research communications
Synthesis, κO}cobalt(II)
Hirshfeld surface analysis and DFT calculations of the coordination compound tetraaquabis{2-[(5-methyl-1,3,4-thiadiazol-2-yl)sulfanyl]acetato-aNational University of Uzbekistan named after Mirzo Ulugbek, 4 University St, Tashkent, 100174, Uzbekistan, bPhysical and Material Chemistry Division, CSIR-National Chemical Laboratory, Pune, 411008, India, cAcademy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India, and dInstitute of Bioorganic Chemistry, Academy of Sciences of Uzbekistan, M. Ulugbek St, 83, Tashkent, 100125, Uzbekistan
*Correspondence e-mail: torambetov_b@mail.ru
A novel coordination compound, [Co(L)2(H2O)4], was synthesized from aqueous solutions of Co(NO3)2 and the ligand 2-[(5-methyl-1,3,4-thiadiazol-2-yl)sulfanyl]acetic acid (HL, C5H6N2O2S2). In the monoclinic crystals (space group P21/c), the cobalt(II) ion is located about a centre of symmetry and is octahedrally coordinated by two L− anions in a monodentate fashion through carboxyl O atoms and by four water molecules. A relatively strong hydrogen bond between one of the water molecules and the non-coordinating carboxylate O atom consolidates the conformation. In the crystal, intermolecular hydrogen bonds lead to the formation of a complex tri-periodic structure. Hirshfeld surface analysis revealed that 30.1% of the intermolecular interactions are from H⋯H contacts and 20.8% are from N⋯H/H⋯N contacts. DFT calculations were performed to assess the stability and chemical reactivity of the compound by determining the energy differences between the HOMO and LUMO.
Keywords: crystal structure; cobalt(II); 1,3,4-thiadiazole; hydrogen bonding; Hirshfeld surface analysis; DFT calculation.
CCDC reference: 2408680
1. Chemical context
1,3,4-Thiadiazole derivatives are versatile compounds with significant applications in various fields, notably as ligands in the formation of metal complexes (Frija et al., 2016). Their ability to coordinate metal ions through multiple donor atoms allows for the creation of stable and diverse complexes (Atashov et al., 2024; Lavrenova et al., 2023; Serbest et al., 2008), which can be tailored for specific applications in medicine (Masaryk et al., 2022; Patil et al., 2020; Karcz et al., 2020), agriculture (Smaili et al., 2017; Chandra et al., 2015) or materials science (Bawazeer et al., 2020; Karasmani et al., 2018; Wang et al., 2012).
[(5-Methyl-1,3,4-thiadiazol-2-yl)sulfanyl]acetic acid (HL) is a derivative of 5-methyl-1,3,4-thiadiazole-2-thiol by S-alkylation. It is a sulfur-containing carboxylic acid, which is widely used due to its unique properties. It is a non-toxic and water-soluble compound in which the substituent is located in the form of a pharmacophore, which can lead to higher reactivity and biological activity through complexation. In this context, we report here on the title coordination compound [Co(L)2(H2O)4].
2. Structural commentary
The molecular structure of [Co(L)2(H2O)4] is shown in Fig. 1. The comprises half a molecule of the complex, with the CoII atom located about a centre of symmetry. The CoII atom exhibits a slightly distorted octahedral coordination environment formed by carboxylate and water O atoms. The carboxylate group coordinates monodentately through O1, O1i together with water O atoms O4 and O4i in the equatorial plane [symmetry code: (i) –x + 1, –y + 1, –z + 1], whereas the two water O atoms O3 and O3i are in axial positions. The corresponding distances are listed in Table 1. The cis-bond angles in the vary from 84.80 (8) to 95.20 (8)°. Bond lengths and angles of the 5-methyl-1,3,4-thiadiazole-2-thiolate ligand are similar to the standard values observed in similar structures (see section 6). The positions of the ligands allow for the formation of one rather strong hydrogen bond between a water molecule (O3—H3B) and the non-coordinating carboxylate O4 atom (Table 2), which is shorter than the stated distance (2.85 Å) in liquid water (Eisenberg & Kauzmann, 2005). This hydrogen bond leads to a six-membered ring motif with designation S(6) (Etter, 1990; Etter et al., 1990; Grabowski, 2020). Moreover, crystal-packing effects result in the C4—H4C⋯S distances (Table 2) being smaller than the sum of the van der Waals radii, and the existing short intramolecular contacts can be considered from a geometrical and topological point of view as a weak hydrogen bond contributing to the overall cohesion of the molecular conformation (Fargher et al., 2022; Domagała et al., 2003; Surange et al., 1997).
