H, C⋯H and S⋯H. Interactions including N⋯H, O⋯H and C⋯C contacts were also observed; however, their contribution to the overall stability of the crystal lattice is minor.
1. Chemical context
Among heterocyclic organic compounds, 1,3,4-oxadiazoles have become an important class of heterocycles because of their broad spectrum of biological activity (De Oliveira et al., 2012 ▸; Vaidya et al., 2020 ▸). Scientists have identified many properties of 1,3,4-oxadiazole derivatives, such as antimicrobial (Bala et al., 2014 ▸; Zachariah et al., 2015 ▸; Ahmed et al., 2017 ▸; Razzoqova et al., 2019 ▸ ), antituberculosis (Makane et al., 2019 ▸; Wang et al., 2022 ▸), anticancer (Alam, 2022 ▸; Vaidya et al., 2020 ▸; Zhang et al., 2005 ▸), anti-inflammatory (Abd-Ellah et al., 2017 ▸), analgesic (Husain & Ajmal, 2009 ▸), herbicidal (Sun et al., 2014 ▸; Duan et al., 2011 ▸) and antifungal (Zhang et al., 2013 ▸; Capoci et al., 2019 ▸) activities. Heterocyclic thiones are an important type of compound in coordination chemistry because of their potential multifunctional donor sites, namely either exocyclic sulfur or endocyclic nitrogen (Reddy et al., 2011 ▸; Wang et al., 2010 ▸). The presence of the 1,3,4-oxadiazole ring affects the physicochemical and pharmacokinetic properties of the entire compound. An exciting feature of these metal complexes is that they can be mononuclear (Singh et al., 2008 ▸; Ouilia et al., 2012 ▸), binuclear (Xiao et al., 2011 ▸; Wang et al., 2007 ▸) and/or polymeric (Beghidja et al., 2007 ▸).
Oxadiazole ligands are ideal objects for creating new coordination compounds with great potential in various fields. Scientists have written extensive literature on the biological properties of oxadiazole-based complex compounds, especially on their anticancer effects. In addition to these, in the field of electrical engineering, metal complexes bearing oxadiazole ligands have been used as emitting particles in light-emitting diodes. The introduction of various functionalized oxadiazole ligands makes it easy to control the emission color, thermal stability, and film-forming properties of such complexes (Salassa & Terenzi, 2019 ▸).
Herein, we report on the synthesis and crystal structure of a new polymeric complex, [ZnL 2] n , with L = 5-phenyl-1,3,4-oxadiazole-2-thiol.
2. Structural commentary
The single crystal X-ray structure of 5-phenyl-1,3,4-oxadiazole-2-thiolate ZnII shows a polymeric structure that crystallizes in the centrosymmetric monoclinic space group C2/c (Table 2 ▸). As seen in Fig. 1 ▸, its asymmetric unit contains half a zinc atom and one ligand anion. The central ZnII atom has a distorted tetrahedral environment comprising two sulfur and two nitrogen atoms. It is coordinated by four crystallographically independent (L) ligands, forming zigzag chains along the [001] direction, which are linked by two sulfur atoms and two nitrogen atoms of four ligands. The Zn1—S1 and Zn1—N1 bond lengths are 2.3370 (5) Å, 2.0184 (14) Å, respectively. In this case, the bond angles of the atom forming the tetrahedral polyhedron are slightly different from the angles of the ideal tetrahedron [N1—Zn1–N1 = 111.37 (9)°, S1—Zn1—S1 = 100.46 (3)° and N1—Zn1—S1 = 108.51 (4)°]. It is known from the literature (Razzoqova et al., 2019 ▸) that the sulfur atom in the 1,3,4-oxadiazole-2-thione molecule is attached to the ring by a double bond. In this polymer complex synthesized based on ZnII ion, the oxadiazole derivative transforms into the thiol tautomeric form and binds to the Zn ion. The N1 atom in the ligand molecule, on the other hand, forms a bond with another ZnII ion due to its high electron-donating property, resulting in an eight-membered [Zn–S–C–N–Zn–S–C–N] chair-like ring with two ZnII atoms and two ligand molecules (Fig. 2 ▸). The dihedral angle between the mean planes of the phenyl (C3–C8) and oxadiazole (C1/O1/C2/N2/N1) rings of the ligand molecule is 13.42 (8)°. The conformation of the oxadiazole-thiol fragment of the ligand is approximately planar (r.m.s. deviation 0.006 Å), with a maximum deviation from the least-squares plane of 0.009 (1) Å for atom O1. The dihedral angle between the planes of the two neighboring independent oxadiazole-thiol (C1/O1/C2/N2/N1/S1) fragments is 64.10 (9)°.
