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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2023 Jul 11;79(Pt 8):714–717. doi: 10.1107/S2056989023005935

Crystal structure of bis­{S-octyl-3-[(thio­phen-2-yl)methyl­idene]di­thio­carbazato-κ2 N 3,S}nickel(II)

Sultana Shakila Khan a, Md Belayet Hossain Howlader a,*, Md Chanmiya Sheikh b, Ryuta Miyatake c, Ennio Zangrando d
Editor: S Parkine
PMCID: PMC10439407  PMID: 37601399

The mononuclear nickel(II) complex is bis-chelated by di­thio­carbazato ligands bearing a thienyl ring and an n-octyl alkyl chain.

Keywords: crystal structure, nickel(II) complex, di­thio­carbazato ligand

Abstract

In the title complex, [Ni(C14H21N2S3)2], the nickel(II) atom is located on a crystallographic inversion center and exhibits a square-planar coordination environment, being coordinated by two negatively charged N,S-chelating ligands in a trans configuration. In the crystal, the non-H atoms of the complex are practically coplanar (r.m.s. deviation of fitted atoms = 0.135 Å), and the angle between the thienyl and the chelating rings is 6.7 (1)°. The mol­ecules stack at a distance of 3.623 (2) Å along the b-axis direction.

1. Chemical context

Thio­semicarbazones, semicarbazones, hydrazide/hydrazones and di­thio­carbazate ligands have been widely employed for the preparation of metal complexes. Over the last few decades, di­thio­carbazate Schiff bases and their metal complexes have gained considerable inter­est because of their promising bioactivities against diverse cancer cell lines (Yusof et al., 2015; Ramilo-Gomes et al., 2021; Low et al., 2016), as well as anti­microbial activity (Zangrando et al., 2017). Clearly, the biological properties of these compounds can be modulated by using different organic substituents, leading to concomitant structural modifications (How et al., 2008; Yusof et al., 2022). A study of structure–activity relationships was described by Beshir et al. (2008). 1.

Therefore, considering the diverse significance of di­thio­carbazate bases and their role in a variety of biological applications, herein we report a novel NiII complex with a di­thio­carbazate Schiff base ligand bearing an octyl alkyl chain and a thienyl ring (Fig. 1).

Figure 1.

Figure 1

An ellipsoid plot (50% probability) of the title compound.

2. Structural commentary

The nickel(II) atom is located on a crystallographic center of symmetry and exhibits a square-planar coordination sphere, being coordinated by two negatively charged N,S-chelating ligands in a trans configuration. The Ni—N1 and Ni—S1 bond distances are 1.9168 (19) and 2.1735 (7) Å, respectively with a chelating N1—Ni—S1 bond angle of 85.88 (6)°. These values agree with those reported in previous papers (Begum et al., 2016; Islam et al., 2014; Howlader et al., 2015) for related compounds. It is worth mentioning that nickel(II) and copper(II) complexes with di­thio­carbazate ligands have been reported to crystallize in both cis and trans configurations, although the latter is slightly more frequent (Begum et al., 2020).

All of the non-H atoms of the complex are almost coplanar, with S1 and C1 [−0.28 Å] and C13, C14 [+0.24, +0.31 Å], respectively deviating the most from its mean plane (r.m.s. deviation of fitted atoms = 0.135 Å). The thienyl ring forms a small dihedral angle of 6.7 (1)° with respect to the chelating five-membered ring. The long alkyl chain is in a staggered conformation with torsion angles along the chain that range between 176.7 (2) and 179.8 (2)°.

The mol­ecule is stabilized by an intra­molecular unconventional hydrogen bond between C5—H5 with S1′ [at 1 − x, 1 − y, 1 − z] of the symmetry-related ligand [C5⋯S1′ distance of 3.067 (3) Å, C5—H5⋯S1′ angle of 125°].