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3. Supramolecular features and energy framework calculations
In the L)2(H2O)4], further hydrogen bonds are observed (Table 2). Neighboring cobalt complexes are connected parallel to the a axis by O4—H4B⋯O1i and O4i—H4Bi ⋯O1 interactions; the corresponding Co1⋯Co1i distance is 5.195 Å (Fig. 2a). Neighboring central atoms are located at distances of 10.035 (1) and 18.909 (1) Å, respectively, along the b- and c-axis directions, and cohesion in the crystal is achieved due to the O3—H3A⋯N1 and O4—H4A⋯N2 hydrogen bonds (Fig. 2b).
of [Co(The interaction energies of the hydrogen-bonding system were calculated using the HF method (HF/3-21G) in CrystalExplorer (Spackman et al., 2021). The result is represented graphically in Fig. 3, showing the total energy (Etot), which is the sum of the Coulombic (Eele), polar (Epol), dispersion (Edis) and repulsive (Erep) contributions. The four energy components were scaled for the total energy calculation (Etot = 1.019Eele + 0.651Epol + 0.901Edis + 0.811Erep). The interaction energies were investigated for a 3.8 Å cluster around the reference molecule and are depicted in Fig. 4a as framework energy diagrams. The components of the interaction energies (E), symmetry operations concerning the reference molecule (Symop), the centroid-to-centroid distances between the reference molecule and interacting molecules (R), and the number of pair(s) of interacting molecules to the reference molecule (N) are listed in Fig. 4b. The total interaction energy is −274.5 kJ mol−1, involving the electrostatic (–257.2 kJ mol−1), polarization (–74.6 kJ mol−1), dispersion (–129.3 kJ mol−1), and repulsion (186.6 kJ mol−1) energies. The main attractive interactions (Coulombic, dispersion and the sum total energy) show a stronger bonding effect along the crystallographic a-axis direction.
4. Hirshfeld surface analysis
To further investigate the intermolecular interactions present in the title compound, a Hirshfeld surface (HS) analysis was performed, and the two-dimensional fingerprint plots were generated with CrystalExplorer (Spackman et al., 2021). Fig. 5 shows the three-dimensional Hirshfeld surface of the complex plotted over dnorm (normalized contact distance). The hydrogen-bonding interactions given in Table 2 play a key role in the molecular packing of the complex.
The overall two-dimensional fingerprint plot and those delineated into interatomic interactions are given in Fig. 5. The HS analysis shows that the most important contributions are from H⋯H, N⋯H/H⋯N, O⋯H/H⋯O and S⋯H/H⋯S contacts, while other contributions (C⋯H/H⋯C, S⋯O/O⋯S, S⋯C/C⋯S and S⋯N/N⋯S) are considered as minor contacts. The percentage contributions of the various interatomic contacts occurring in the crystal are also shown in Fig. 5.