Table 2. Experimental details.
| Crystal data | |
| Chemical formula | [Zn(C8H5N2OS)2] |
| M r | 419.79 |
| Crystal system, space group | Monoclinic, C2/c |
| Temperature (K) | 293 |
| a, b, c (Å) | 20.4223 (3), 11.3260 (2), 7.4019 (1) |
| β (°) | 98.310 (1) |
| V (Å3) | 1694.11 (5) |
| Z | 4 |
| Radiation type | Cu Kα |
| μ (mm−1) | 4.48 |
| Crystal size (mm) | 0.60 × 0.14 × 0.08 |
| Data collection | |
| Diffractometer | XtaLAB Synergy, single source at home/near, HyPix3000 |
| Absorption correction | Multi-scan (CrysAlis PRO; Rigaku OD, 2020 ▸) |
| T min, T max | 0.099, 1.000 |
| No. of measured, independent and observed [I > 2σ(I)] reflections | 7033, 1634, 1536 |
| R int | 0.028 |
| (sin θ/λ)max (Å−1) | 0.615 |
| Refinement | |
| R[F 2 > 2σ(F 2)], wR(F 2), S | 0.026, 0.073, 1.09 |
| No. of reflections | 1634 |
| No. of parameters | 134 |
| H-atom treatment | All H-atom parameters refined |
| Δρmax, Δρmin (e Å−3) | 0.26, −0.33 |
Figure 1.
The molecular structure of [Zn0.5 L] with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are displayed as small spheres of arbitrary radii.
Figure 2.
The view of the molecular packing showing the polymeric chain extended along the c-axis.
3. Supramolecular features
The [(ZnL 2) n ] unit is given as a monomer of the polymeric chain that extends parallel to the c-axis. Along the polymeric chain, the hydrophilic groups are concentrated within the core of the chain while the phenyl rings project approximately normal to the chain. Neighboring chains across the ab plane are loosely connected via a rather weak C6—H6⋯S1 hydrogen bond (Table 1 ▸, Fig. 3 ▸).
Table 1. Hydrogen-bond geometry (Å, °).
| D—H⋯A | D—H | H⋯A | D⋯A | D—H⋯A |
|---|---|---|---|---|
| C6—H6⋯S1i | 1.00 (3) | 2.86 (3) | 3.608 (2) | 132 (2) |
Symmetry code: (i)
.
Figure 3.
Crystal packing of the polymeric chains in the [(ZnL 2) n ] structure. The projection is along the [001] direction. Hydrogen bonds are shown by cyan lines.
4. Hirshfeld surface analysis
To further investigate the intermolecular interactions present in the title compound, a Hirshfeld surface analysis was performed, and the two-dimensional fingerprint plots were generated with CrystalExplorer17 (Turner et al., 2017 ▸). The Hirshfeld surface mapped over d norm and corresponding colors representing various interactions are shown in Fig. 4 ▸. We chose the ZnL 2 molecular fragment as the monomer unit for calculating the Hirshfeld surface of this polymer complex.
Figure 4.
Hirshfeld surfaces mapped over d norm calculated for the monomer part of the polymer molecule.
The large red areas on the Hirshfeld surface correspond to the Zn⋯N interactions. The two-dimensional (2D) fingerprint plots (McKinnon et al., 2007 ▸) are shown in Fig. 5 ▸. On the Hirshfeld surface, the largest contributions (19.2%, 19.5% and 19%) come from short contacts such as van der Waals forces, H⋯H, C⋯H and S⋯H contacts. N⋯H (8.1%), O⋯H (8%) and C⋯C (4.7%) contacts are also observed. These interactions play a crucial role in the overall stabilization of the crystal packing.
Figure 5.
Contributions of the various contacts to the fingerprint plot built using the Hirshfeld surface of the title compound.