3. Supra­molecular features

The mol­ecules stack with an inter­planar distance of 3.623 (2) Å, and the crystal packing shows that all hydro­phobic n-octyl chains segregate together, so as to share the same regions of space (Fig. 2), as already observed in similar complexes (Begum et al., 2016). Fig. 3 overlays this structure of the complex superimposed onto that of a 4-meth­oxy­benzyl derivative (WEGKEB: Begum et al., 2018), where it is worth noting the different orientation of octyl chains in the two cases. This is due to the different torsion angle C6—S2—C7—C8 of −177.36 (18)° in this structure vs 86.8 (6)° and −160.0 (9)° (for the two disorder components of the equivalent torsion angle in WEGKEB), likely induced by crystal-packing requirements. Details of hydrogen-bonding inter­actions are given in Table 1.

Figure 2.

Figure 2

A partial packing view showing complexes stacked in the b-axis direction.

Figure 3.

Figure 3

Superposition of this structure with the 4-meth­oxy­benzyl derivative WEGKEB (Begum et al., 2018; only one disorder component shown), where it is worth noting the different orientation of the octyl moiety, likely induced by crystal-packing requirements.

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA D—H⋯A
C2—H2⋯S1i 0.95 3.00 3.684 (3) 131
C2—H2⋯S2ii 0.95 2.93 3.752 (3) 146
C5—H5⋯S1iii 0.95 2.42 3.067 (3) 125
C7—H7A⋯S3 0.99 2.93 3.406 (3) 110

Symmetry codes: (i) Inline graphic ; (ii) Inline graphic ; (iii) Inline graphic .

4. Database survey

For comparison, NiII complexes with comparable ligands bearing long alkyl chains have been reported from these laboratories (Begum et al., 2016, 2017, 2018, 2020, 2023; CSD refcodes = JUYCAJ, WEGKEB, BIQTIH, TILVUJ and PICMOH, respectively).

5. Synthesis and crystallization

A solution of Ni(CH3COO)2·4H2O (0.12 g, 0.5 mmol in 10 mL methanol) was added to a solution of S-octyl-β-N-(2-thien­yl)methyl­enedi­thio­carbazate (0.314 g, 1.0 mmol in 30 mL of methanol). The resulting mixture was stirred at room temperature for 4 h. The dark-orange precipitate that formed was filtered off, washed with methanol and dried in vacuo over anhydrous CaCl2. Orange needle-shaped single crystals, suitable for X-ray diffraction, were obtained by slow evaporation of the compound from a mixture of chloro­form and aceto­nitrile (4:1, v/v) after 14 days. Yield: 66%; m. p. (377-378) K.

FT–IR (KBr, cm−1): 2920 ν(C—H, alk­yl), 1639, 1572 ν(C=N—N=C).

1H NMR (400 MHz, CDCl3, ppm) δ: 7.999 (s, 2×1H, CH=N, C-5), 7.715 (d, 2×1H, C-1, J = 5.2 Hz), 7.468 (d, 2×1H, C-3, J = 5.2 Hz), 7.103 (t, 2×1H, C-2), 3.269 (t, 2×2H, –SCH2, C-7), 1.764 (p, 2×2H, C-8), 1.460 (p, 2×2H, C-9), 1.318–1.270 (m, 2×8H, C-10, 11, 12, 13), 0.878 (t, 2×3H, C-14).

UV–Vis spectrum [CHCl3, λmax nm]: 475, 400, 276.

HRMS (FAB) Calculated for C28H42N4NiS6 [M+H]+: 685.11599, found [M+H]+: 685.11549.

6. Refinement

Crystal data, data collection and structure refinement are summarized in Table 2. Hydrogen atoms were placed at calculated positions (C–H = 0.95–0.99 Å) and refined as riding with U iso(H) = 1.2–1.5U eq(C).

Table 2. Experimental details.