5. Density functional theory (DFT) calculations
The molecular structure of the complex was optimized in the gas phase by the B3LYP (Lee et al., 1988) DFT method using the LanL2dz basis set (Grimme, 2006) for the Co atom and 6-311G (d,p) basis set (de Castro & Jorge, 1998) for non-metal atoms. Calculations were conducted using the Gaussian09 program (Frisch et al., 2009) to evaluate the stability of the compound and its chemical reactivity by determining the HOMO–LUMO (highest occupied molecular orbital - lowest unoccupied molecular orbital) energy differences, the (I), the affinity electronics (A), the index (ω), the (μ), the hardness (η) and the softness (S). The optimized potential surface molecular electrostatic potential (MEP) was also determined to characterize the effects of various substituent groups. Additionally, an analysis was performed to identify regions of electron richness and deficiency.
It is well known that for a closed-shell molecule (all electrons are paired) the HOMO–LUMO energy gap is related to its stability. The same argument is used for open-shell systems (unrestricted calculation). In this case, it is taken into account that the energies of both α- and β-spin orbitals designate the orbital with the highest energy as SOMO (singly occupied molecular orbital). Similarly, the LUMO is defined among both α and β, and the corresponding gap is considered as the SOMO–LUMO gap (Abella et al., 2021). Fig. 6 shows the SOMO and LUMO of the title cobalt complex, as well as the DOS (density of states) spectrum displaying the group contributions to the molecular orbitals and the calculation of the (Gauss-Sum 3.0). The DOS spectra were obtained by combining the molecular orbital information with the extraction from Gaussian (O'boyle et al., 2008). The descriptors of the reactivity of the complex derived from the electronic properties of the specified molecule (Padmanabhan et al., 2007; Hekim & Pekdemir, 2022) based on the energies of the HOMO (SOMO) and LUMO orbitals, are shown in Table 3.
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The electrophilic and nucleophilic nature of the interactions, as well as hydrogen bonds, can be explained using the molecular electrostatic potential (MEP), which is related to the electron density. The total electron density surface and the surface of the contour in the form of two-dimensional surface curves of the title complex is given in Fig. 7, which has color codes from red to blue, representing negative to positive potential distributions. The optimum electrophilic reaction zones are localized on N atoms, the maximum positive regions that determine nucleophilic reactions are concentrated at the hydrogen atoms of the water molecules. These locations provide insight into the regions of the molecule that engage in non-covalent interactions.
6. Database survey
A survey of the Cambridge Structural Database (CSD, Version 5.45, last updated March 2024; Groom et al., 2016) indicates that crystal structures have been reported for complexes of 2-methyl-1,3,4-thiadiazole derivatives with several metal ions, including Co, Ni, Cu, Zn, Ru, Ag, Pd, Cd, Sn, Pr, Nd, Pt, Hg, and Bi. Notably, there are ten reported metal complex structures featuring 2-[(5-methyl-1,3,4-thiadiazol-2-yl)thio]acetate (denoted as L), specifically: DEKGAE, DEKGEI (Pan & Zheng, 2017); ICOVED, ICOVIH (Pan, 2011); QAFRAS, QAFREW (Pan et al., 2010) and UNENAD, UNENEH, UNENIL, UNENOR (Ma et al., 2010). In these structures, L coordinates to the metal ions through the oxygen atom of the carboxylic group. Notably, in the UNENEH structure, L does not directly coordinate to the CoII cation. It is interesting to note that the title compound differs from the UNENAD structure by the absence of one water molecule.
7. Synthesis and crystallization
A solution of Co(NO3)2·6H2O (0.291 g, 0.1 mmol) in C2H5OH (3 ml) was added to a solution of HL (0.38 g, 0.2 mmol) in C2H5OH/H2O (5 ml, 1:1), the pH of which was adjusted to 7.0 with dilute sodium hydroxide (1 mol/l). The mixture was stirred at room temperature for 5 h to obtain a clear solution, which was then filtered. Slow evaporation of the filtrate after two weeks gave pink single crystals in the form of blocks suitable for X-ray diffraction. Yield: 0.367 g (72%).
