research communications
Synthesis, catena-poly[[bis(semicarbazide-κ2N,O)copper(II)]-μ-sulfato-κ2O:O′]
and Hirshfeld surface analysis ofaInstitute of General and Inorganic Chemistry of the Uzbekistan Academy of Sciences, M. Ulugbek Str. 77a, Tashkent 700125, Uzbekistan, and bInstitute of Bioorganic Chemistry Academy of Sciences of Uzbekistan, M. Ulugbek Str. 83, Tashkent 700125, Uzbekistan
*Correspondence e-mail: atom.uz@mail.ru
The title polymer, [Cu(SO4)(CH5N3O)2]n, has been synthesized from aqueous solutions of CuSO4 and semicarbazide. In the the CuII atoms are chelated by two neutral semicarbazide molecules through the oxygen atom and a nitrogen atom of the amino group. The remaining two positions of the Jahn–Teller-distorted octahedral coordination sphere are occupied by oxygen atoms of two sulfate anions in the axial positions. The coordination bonds of the latter associate the polyhedra into polymeric chains running parallel to the c axis. There is a weak intramolecular hydrogen bond between the N—H group and an oxygen atom of the SO42– anion. Thirteen relatively weak intermolecular hydrogen-bonding interactions link the chains into a three-dimensional network. Hirshfeld surface analysis revealed that 64.7% of the intermolecular interactions are from O⋯H/H⋯O contacts and 20.1% from H⋯H contacts. Other interactions such as N⋯H/H⋯N or C⋯H/H⋯C contribute less to the crystal packing.
Keywords: semicarbazide; copper complex; crystal structure; Hirshfeld surface analysis; intermolecular interactions.
CCDC reference: 2213165
1. Chemical context
Semicarbazide (SEC), a water-soluble white solid, is a derivative of urea with formula O=C(NH2)(N2H3). It is used in the preparation of pharmaceuticals including nitrofuran antibacterials (furazolidone, nitrofurazone, nitrofurantoin) and related compounds (Vass et al., 2008). Originally, SEC was primarily detected as a nitrofurazone veterinary metabolite, but over time it was found that azodicarbonamide and flour stored in sealed cans could lead to the formation of SEC as well (Tian et al., 2014). Therefore, the toxicity of SEC as a food contaminant is of crucial interest. SEC hydrochloride has an oral LD50 of 225 mg kg−1 in mice and 123 mg kg−1 in the rat. Some studies suggest that SEC hydrochloride is a mutagen, an animal carcinogen and a teratogen. As a result of the lack of data in humans and an overall limited evidence of carcinogenicity in animals, SEC was classified by the International Agency for Research on Cancer as a Group 3 agent, i.e. not classifiable as to its carcinogenicity to humans (Takahashi et al., 2014). However, SEC products (semicarbazones and thiosemicarbazones) are known to have antiviral, anti-infective and antineoplastic activities through binding to copper or iron in cells (Becalski et al., 2004; Tian et al., 2014). It is well known that the biopharmaceutical properties of active pharmaceutical ingredients may be improved by metal complex formation (Khudoyberganov et al., 2022; Ruzmetov et al., 2022a,b). In turn, this phenomenon may lead to a reduction in the toxicity of hazardous organic substances in coordination compounds (Egorova & Ananikov, 2017; Flora & Pachauri et al., 2010; Ahmed et al., 2020). Therefore, it is of great interest to study the metal complex formation of SEC. In this context, we report here the synthesis, and Hirshfeld surface analysis of a new copper complex of SEC with sulfate anions as co-ligands, [Cu(CH5N3O)2(SO4)]n.
2. Structural commentary
The expanded . The CuII atom is chelated by two SEC molecules through the oxygen atoms (O1 and O2) and the nitrogen atoms (N1 and N4) of NH2 groups, leading to a slightly distorted square-planar coordination environment with bond lengths in the range between 1.9218 (17) and 2.015 (2) Å and bond angles between 81.50 (7) and 101.89 (8)°. Two remote oxygen atoms, O6 and O3i, of two SO42– anions augment the coordination sphere (Table 1). As a result of the Jahn–Teller effect, a substantial elongation of the two axial Cu—O bonds is observed and the coordination sphere around CuII becomes a distinctly distorted octahedron.
of the title polymer is shown in Fig. 1
|
Coordination bonds involving the SO42– ligands associate individual polyhedra into polymeric chains running parallel to the c axis (Fig. 2). A weak intramolecular hydrogen bond between N4—H4 and oxygen atom O4 of the SO4 anion (Table 2), enclosing a six-membered ring with graph-set notation S11(6) (Etter, 1990), consolidates the conformation (Fig. 1). The lengths of the S—O bonds are very similar, showing a distribution between 1.4702 (17) and 1.4769 (17) Å, in very good agreement with the mean value of 1.473 Å for S—O bonds (Gagné & Hawthorne, 2018).