Crystal data
Chemical formula [Ni(C14H21N2S3)2]
M r 685.72
Crystal system, space group Monoclinic, P21/c
Temperature (K) 173
a, b, c (Å) 15.5444 (6), 5.5388 (3), 20.1592 (8)
β (°) 103.675 (7)
V3) 1686.44 (13)
Z 2
Radiation type Mo Kα
μ (mm−1) 0.97
Crystal size (mm) 0.08 × 0.02 × 0.01
 
Data collection
Diffractometer Rigaku R-AXIS RAPID
Absorption correction Multi-scan (ABSCOR; Rigaku, 1995)
T min, T max 0.815, 0.990
No. of measured, independent and observed [I > 2σ(I)] reflections 15791, 3850, 2621
R int 0.077
(sin θ/λ)max−1) 0.649
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.045, 0.079, 1.00
No. of reflections 3850
No. of parameters 179
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.44, −0.27

Computer programs: RAPID-AUTO (Rigaku, 2018), SHELXT (Sheldrick, 2015a ), SHELXL2019/2 (Sheldrick, 2015b ), DIAMOND (Brandenburg, 1999) and WinGX (Farrugia, 2012).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989023005935/pk2690sup1.cif

e-79-00714-sup1.cif (495.6KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989023005935/pk2690Isup2.hkl

e-79-00714-Isup2.hkl (307.1KB, hkl)

CCDC reference: 2254902

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

MBHH and SSK are grateful to the Department of Chemistry, Rajshahi University for the provision of laboratory facilities. MCS and RM acknowledge the Center for Environmental Conservation and Research Safety, University of Toyama, for providing facilities for single-crystal X-ray analyses.

supplementary crystallographic information

Crystal data

[Ni(C14H21N2S3)2] F(000) = 724
Mr = 685.72 Dx = 1.350 Mg m3
Monoclinic, P21/c Mo Kα radiation, λ = 0.71075 Å
a = 15.5444 (6) Å Cell parameters from 10434 reflections
b = 5.5388 (3) Å θ = 2.1–27.5°
c = 20.1592 (8) Å µ = 0.97 mm1
β = 103.675 (7)° T = 173 K
V = 1686.44 (13) Å3 Needle, orange
Z = 2 0.08 × 0.02 × 0.01 mm

Data collection

Rigaku R-AXIS RAPID diffractometer 2621 reflections with I > 2σ(I)
Detector resolution: 10.000 pixels mm-1 Rint = 0.077
ω scans θmax = 27.5°, θmin = 2.7°
Absorption correction: multi-scan (ABSCOR; Rigaku, 1995) h = −19→20
Tmin = 0.815, Tmax = 0.990 k = −7→7
15791 measured reflections l = −26→25
3850 independent reflections

Refinement

Refinement on F2 0 restraints
Least-squares matrix: full Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.045 H-atom parameters constrained
wR(F2) = 0.079 w = 1/[σ2(Fo2) + (0.0329P)2 + 0.0128P] where P = (Fo2 + 2Fc2)/3
S = 1.00 (Δ/σ)max = 0.001
3850 reflections Δρmax = 0.44 e Å3
179 parameters Δρmin = −0.27 e Å3