8. Refinement
Crystal data, data collection and structure . All hydrogen atoms were located in difference-Fourier maps and refined using an isotropic approximation. The water hydrogen atoms were constrained to an ideal geometry with distances fixed at 0.87 (4) Å and Uiso(H) = 1.5Ueq(O). Two reflections ( 10 9; 11 11) were omitted from the refinement..
details are summarized in Table 4Supporting information
CCDC reference: 2408680
https://doi.org/10.1107/S2056989024011939/wm5739sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989024011939/wm5739Isup3.hkl
[Co(C5H5N2O2S2)2(H2O)4] | F(000) = 522 |
Mr = 509.45 | Dx = 1.717 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54184 Å |
a = 5.1950 (2) Å | Cell parameters from 2568 reflections |
b = 10.0347 (3) Å | θ = 4.4–74.9° |
c = 18.9090 (6) Å | µ = 11.23 mm−1 |
β = 91.892 (3)° | T = 293 K |
V = 985.19 (6) Å3 | Block, pink |
Z = 2 | 0.08 × 0.06 × 0.04 mm |
Xcalibur, Ruby diffractometer | 2023 independent reflections |
Radiation source: fine-focus sealed X-ray tube, Enhance (Cu) X-ray Source | 1770 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.055 |
Detector resolution: 10.2576 pixels mm-1 | θmax = 76.1°, θmin = 4.7° |
ω scans | h = −6→5 |
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2021) | k = −12→7 |
Tmin = 0.808, Tmax = 1.000 | l = −22→23 |
6554 measured reflections |
Refinement on F2 | Hydrogen site location: mixed |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.038 | w = 1/[σ2(Fo2) + (0.0423P)2 + 0.2531P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.098 | (Δ/σ)max < 0.001 |
S = 1.06 | Δρmax = 0.34 e Å−3 |
2023 reflections | Δρmin = −0.27 e Å−3 |
137 parameters | Extinction correction: SHELXL (Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
1 restraint | Extinction coefficient: 0.0100 (6) |
Primary atom site location: dual |
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. |
x | y | z | Uiso*/Ueq | ||
Co1 | 0.500000 | 0.500000 | 0.500000 | 0.0225 (2) | |
S2 | 0.93444 (16) | 0.67263 (8) | 0.23436 (4) | 0.0363 (2) | |
S1 | 0.51630 (16) | 0.46582 (8) | 0.19232 (4) | 0.0352 (2) | |
O1 | 0.7298 (4) | 0.4971 (2) | 0.41151 (11) | 0.0301 (5) | |
O3 | 0.3120 (5) | 0.6845 (2) | 0.47316 (12) | 0.0319 (5) | |
O2 | 0.5470 (5) | 0.6628 (2) | 0.34843 (12) | 0.0381 (5) | |
O4 | 0.7849 (4) | 0.5994 (2) | 0.55445 (14) | 0.0403 (6) | |