3. Supramolecular features
For hydrogen-bonding interactions, there are six proton acceptor and ten proton donor functionalities, forming a complex system of 13 intermolecular hydrogen bonds (Table 2). Within this network, bifurcated hydrogen bonds involving hydrogen atoms H4A, H5 and H6A are noted. Each of the atoms O4 and O5 is an acceptor for four hydrogen bonds whereas atoms O1 and O6 are hydrogen-bonded to two hydrogen atoms, and O2 and O3 to one hydrogen atom each. The hydrogen bonds form numerous different associates with various dimensions, e.g. there are many rings with graph-set notations ranging from R11(n) to R66(n). The hydrogen bonds indicated in Table 2 link the polymeric chains into a three-dimensional network (Fig. 3).
4. Hirshfeld surface analysis
Hirshfeld surfaces were calculated and two-dimensional fingerprints generated using CrystalExplorer2021 (Spackman et al., 2021). Fig. 4 shows the Hirshfeld surface of the title compound with dnorm (normalized contact distance) plotted over the range −0.5974 to 1.0842 a.u. The interactions given in Table 2 play a key role in the molecular packing of the complex, and nearly two thirds (or 64.7%) of intermolecular interactions correspond to O⋯H/H⋯O contacts The overall two-dimensional fingerprint plot and those delineated into O⋯H/H⋯O, H⋯H, N⋯H/H⋯N, C⋯H/H⋯C and Cu⋯O/O⋯C interactions are shown in Fig. 5. The 2.5% contribution of the Cu⋯O/O⋯Cu contact is explained by the existence of the very long Cu—O3 bond, which is considered by CrystalExplorer to be an intermolecular contact.
5. Database survey
A search of the Cambridge Structural Database (CSD, Version 5.43, update of November 2021; Groom et al., 2016) for semicarbazide metal complexes gave 45 hits. In all entries, neutral semicarbazide molecules coordinate in a chelating fashion enclosing five-membered rings with exception of the Pd complex NAZYES (Bergs et al., 1997) where a single semicarbazide molecule coordinates monodentately through an NH2 group. In 21 mixed-ligand complexes, chloride ions serve as co-ligands except in the structure with refcode SEGWAC (Chuklanova et al., 1988) where all four ligand positions of the ZnII atom are occupied by Cl− ligands and protonated semicarbazide molecules present as non-coordinating molecules. Chloride anions likewise are non-coordinating in four cases, and NO3− anions in five structures. Water molecules of crystallization are encountered in 13 complexes. There is only one coordination polymer among the identified compounds, SCACCU10 (Chiesi Villa et al., 1971). The of most of the metal complexes is an octahedron while a tetrahedron is revealed in six cases and penta-coordination is found in three structures. Inclusion of the SO42− anion into the coordination sphere of the central metal cation is reported only for the title compound.
6. Synthesis and crystallization
0.02 g (0.2 mol) of semicarbazide hydrochloride, 0.022 g (0.09 mol) of copper sulfate and 0.0054 g (0.09 mol) of monoethanolamine were dissolved separately in 1 ml of water at room temperature. The three solutions were mixed and left in a thermostat at 298 K. After two days, blue crystals started to precipitate. The crystals were filtered off, washed with ethanol and dried.
7. Refinement
Crystal data, data collection and structure . N-bound hydrogen atoms were placed in calculated positions and refined in the riding-model approximation with Uiso(H) = 1.2Ueq(N), N—H = 0.89 Å for the N1 and N4 nitrogen atoms and N—H = 0.86 for the remaining nitrogen atoms.