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
Ni1 0.500000 0.500000 0.500000 0.02461 (12)
S1 0.43249 (4) 0.34173 (13) 0.57239 (3) 0.03295 (17)
S2 0.30020 (4) −0.04469 (12) 0.55073 (3) 0.03283 (17)
S3 0.33321 (4) −0.17114 (13) 0.33566 (3) 0.03364 (17)
N1 0.43677 (12) 0.2681 (4) 0.43617 (10) 0.0263 (5)
N2 0.37776 (13) 0.1034 (4) 0.45452 (10) 0.0274 (5)
C1 0.32299 (17) −0.2689 (5) 0.25377 (13) 0.0364 (7)
H1 0.290649 −0.408991 0.235505 0.044*
C2 0.36579 (17) −0.1259 (5) 0.21773 (13) 0.0384 (7)
H2 0.366185 −0.152919 0.171263 0.046*
C3 0.40956 (16) 0.0668 (5) 0.25668 (12) 0.0331 (6)
H3 0.443110 0.184342 0.239444 0.040*
C4 0.39872 (15) 0.0677 (4) 0.32296 (12) 0.0273 (6)
C5 0.44139 (15) 0.2400 (5) 0.37290 (12) 0.0289 (6)
H5 0.478965 0.351305 0.357540 0.035*
C6 0.37280 (14) 0.1323 (4) 0.51739 (12) 0.0255 (5)
C7 0.25455 (16) −0.2377 (5) 0.47858 (12) 0.0317 (6)
H7A 0.228117 −0.136545 0.438453 0.038*
H7B 0.302730 −0.334361 0.467263 0.038*
C8 0.18415 (17) −0.4070 (5) 0.49347 (13) 0.0338 (6)
H8A 0.210547 −0.512821 0.532553 0.041*
H8B 0.136169 −0.311795 0.505600 0.041*
C9 0.14665 (17) −0.5596 (5) 0.43057 (13) 0.0364 (7)
H9A 0.123844 −0.450452 0.391478 0.044*
H9B 0.195365 −0.655482 0.419806 0.044*
C10 0.07291 (17) −0.7307 (5) 0.43757 (13) 0.0368 (6)
H10A 0.025185 −0.637168 0.450618 0.044*
H10B 0.096283 −0.847621 0.474588 0.044*
C11 0.03444 (17) −0.8679 (5) 0.37195 (13) 0.0393 (7)
H11A 0.011898 −0.749798 0.335090 0.047*
H11B 0.082584 −0.960448 0.359172 0.047*
C12 −0.03979 (17) −1.0408 (5) 0.37605 (14) 0.0403 (7)
H12A −0.016871 −1.163148 0.411632 0.048*
H12B −0.087282 −0.949827 0.390228 0.048*
C13 −0.0790 (2) −1.1686 (7) 0.30929 (15) 0.0569 (9)
H13A −0.102651 −1.046174 0.273913 0.068*
H13B −0.031228 −1.257274 0.294768 0.068*
C14 −0.1521 (2) −1.3442 (7) 0.31334 (18) 0.0693 (11)
H14A −0.128788 −1.469718 0.347054 0.083*
H14B −0.174872 −1.418856 0.268549 0.083*
H14C −0.200158 −1.257687 0.327044 0.083*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
Ni1 0.0294 (2) 0.0213 (3) 0.0228 (2) −0.0016 (2) 0.00554 (18) −0.00261 (19)
S1 0.0420 (4) 0.0320 (4) 0.0256 (3) −0.0103 (3) 0.0095 (3) −0.0052 (3)
S2 0.0415 (4) 0.0294 (4) 0.0287 (3) −0.0086 (3) 0.0105 (3) 0.0004 (3)
S3 0.0419 (4) 0.0278 (4) 0.0300 (3) −0.0062 (3) 0.0062 (3) −0.0026 (3)
N1 0.0299 (11) 0.0220 (12) 0.0270 (11) −0.0014 (9) 0.0067 (9) −0.0013 (9)
N2 0.0345 (11) 0.0225 (12) 0.0265 (11) −0.0050 (9) 0.0098 (9) −0.0008 (9)
C1 0.0406 (15) 0.0330 (17) 0.0324 (14) −0.0041 (13) 0.0021 (12) −0.0101 (12)
C2 0.0391 (15) 0.0460 (19) 0.0297 (13) −0.0038 (13) 0.0076 (13) −0.0126 (13)
C3 0.0365 (14) 0.0368 (17) 0.0265 (12) −0.0044 (12) 0.0087 (12) −0.0051 (11)
C4 0.0298 (13) 0.0232 (14) 0.0278 (12) −0.0008 (10) 0.0046 (11) −0.0025 (10)
C5 0.0327 (13) 0.0260 (15) 0.0298 (13) −0.0038 (11) 0.0109 (11) −0.0015 (11)
C6 0.0270 (12) 0.0202 (14) 0.0285 (13) 0.0008 (10) 0.0049 (11) 0.0037 (10)
C7 0.0377 (14) 0.0261 (15) 0.0306 (13) −0.0045 (11) 0.0068 (12) −0.0009 (11)
C8 0.0373 (14) 0.0291 (15) 0.0347 (14) −0.0064 (11) 0.0077 (12) 0.0019 (11)
C9 0.0379 (14) 0.0314 (17) 0.0398 (15) −0.0074 (12) 0.0091 (13) −0.0027 (12)
C10 0.0397 (14) 0.0300 (16) 0.0421 (15) −0.0072 (12) 0.0122 (13) −0.0020 (12)
C11 0.0396 (15) 0.0370 (18) 0.0405 (15) −0.0097 (13) 0.0078 (13) −0.0037 (13)
C12 0.0419 (15) 0.0355 (18) 0.0430 (15) −0.0089 (13) 0.0090 (13) −0.0027 (13)
C13 0.0565 (19) 0.060 (2) 0.0522 (19) −0.0206 (17) 0.0084 (16) −0.0114 (17)
C14 0.063 (2) 0.062 (3) 0.072 (2) −0.0261 (19) −0.0053 (19) −0.009 (2)