5. Database survey
A survey of the Cambridge Structural Database (CSD, version 5.43, update of November 2021; Groom et al., 2016 ▸) revealed that crystal structures had been reported for complexes of 1,3,4-oxadiazole derivatives and a number of metal ions, including zinc, copper, nickel, manganese, cadmium, cobalt and silver. No polymer complexes containing [M–S–C–N–M–S–C–N] eight-membered cyclization have been reported. The structures of complexes of Pt, Sn and Au based on 5-phenyl-1,3,4-oxadiazole-2-thiole with additional ligands have been deposited in the CSD (FATNIZ, Al-Jibori et al., 2012 ▸; HAXTAC, Ma et al., 2005 ▸; and YIVVEG, Chaves et al., 2014 ▸). However, no complexes containing only the zinc ion and 5-phenyl-1,3,4-oxadiazole-2-thiolate have been documented in the CSD.
6. Synthesis and crystallization
ZnCl2 (0.136 g, 0.001 mol) and 5-phenyl-1,3,4-oxadiazole-2-thiol (ligand) (0.354 g, 0.002 mol) were dissolved separately in ethanol (10 mL). To a solution of the ligand, an aqueous solution of KOH (0.112 g, 0.002 mol) was added. The obtained solutions were mixed together and stirred at 323 K for 20 min. A white precipitate was obtained. The precipitate was filtered and allowed to dry. The solid residue was dissolved in DMF to crystallize for the single crystal X-ray diffraction studies. X-ray quality single crystals were produced after 10 days by slow evaporation of the solution.
7. Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. All the hydrogen atoms were located in difference-Fourier maps and refined isotropically.
Supplementary Material
Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989022006922/dj2049sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989022006922/dj2049Isup2.hkl
CCDC reference: 2184492
Additional supporting information: crystallographic information; 3D view; checkCIF report
supplementary crystallographic information
Crystal data
| [Zn(C8H5N2OS)2] | F(000) = 848 |
| Mr = 419.79 | Dx = 1.646 Mg m−3 |
| Monoclinic, C2/c | Cu Kα radiation, λ = 1.54184 Å |
| a = 20.4223 (3) Å | Cell parameters from 5128 reflections |
| b = 11.3260 (2) Å | θ = 4.4–71.1° |
| c = 7.4019 (1) Å | µ = 4.48 mm−1 |
| β = 98.310 (1)° | T = 293 K |
| V = 1694.11 (5) Å3 | Block, colourless |
| Z = 4 | 0.60 × 0.14 × 0.08 mm |
Data collection
| XtaLAB Synergy, single source at home/near, HyPix3000 diffractometer | 1634 independent reflections |
| Radiation source: micro-focus sealed X-ray tube, PhotonJet (Cu) X-ray Source | 1536 reflections with I > 2σ(I) |
| Mirror monochromator | Rint = 0.028 |
| Detector resolution: 10.0000 pixels mm-1 | θmax = 71.5°, θmin = 4.4° |
| ω scans | h = −25→23 |
| Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2020) | k = −13→13 |
| Tmin = 0.099, Tmax = 1.000 | l = −9→8 |
| 7033 measured reflections |
Refinement