details are summarized in Table 3
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Supporting information
CCDC reference: 2213165
https://doi.org/10.1107/S2056989022010040/wm5662sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989022010040/wm5662Isup3.hkl
Data collection: CrysAlis PRO (Rigaku, 2020); cell
CrysAlis PRO (Rigaku, 2020); data reduction: CrysAlis PRO (Rigaku, 2020); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).[Cu(SO4)(CH5N3O)2] | F(000) = 628 |
Mr = 309.76 | Dx = 2.219 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54184 Å |
a = 10.5555 (2) Å | Cell parameters from 4840 reflections |
b = 6.8624 (1) Å | θ = 3.5–70.8° |
c = 12.9061 (2) Å | µ = 5.82 mm−1 |
β = 97.265 (2)° | T = 293 K |
V = 927.36 (3) Å3 | Block, light blue |
Z = 4 | 0.18 × 0.16 × 0.14 mm |
XtaLAB Synergy, Single source at home/near, HyPix3000 diffractometer | 1785 independent reflections |
Radiation source: micro-focus sealed X-ray tube, PhotonJet (Cu) X-ray Source | 1656 reflections with I > 2σ(I) |
Mirror monochromator | Rint = 0.037 |
Detector resolution: 10.0000 pixels mm-1 | θmax = 71.1°, θmin = 4.2° |
ω scans | h = −12→12 |
Absorption correction: multi-scan (CrysAlisPro; Rigaku, 2020) | k = −8→6 |
Tmin = 0.084, Tmax = 1.000 | l = −15→15 |
8102 measured reflections |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.029 | w = 1/[σ2(Fo2) + (0.0437P)2 + 0.5652P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.080 | (Δ/σ)max < 0.001 |
S = 1.07 | Δρmax = 0.32 e Å−3 |
1785 reflections | Δρmin = −0.41 e Å−3 |
146 parameters | Extinction correction: SHELXL-2018/3 (Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
0 restraints | Extinction coefficient: 0.0019 (3) |
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 | ||
Cu1 | 0.25619 (3) | 0.28648 (5) | 0.38274 (3) | 0.02624 (15) | |
S1 | 0.15524 (5) | 0.43123 (8) | 0.62353 (4) | 0.02198 (17) | |
O1 | 0.40378 (15) | 0.4485 (2) | 0.36355 (13) | 0.0265 (4) | |
O2 | 0.36126 (16) | 0.0997 (2) | 0.46464 (15) | 0.0320 (4) | |
O4 | 0.06548 (18) | 0.2652 (3) | 0.61509 (14) | 0.0327 (4) | |
O3 | 0.26979 (17) | 0.3862 (3) | 0.69698 (15) | 0.0390 (5) | |
N1 | 0.16194 (18) | 0.4839 (3) | 0.29178 (15) | 0.0240 (4) | |
H1A | 0.129486 | 0.430444 | 0.231376 | 0.029* | |
H1B | 0.098181 | 0.533034 | 0.322557 | 0.029* | |
N4 | 0.11789 (19) | 0.0915 (3) | 0.40077 (17) | 0.0284 (4) | |
H4A | 0.057785 | 0.146007 | 0.433787 | 0.034* | |
H4B | 0.081860 | 0.049058 | 0.338815 | 0.034* | |
N5 | 0.1763 (2) | −0.0647 (3) | 0.46025 (18) | 0.0311 (5) | |
H5 | 0.132873 | −0.161448 | 0.479156 | 0.037* | |
N2 | 0.2496 (2) | 0.6315 (3) | 0.27463 (18) | 0.0333 (5) | |