Geometric parameters (Å, º)

Ni1—N1i 1.9168 (19) C7—H7B 0.9900
Ni1—N1 1.9168 (19) C8—C9 1.521 (3)
Ni1—S1i 2.1735 (7) C8—H8A 0.9900
Ni1—S1i 2.1735 (7) C8—H8B 0.9900
Ni1—S1 2.1735 (7) C9—C10 1.519 (3)
S1—C6 1.717 (2) C9—H9A 0.9900
S2—C6 1.745 (2) C9—H9B 0.9900
S2—C7 1.809 (2) C10—C11 1.520 (3)
S3—C1 1.709 (3) C10—H10A 0.9900
S3—C4 1.725 (3) C10—H10B 0.9900
N1—C5 1.304 (3) C11—C12 1.516 (4)
N1—N2 1.404 (3) C11—H11A 0.9900
N2—C6 1.298 (3) C11—H11B 0.9900
C1—C2 1.351 (4) C12—C13 1.515 (4)
C1—H1 0.9500 C12—H12A 0.9900
C2—C3 1.402 (4) C12—H12B 0.9900
C2—H2 0.9500 C13—C14 1.513 (4)
C3—C4 1.386 (3) C13—H13A 0.9900
C3—H3 0.9500 C13—H13B 0.9900
C4—C5 1.431 (3) C14—H14A 0.9800
C5—H5 0.9500 C14—H14B 0.9800
C7—C8 1.524 (3) C14—H14C 0.9800
C7—H7A 0.9900
N1i—Ni1—N1 180.0 C9—C8—H8A 109.8
N1i—Ni1—S1i 85.88 (6) C7—C8—H8A 109.8
N1—Ni1—S1i 94.12 (6) C9—C8—H8B 109.8
N1i—Ni1—S1i 85.88 (6) C7—C8—H8B 109.8
N1—Ni1—S1i 94.12 (6) H8A—C8—H8B 108.3
S1i—Ni1—S1i 0.00 (2) C10—C9—C8 114.7 (2)
N1i—Ni1—S1 94.12 (6) C10—C9—H9A 108.6
N1—Ni1—S1 85.88 (6) C8—C9—H9A 108.6
S1i—Ni1—S1 180.0 C10—C9—H9B 108.6
S1i—Ni1—S1 180.0 C8—C9—H9B 108.6
C6—S1—Ni1 96.42 (8) H9A—C9—H9B 107.6
C6—S2—C7 100.88 (12) C9—C10—C11 112.4 (2)
C1—S3—C4 91.32 (13) C9—C10—H10A 109.1
C5—N1—N2 111.8 (2) C11—C10—H10A 109.1
C5—N1—Ni1 126.77 (17) C9—C10—H10B 109.1
N2—N1—Ni1 121.46 (14) C11—C10—H10B 109.1
C6—N2—N1 111.74 (19) H10A—C10—H10B 107.9
C2—C1—S3 112.9 (2) C12—C11—C10 114.6 (2)
C2—C1—H1 123.6 C12—C11—H11A 108.6
S3—C1—H1 123.6 C10—C11—H11A 108.6
C1—C2—C3 112.4 (2) C12—C11—H11B 108.6
C1—C2—H2 123.8 C10—C11—H11B 108.6
C3—C2—H2 123.8 H11A—C11—H11B 107.6
C4—C3—C2 112.9 (2) C13—C12—C11 113.4 (2)
C4—C3—H3 123.5 C13—C12—H12A 108.9
C2—C3—H3 123.5 C11—C12—H12A 108.9
C3—C4—C5 122.6 (2) C13—C12—H12B 108.9
C3—C4—S3 110.53 (18) C11—C12—H12B 108.9
C5—C4—S3 126.78 (19) H12A—C12—H12B 107.7
N1—C5—C4 130.1 (2) C14—C13—C12 113.7 (3)