H4A | 0.754101 | 0.661162 | 0.583781 | 0.060* | |
H4B | 0.939850 | 0.576984 | 0.564102 | 0.060* | |
N2 | 0.6147 (6) | 0.6755 (3) | 0.12306 (16) | 0.0439 (7) | |
N1 | 0.4211 (7) | 0.6115 (3) | 0.08461 (16) | 0.0466 (7) | |
C5 | 0.7135 (6) | 0.5770 (3) | 0.35950 (15) | 0.0261 (6) | |
C4 | 0.9347 (6) | 0.5598 (3) | 0.30843 (16) | 0.0308 (6) | |
H4C | 0.929270 | 0.469381 | 0.290307 | 0.037* | |
H4D | 1.096227 | 0.570265 | 0.335059 | 0.037* | |
C2 | 0.6821 (6) | 0.6126 (3) | 0.18058 (16) | 0.0314 (6) | |
C1 | 0.3501 (7) | 0.5011 (3) | 0.11352 (17) | 0.0350 (7) | |
C3 | 0.1401 (8) | 0.4148 (4) | 0.0839 (2) | 0.0464 (8) | |
H3C | 0.208492 | 0.355386 | 0.049477 | 0.070* | |
H3D | 0.008604 | 0.469362 | 0.061893 | 0.070* | |
H3E | 0.067607 | 0.363860 | 0.121388 | 0.070* | |
H3A | 0.311 (9) | 0.750 (5) | 0.501 (2) | 0.061 (14)* | |
H3B | 0.383 (9) | 0.707 (5) | 0.4341 (17) | 0.070 (15)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Co1 | 0.0219 (3) | 0.0233 (3) | 0.0222 (3) | 0.0038 (2) | −0.0007 (2) | −0.0002 (2) |
S2 | 0.0405 (5) | 0.0368 (4) | 0.0316 (4) | −0.0094 (3) | 0.0025 (3) | 0.0057 (3) |
S1 | 0.0430 (5) | 0.0323 (4) | 0.0301 (4) | −0.0059 (3) | −0.0032 (3) | 0.0096 (3) |
O1 | 0.0298 (11) | 0.0348 (11) | 0.0259 (10) | 0.0063 (8) | 0.0038 (8) | 0.0037 (8) |
O3 | 0.0374 (13) | 0.0277 (10) | 0.0304 (11) | 0.0073 (9) | −0.0013 (9) | −0.0001 (8) |
O2 | 0.0392 (13) | 0.0426 (12) | 0.0326 (11) | 0.0156 (10) | 0.0032 (10) | 0.0060 (9) |
O4 | 0.0248 (11) | 0.0418 (13) | 0.0534 (15) | 0.0074 (9) | −0.0121 (10) | −0.0217 (10) |
N2 | 0.0510 (18) | 0.0427 (16) | 0.0375 (15) | −0.0075 (13) | −0.0077 (13) | 0.0156 (12) |
N1 | 0.0571 (19) | 0.0473 (17) | 0.0348 (15) | −0.0039 (14) | −0.0077 (14) | 0.0123 (13) |
C5 | 0.0263 (14) | 0.0275 (13) | 0.0242 (13) | −0.0011 (11) | −0.0008 (11) | −0.0012 (10) |
C4 | 0.0299 (15) | 0.0350 (15) | 0.0276 (14) | 0.0044 (12) | 0.0018 (11) | 0.0022 (11) |
C2 | 0.0373 (17) | 0.0302 (14) | 0.0270 (14) | 0.0016 (12) | 0.0036 (12) | 0.0062 (11) |
C1 | 0.0422 (19) | 0.0347 (16) | 0.0281 (15) | 0.0056 (13) | 0.0010 (13) | 0.0047 (11) |
C3 | 0.048 (2) | 0.0464 (19) | 0.0437 (19) | −0.0003 (16) | −0.0115 (16) | 0.0015 (15) |
Co1—O1i | 2.088 (2) | O2—C5 | 1.233 (4) |
Co1—O1 | 2.088 (2) | O4—H4A | 0.8501 |
Co1—O3 | 2.146 (2) | O4—H4B | 0.8500 |
Co1—O3i | 2.146 (2) | N2—N1 | 1.380 (4) |
Co1—O4 | 2.036 (2) | N2—C2 | 1.296 (4) |
Co1—O4i | 2.036 (2) | N1—C1 | 1.295 (4) |