H2 | 0.225589 | 0.736581 | 0.241505 | 0.040* | |
N6 | 0.3650 (2) | −0.2015 (3) | 0.53428 (18) | 0.0318 (5) | |
H6A | 0.446089 | −0.194830 | 0.552441 | 0.038* | |
H6B | 0.323773 | −0.304631 | 0.547814 | 0.038* | |
N3 | 0.4573 (2) | 0.7341 (3) | 0.29420 (19) | 0.0369 (5) | |
H3A | 0.536565 | 0.718013 | 0.317642 | 0.044* | |
H3B | 0.433312 | 0.836957 | 0.258968 | 0.044* | |
C1 | 0.3723 (2) | 0.6007 (3) | 0.31234 (18) | 0.0238 (5) | |
C2 | 0.3037 (2) | −0.0535 (3) | 0.48563 (18) | 0.0240 (5) | |
O5 | 0.09208 (18) | 0.6011 (3) | 0.66402 (17) | 0.0407 (5) | |
O6 | 0.19228 (18) | 0.4786 (3) | 0.52040 (13) | 0.0333 (4) |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cu1 | 0.0189 (2) | 0.0213 (2) | 0.0375 (2) | −0.00162 (12) | −0.00018 (15) | 0.00774 (14) |
S1 | 0.0190 (3) | 0.0238 (3) | 0.0234 (3) | −0.0045 (2) | 0.0034 (2) | −0.0019 (2) |
O1 | 0.0184 (8) | 0.0231 (8) | 0.0378 (9) | 0.0007 (6) | 0.0025 (7) | 0.0065 (7) |
O2 | 0.0225 (9) | 0.0225 (8) | 0.0491 (11) | −0.0053 (7) | −0.0035 (8) | 0.0109 (8) |
O4 | 0.0322 (10) | 0.0292 (9) | 0.0356 (10) | −0.0134 (7) | 0.0001 (8) | 0.0053 (7) |
O3 | 0.0233 (9) | 0.0524 (12) | 0.0391 (10) | −0.0035 (8) | −0.0043 (8) | 0.0060 (9) |
N1 | 0.0187 (10) | 0.0263 (10) | 0.0271 (10) | 0.0015 (8) | 0.0036 (8) | −0.0003 (8) |
N4 | 0.0196 (10) | 0.0276 (10) | 0.0374 (11) | −0.0021 (8) | 0.0007 (8) | −0.0011 (9) |
N5 | 0.0251 (11) | 0.0225 (9) | 0.0453 (12) | −0.0067 (8) | 0.0030 (9) | 0.0045 (9) |
N2 | 0.0246 (11) | 0.0277 (11) | 0.0468 (13) | 0.0013 (8) | 0.0014 (9) | 0.0164 (10) |
N6 | 0.0282 (12) | 0.0234 (10) | 0.0432 (13) | −0.0014 (8) | 0.0016 (9) | 0.0102 (9) |
N3 | 0.0319 (13) | 0.0342 (12) | 0.0446 (13) | −0.0088 (9) | 0.0050 (10) | 0.0145 (10) |
C1 | 0.0240 (12) | 0.0231 (11) | 0.0256 (11) | 0.0011 (9) | 0.0086 (9) | 0.0000 (9) |
C2 | 0.0250 (12) | 0.0212 (11) | 0.0262 (11) | −0.0032 (9) | 0.0040 (9) | −0.0011 (9) |
O5 | 0.0284 (10) | 0.0392 (10) | 0.0548 (12) | −0.0009 (8) | 0.0065 (9) | −0.0220 (9) |
O6 | 0.0425 (11) | 0.0316 (9) | 0.0276 (9) | −0.0112 (8) | 0.0115 (8) | −0.0017 (7) |
Cu1—O1 | 1.9549 (17) | N1—N2 | 1.408 (3) |
Cu1—O2 | 1.9218 (17) | N4—H4A | 0.8900 |
Cu1—N1 | 1.9769 (19) | N4—H4B | 0.8900 |
Cu1—N4 | 2.015 (2) | N4—N5 | 1.414 (3) |
Cu1—O6 | 2.3776 (18) | N5—H5 | 0.8600 |
Cu1—O3i | 2.6947 (19) | N5—C2 | 1.345 (3) |
S1—O4 | 1.4769 (17) | N2—H2 | 0.8600 |
S1—O3 | 1.4719 (18) | N2—C1 | 1.341 (3) |
S1—O5 | 1.4714 (19) | N6—H6A | 0.8600 |
S1—O6 | 1.4702 (17) | N6—H6B | 0.8600 |
O1—C1 | 1.258 (3) | N6—C2 | 1.320 (3) |
O2—C2 | 1.261 (3) | N3—H3A | 0.8600 |
N1—H1A | 0.8900 | N3—H3B | 0.8600 |
N1—H1B | 0.8900 | N3—C1 | 1.324 (3) |
O1—Cu1—N1 | 83.36 (7) | N2—N1—H1A | 110.3 |