| Refinement on F2 | Primary atom site location: structure-invariant direct methods |
| Least-squares matrix: full | Hydrogen site location: difference Fourier map |
| R[F2 > 2σ(F2)] = 0.026 | All H-atom parameters refined |
| wR(F2) = 0.073 | w = 1/[σ2(Fo2) + (0.0425P)2 + 0.6399P] where P = (Fo2 + 2Fc2)/3 |
| S = 1.09 | (Δ/σ)max = 0.001 |
| 1634 reflections | Δρmax = 0.26 e Å−3 |
| 134 parameters | Δρmin = −0.33 e Å−3 |
| 0 restraints |
Special details
| 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)
| x | y | z | Uiso*/Ueq | ||
| Zn1 | 0.500000 | 0.42861 (3) | 0.750000 | 0.03700 (13) | |
| S1 | 0.52858 (2) | 0.70338 (4) | 0.49120 (6) | 0.04489 (15) | |
| O1 | 0.64980 (6) | 0.66497 (11) | 0.66937 (16) | 0.0378 (3) | |
| N1 | 0.57974 (7) | 0.52907 (14) | 0.7241 (2) | 0.0381 (3) | |
| N2 | 0.64167 (7) | 0.49941 (14) | 0.8226 (2) | 0.0402 (3) | |
| C2 | 0.68103 (8) | 0.58151 (15) | 0.7854 (2) | 0.0360 (4) | |
| C3 | 0.75171 (8) | 0.59280 (16) | 0.8505 (2) | 0.0370 (4) | |
| C1 | 0.58617 (8) | 0.62555 (15) | 0.6334 (2) | 0.0362 (4) | |
| C8 | 0.78515 (9) | 0.49670 (18) | 0.9351 (3) | 0.0442 (4) | |
| C4 | 0.78562 (10) | 0.69688 (18) | 0.8287 (3) | 0.0472 (4) | |
| C7 | 0.85194 (10) | 0.5044 (2) | 0.9992 (3) | 0.0572 (5) | |
| C5 | 0.85239 (11) | 0.7043 (2) | 0.8940 (3) | 0.0578 (5) | |
| C6 | 0.88524 (10) | 0.6091 (2) | 0.9798 (3) | 0.0613 (6) | |
| H8 | 0.7634 (11) | 0.4299 (18) | 0.946 (3) | 0.042 (6)* | |
| H5 | 0.8723 (13) | 0.772 (3) | 0.874 (3) | 0.068 (7)* | |
| H4 | 0.7642 (12) | 0.761 (2) | 0.771 (3) | 0.059 (7)* | |
| H7 | 0.8758 (14) | 0.443 (2) | 1.056 (4) | 0.074 (8)* | |
| H6 | 0.9339 (15) | 0.614 (3) | 1.020 (4) | 0.088 (9)* |
Atomic displacement parameters (Å2)
| U11 | U22 | U33 | U12 | U13 | U23 | |
| Zn1 | 0.02217 (18) | 0.0460 (2) | 0.0416 (2) | 0.000 | 0.00048 (13) | 0.000 |
| S1 | 0.0363 (3) | 0.0440 (3) | 0.0508 (3) | 0.00848 (17) | −0.00577 (19) | −0.00479 (18) |
| O1 | 0.0309 (6) | 0.0384 (6) | 0.0423 (6) | −0.0034 (5) | −0.0009 (5) | 0.0004 (5) |
| N1 | 0.0228 (7) | 0.0461 (8) | 0.0440 (8) | −0.0019 (6) | 0.0001 (6) | 0.0003 (6) |
| N2 | 0.0243 (7) | 0.0483 (8) | 0.0462 (8) | −0.0030 (6) | −0.0012 (6) | 0.0056 (6) |
| C2 | 0.0291 (8) | 0.0410 (9) | 0.0368 (8) | −0.0004 (6) | 0.0010 (7) | −0.0010 (6) |
| C3 | 0.0276 (8) | 0.0468 (9) | 0.0359 (8) | −0.0050 (7) | 0.0019 (6) | −0.0033 (7) |
| C1 | 0.0273 (8) | 0.0418 (9) | 0.0386 (8) | 0.0008 (7) | 0.0013 (6) | −0.0070 (7) |
| C8 | 0.0357 (9) | 0.0498 (11) | 0.0459 (9) | −0.0059 (8) | 0.0012 (7) | 0.0053 (8) |
| C4 | 0.0380 (10) | 0.0446 (10) | 0.0578 (11) | −0.0048 (8) | 0.0027 (8) | 0.0008 (9) |
| C7 | 0.0363 (10) | 0.0697 (14) | 0.0620 (12) | 0.0004 (10) | −0.0044 (9) | 0.0124 (11) |
| C5 | 0.0393 (11) | 0.0591 (13) | 0.0741 (14) | −0.0179 (9) | 0.0052 (10) | −0.0027 (11) |
| C6 | 0.0288 (10) | 0.0797 (15) | 0.0722 (14) | −0.0108 (10) | −0.0035 (9) | 0.0046 (12) |