S2—C4 | 1.801 (3) | C5—C4 | 1.535 (4) |
S2—C2 | 1.740 (3) | C4—H4C | 0.9700 |
S1—C2 | 1.724 (3) | C4—H4D | 0.9700 |
S1—C1 | 1.734 (3) | C1—C3 | 1.488 (5) |
O1—C5 | 1.270 (3) | C3—H3C | 0.9600 |
O3—H3A | 0.84 (5) | C3—H3D | 0.9600 |
O3—H3B | 0.868 (19) | C3—H3E | 0.9600 |
O1i—Co1—O1 | 180.0 | C2—N2—N1 | 112.8 (3) |
O1—Co1—O3 | 95.20 (8) | C1—N1—N2 | 112.9 (3) |
O1i—Co1—O3i | 95.20 (8) | O1—C5—C4 | 112.6 (2) |
O1—Co1—O3i | 84.80 (8) | O2—C5—O1 | 127.0 (3) |
O1i—Co1—O3 | 84.80 (8) | O2—C5—C4 | 120.5 (3) |
O3—Co1—O3i | 180.0 | S2—C4—H4C | 108.3 |
O4—Co1—O1i | 90.76 (10) | S2—C4—H4D | 108.3 |
O4i—Co1—O1 | 90.76 (10) | C5—C4—S2 | 115.9 (2) |
O4i—Co1—O1i | 89.24 (10) | C5—C4—H4C | 108.3 |
O4—Co1—O1 | 89.24 (10) | C5—C4—H4D | 108.3 |
O4—Co1—O3 | 90.83 (9) | H4C—C4—H4D | 107.4 |
O4—Co1—O3i | 89.17 (9) | S1—C2—S2 | 126.18 (18) |
O4i—Co1—O3 | 89.17 (9) | N2—C2—S2 | 120.0 (2) |
O4i—Co1—O3i | 90.83 (9) | N2—C2—S1 | 113.7 (3) |
O4—Co1—O4i | 180.00 (11) | N1—C1—S1 | 113.4 (3) |
C2—S2—C4 | 102.60 (15) | N1—C1—C3 | 123.7 (3) |
C2—S1—C1 | 87.22 (15) | C3—C1—S1 | 122.8 (2) |
C5—O1—Co1 | 125.90 (19) | C1—C3—H3C | 109.5 |
Co1—O3—H3A | 123 (3) | C1—C3—H3D | 109.5 |
Co1—O3—H3B | 103 (3) | C1—C3—H3E | 109.5 |
H3A—O3—H3B | 109 (4) | H3C—C3—H3D | 109.5 |
Co1—O4—H4A | 122.5 | H3C—C3—H3E | 109.5 |
Co1—O4—H4B | 130.3 | H3D—C3—H3E | 109.5 |
H4A—O4—H4B | 104.5 | ||
Co1—O1—C5—O2 | −6.9 (4) | C4—S2—C2—S1 | −8.8 (3) |
Co1—O1—C5—C4 | 171.97 (18) | C4—S2—C2—N2 | 176.0 (3) |
O1—C5—C4—S2 | −178.0 (2) | C2—S2—C4—C5 | −73.2 (2) |
O2—C5—C4—S2 | 0.9 (4) | C2—S1—C1—N1 | 0.1 (3) |
N2—N1—C1—S1 | 0.4 (4) | C2—S1—C1—C3 | −177.7 (3) |
N2—N1—C1—C3 | 178.3 (3) | C2—N2—N1—C1 | −1.0 (5) |
N1—N2—C2—S2 | 176.8 (2) | C1—S1—C2—S2 | −176.1 (2) |
N1—N2—C2—S1 | 1.1 (4) | C1—S1—C2—N2 | −0.7 (3) |
Symmetry code: (i) −x+1, −y+1, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3B···O2 | 0.87 (2) | 1.91 (3) | 2.700 (3) | 151 (5) |
C4—H4C···S1 | 0.97 | 2.79 | 3.181 (3) | 105 |
O4—H4A···N2ii | 0.85 | 1.95 | 2.764 (4) | 160 |
O4—H4B···O1iii | 0.85 | 1.91 | 2.757 (3) | 172 |
O3—H3A···N1ii | 0.84 (5) | 2.17 (5) | 2.979 (4) | 162 (5) |
Symmetry codes: (ii) x, −y+3/2, z+1/2; (iii) −x+2, −y+1, −z+1. |
E SOMO (eV) | -6.64 |
E LUMO (eV) | -2.39 |
ΔE | 4.25 |
I | 6.64 |
A | 2.39 |
χ | 4.515 |
η | 2.125 |
µ | -4.515 |
S | 0.235 |
ω | 0.235 |
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