N1—C5—H5 115.0 C14—C13—H13A 108.8
C4—C5—H5 115.0 C12—C13—H13A 108.8
N2—C6—S1 124.49 (19) C14—C13—H13B 108.8
N2—C6—S2 119.99 (18) C12—C13—H13B 108.8
S1—C6—S2 115.51 (14) H13A—C13—H13B 107.7
C8—C7—S2 111.63 (17) C13—C14—H14A 109.5
C8—C7—H7A 109.3 C13—C14—H14B 109.5
S2—C7—H7A 109.3 H14A—C14—H14B 109.5
C8—C7—H7B 109.3 C13—C14—H14C 109.5
S2—C7—H7B 109.3 H14A—C14—H14C 109.5
H7A—C7—H7B 108.0 H14B—C14—H14C 109.5
C9—C8—C7 109.2 (2)
C5—N1—N2—C6 −179.6 (2) N1—N2—C6—S1 −1.3 (3)
Ni1—N1—N2—C6 0.4 (3) N1—N2—C6—S2 177.52 (15)
C4—S3—C1—C2 −1.0 (2) Ni1—S1—C6—N2 1.4 (2)
S3—C1—C2—C3 0.9 (3) Ni1—S1—C6—S2 −177.45 (11)
C1—C2—C3—C4 −0.3 (3) C7—S2—C6—N2 2.3 (2)
C2—C3—C4—C5 176.5 (2) C7—S2—C6—S1 −178.84 (14)
C2—C3—C4—S3 −0.5 (3) C6—S2—C7—C8 −177.36 (18)
C1—S3—C4—C3 0.8 (2) S2—C7—C8—C9 178.55 (18)
C1—S3—C4—C5 −176.0 (2) C7—C8—C9—C10 −177.8 (2)
N2—N1—C5—C4 −2.1 (4) C8—C9—C10—C11 176.7 (2)
Ni1—N1—C5—C4 177.9 (2) C9—C10—C11—C12 −179.8 (2)
C3—C4—C5—N1 178.5 (3) C10—C11—C12—C13 178.0 (3)
S3—C4—C5—N1 −5.1 (4) C11—C12—C13—C14 179.1 (3)

Symmetry code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
C2—H2···S1ii 0.95 3.00 3.684 (3) 131
C2—H2···S2iii 0.95 2.93 3.752 (3) 146
C5—H5···S1i 0.95 2.42 3.067 (3) 125
C7—H7A···S3 0.99 2.93 3.406 (3) 110

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

References

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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) global, I. DOI: 10.1107/S2056989023005935/pk2690sup1.cif

e-79-00714-sup1.cif (495.6KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989023005935/pk2690Isup2.hkl

e-79-00714-Isup2.hkl (307.1KB, hkl)

CCDC reference: 2254902

Additional supporting information: crystallographic information; 3D view; checkCIF report


Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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