Geometric parameters (Å, º)
| Zn1—S1i | 2.3370 (5) | C3—C8 | 1.385 (3) |
| Zn1—S1ii | 2.3370 (5) | C3—C4 | 1.388 (3) |
| Zn1—N1 | 2.0184 (14) | C8—C7 | 1.381 (3) |
| Zn1—N1iii | 2.0184 (14) | C8—H8 | 0.89 (2) |
| S1—C1 | 1.7059 (17) | C4—C5 | 1.382 (3) |
| O1—C2 | 1.371 (2) | C4—H4 | 0.92 (3) |
| O1—C1 | 1.3635 (19) | C7—C6 | 1.384 (3) |
| N1—N2 | 1.4062 (18) | C7—H7 | 0.92 (3) |
| N1—C1 | 1.299 (2) | C5—C6 | 1.376 (4) |
| N2—C2 | 1.285 (2) | C5—H5 | 0.89 (3) |
| C2—C3 | 1.460 (2) | C6—H6 | 1.00 (3) |
| S1i—Zn1—S1ii | 100.46 (3) | O1—C1—S1 | 120.26 (13) |
| N1—Zn1—S1ii | 108.51 (4) | N1—C1—S1 | 129.90 (13) |
| N1—Zn1—S1i | 113.82 (4) | N1—C1—O1 | 109.83 (14) |
| N1iii—Zn1—S1i | 108.50 (4) | C3—C8—H8 | 119.3 (14) |
| N1iii—Zn1—S1ii | 113.82 (5) | C7—C8—C3 | 120.24 (19) |
| N1—Zn1—N1iii | 111.37 (9) | C7—C8—H8 | 120.5 (14) |
| C1—S1—Zn1i | 102.39 (6) | C3—C4—H4 | 120.8 (16) |
| C1—O1—C2 | 103.92 (13) | C5—C4—C3 | 119.6 (2) |
| N2—N1—Zn1 | 119.57 (11) | C5—C4—H4 | 119.6 (16) |
| C1—N1—Zn1 | 131.80 (12) | C8—C7—C6 | 119.6 (2) |
| C1—N1—N2 | 108.57 (13) | C8—C7—H7 | 122.8 (17) |
| C2—N2—N1 | 105.05 (14) | C6—C7—H7 | 117.6 (17) |
| O1—C2—C3 | 119.65 (15) | C4—C5—H5 | 116.4 (17) |
| N2—C2—O1 | 112.61 (14) | C6—C5—C4 | 120.3 (2) |
| N2—C2—C3 | 127.75 (16) | C6—C5—H5 | 123.3 (17) |
| C8—C3—C2 | 118.67 (16) | C7—C6—H6 | 119.8 (18) |
| C8—C3—C4 | 119.85 (17) | C5—C6—C7 | 120.33 (19) |
| C4—C3—C2 | 121.48 (17) | C5—C6—H6 | 119.8 (18) |
| Zn1i—S1—C1—O1 | 116.48 (12) | C2—O1—C1—S1 | −179.75 (12) |
| Zn1i—S1—C1—N1 | −65.24 (17) | C2—O1—C1—N1 | 1.66 (18) |
| Zn1—N1—N2—C2 | −176.89 (12) | C2—C3—C8—C7 | −179.66 (19) |
| Zn1—N1—C1—S1 | −2.7 (3) | C2—C3—C4—C5 | 179.34 (19) |
| Zn1—N1—C1—O1 | 175.68 (11) | C3—C8—C7—C6 | 0.5 (3) |
| O1—C2—C3—C8 | −166.60 (16) | C3—C4—C5—C6 | 0.2 (3) |
| O1—C2—C3—C4 | 13.2 (3) | C1—O1—C2—N2 | −1.25 (19) |
| N1—N2—C2—O1 | 0.4 (2) | C1—O1—C2—C3 | 178.37 (15) |
| N1—N2—C2—C3 | −179.19 (17) | C1—N1—N2—C2 | 0.68 (19) |
| N2—N1—C1—S1 | −179.91 (13) | C8—C3—C4—C5 | −0.9 (3) |
| N2—N1—C1—O1 | −1.49 (19) | C8—C7—C6—C5 | −1.2 (4) |
| N2—C2—C3—C8 | 13.0 (3) | C4—C3—C8—C7 | 0.6 (3) |
| N2—C2—C3—C4 | −167.27 (19) | C4—C5—C6—C7 | 0.9 (4) |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x, −y+1, z+1/2; (iii) −x+1, y, −z+3/2.
Hydrogen-bond geometry (Å, º)
| D—H···A | D—H | H···A | D···A | D—H···A |
| C6—H6···S1iv | 1.00 (3) | 2.86 (3) | 3.608 (2) | 132 (2) |
Symmetry code: (iv) x+1/2, −y+3/2, z+1/2.
Funding Statement
This work was supported by Uzbekistan Ministry of Innovation Development.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989022006922/dj2049sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989022006922/dj2049Isup2.hkl
CCDC reference: 2184492
Additional supporting information: crystallographic information; 3D view; checkCIF report