O1—Cu1—N4 | 173.06 (8) | N2—N1—H1B | 110.3 |
O1—Cu1—O6 | 94.90 (7) | Cu1—N4—H4A | 110.3 |
O2—Cu1—O1 | 92.02 (7) | Cu1—N4—H4B | 110.3 |
O2—Cu1—N1 | 174.70 (8) | H4A—N4—H4B | 108.6 |
O2—Cu1—N4 | 82.52 (8) | N5—N4—Cu1 | 107.04 (14) |
O2—Cu1—O6 | 99.05 (7) | N5—N4—H4A | 110.3 |
N1—Cu1—N4 | 101.89 (8) | N5—N4—H4B | 110.3 |
N1—Cu1—O6 | 83.95 (7) | N4—N5—H5 | 121.8 |
N4—Cu1—O6 | 90.21 (8) | C2—N5—N4 | 116.32 (19) |
O2—Cu1—O3i | 96.00 (7) | C2—N5—H5 | 121.8 |
O1—Cu1—O3i | 90.24 (7) | N1—N2—H2 | 121.5 |
N1—Cu1—O3i | 81.50 (7) | C1—N2—N1 | 116.94 (19) |
N4—Cu1—O3i | 86.13 (9) | C1—N2—H2 | 121.5 |
O6—Cu1—O3i | 163.90 (6) | H6A—N6—H6B | 120.0 |
O3—S1—O4 | 110.64 (11) | C2—N6—H6A | 120.0 |
O5—S1—O4 | 108.79 (11) | C2—N6—H6B | 120.0 |
O5—S1—O3 | 108.05 (12) | H3A—N3—H3B | 120.0 |
O6—S1—O4 | 110.20 (10) | C1—N3—H3A | 120.0 |
O6—S1—O3 | 109.80 (11) | C1—N3—H3B | 120.0 |
O6—S1—O5 | 109.31 (12) | O1—C1—N2 | 120.0 (2) |
C1—O1—Cu1 | 112.13 (15) | O1—C1—N3 | 121.8 (2) |
C2—O2—Cu1 | 114.46 (15) | N3—C1—N2 | 118.2 (2) |
Cu1—N1—H1A | 110.3 | O2—C2—N5 | 119.3 (2) |
Cu1—N1—H1B | 110.3 | O2—C2—N6 | 121.6 (2) |
H1A—N1—H1B | 108.5 | N6—C2—N5 | 119.1 (2) |
N2—N1—Cu1 | 107.15 (14) | S1—O6—Cu1 | 133.39 (11) |
Cu1—O1—C1—N2 | −2.6 (3) | O3—S1—O6—Cu1 | 76.86 (17) |
Cu1—O1—C1—N3 | 177.26 (19) | N1—N2—C1—O1 | −2.4 (3) |
Cu1—O2—C2—N5 | −7.0 (3) | N1—N2—C1—N3 | 177.7 (2) |
Cu1—O2—C2—N6 | 174.70 (19) | N4—N5—C2—O2 | 6.7 (3) |
Cu1—N1—N2—C1 | 5.9 (3) | N4—N5—C2—N6 | −175.0 (2) |
Cu1—N4—N5—C2 | −2.9 (2) | O5—S1—O6—Cu1 | −164.78 (14) |
O4—S1—O6—Cu1 | −45.26 (18) |
Symmetry code: (i) x, −y+1/2, z−1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···O4i | 0.89 | 2.06 | 2.928 (3) | 164 |
N1—H1B···O4ii | 0.89 | 2.43 | 3.302 (3) | 167 |
N1—H1B···O5ii | 0.89 | 2.24 | 2.871 (3) | 128 |
N2—H2···O5iii | 0.86 | 1.97 | 2.751 (3) | 151 |
N3—H3A···O3iv | 0.86 | 2.20 | 2.985 (3) | 152 |
N3—H3B···O1v | 0.86 | 2.59 | 3.036 (3) | 113 |
N4—H4A···O4 | 0.89 | 2.47 | 3.125 (3) | 131 |
N4—H4A···O5ii | 0.89 | 2.57 | 3.097 (3) | 119 |
N4—H4B···O5i | 0.89 | 2.49 | 3.309 (3) | 152 |
N5—H5···O6vi | 0.86 | 2.59 | 3.228 (3) | 132 |
N5—H5···O4vii | 0.86 | 2.39 | 2.954 (3) | 123 |
N6—H6A···O1viii | 0.86 | 2.51 | 3.123 (3) | 129 |
N6—H6A···O2viii | 0.86 | 2.17 | 2.971 (3) | 154 |
N6—H6A···O6vi | 0.86 | 2.03 | 2.845 (3) | 157 |
Symmetry codes: (i) x, −y+1/2, z−1/2; (ii) −x, −y+1, −z+1; (iii) x, −y+3/2, z−1/2; (iv) −x+1, −y+1, −z+1; (v) −x+1, y+1/2, −z+1/2; (vi) x, y−1, z; (vii) −x, −y, −z+1; (viii) −x+1, −y, −z+1. |
Funding information
The authors would like to thank the Uzbekistan government for direct financial support of this research.
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