trans-Di­chlorido­bis­(secnidazole-κN3)copper(II)

Angel-Nieto, I.; Arroyo-Carmona, R.E.; Pérez-Benítez, A.; Aguirre-Hernández, G.; Bernès, S.

doi:10.1107/S2414314624003766

metal-organic compounds

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ISSN: 2414-3146

Volume 9| Part 5| May 2024| x240376

https://doi.org/10.1107/S2414314624003766

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trans-Dichloridobis(secnidazole-κN³)copper(II)

Ismael Angel-Nieto,^a Rosa Elena Arroyo-Carmona,^b Aarón Pérez-Benítez,^b Gerardo Aguirre-Hernández ^c and Sylvain Bernès ^a ^*

^aInstituto de Física, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y 18 Sur, 72570 Puebla, Pue., Mexico, ^bFacultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, 72570 Puebla, Pue., Mexico, and ^cTecnológico Nacional de México, Instituto Tecnológico de Tijuana, Centro de Graduados e Investigación en Química, 22444 Tijuana BC, Mexico
^*Correspondence e-mail: sylvain_bernes@hotmail.com

Edited by I. Brito, University of Antofagasta, Chile (Received 15 April 2024; accepted 24 April 2024; online 3 May 2024)

The use of acetic acid (HOAc) in a reaction between CuCl₂·2H₂O and secnidazole, an active pharmaceutical ingredient useful in the treatment against a variety of anaerobic Gram-positive and Gram-negative bacteria, affords the title complex, [CuCl₂(C₇H₁₁N₃O₃)₂]. This compound was previously synthesized using ethanol as solvent, although its crystal structure was not reported [Betanzos-Lara et al. (2013 ). Inorg. Chim. Acta, 397, 94–100]. In the molecular complex, the Cu²⁺ cation is situated at an inversion centre and displays a square-planar coordination environment. There is a hydrogen-bonded framework based on intermolecular O—H⋯Cl interactions, characterized by H⋯Cl separations of 2.28 (4) Å and O—H⋯Cl angles of 175 (3)°. The resulting supramolecular network is based on R₂²(18) ring motifs, forming chains in the [010] direction.

Keywords: crystal structure; coordination compound; secnidazole; supramolecular structure; hydrogen bonds.

CCDC reference: 2350906

Structure description

Secnidazole [C₇H₁₁N₃O₃, IUPAC name: 1-(2-methyl-5-nitro-1H-imidazol-1-yl)propan-2-ol, abbreviated secnim] is an active pharmaceutical ingredient used in the treatment against a variety of anaerobic Gram-positive and Gram-negative bacteria (Gillis & Wiseman, 1996 ). Some coordination complexes including secnidazole as a ligand were synthesized with late transition metals, Co²⁺, Ni²⁺, Cu²⁺ and Zn²⁺ (Betanzos-Lara et al., 2013). Following the ideas of that group, the aim of this study is to obtain new complexes, to evaluate the synergistic effect of coordination of secnidazole to copper(II) on the antimicrobial activity.

In the literature, only one crystal structure of a secnidazole metallic complex has been reported (CSD refcode KICFUZ; Betanzos-Lara et al., 2013). The complex consists of a dinuclear cluster of Cu²⁺ surrounded by four acetate anions OAc⁻ and two secnidazole molecules bonded in terminal positions, to give [Cu₂(secnim)₂(μ₂-OAc)₄]. The same authors synthesized [Cu(secnim)₂Cl₂], although they did not determine its crystal structure. We have now obtained the same mononuclear complex using a simple synthetic route (see Experimental), and determined its molecular and crystal structure.

The mononuclear Cu²⁺ ion is surrounded by two secnim molecules trans-coordinated through the imidazolic nitrogen atom N3, and two chloride ions, giving a distorted square-plane geometry for Cu^II, with Cu1—N3 and Cu1—Cl1 bond lengths being 1.9953 (19) Å and 2.2586 (6) Å, respectively. The metal is located at an inversion centre in space group P $[\overline{1}]$ , and the asymmetric unit contains half a molecule (Fig. 1). A molecular overlay shows that the global conformation of the secnim free ligand (Novoa de Armas et al., 1997 ) is not altered by coordination to the central metal (Fig. 2). The most significant modification is related to the free rotation of the NO₂ group bonded to C5 in the ligand. The dihedral angle between the nitro group and the mean plane of the imidazole ring is 1.0° in the non-coordinating ligand, while this angle is 15.2 (4)° in the complex. Such a rotation could be a consequence of a steric hindrance between the nitro group and the propan-2-ol lateral chain in a neighbouring molecule in the crystal (Table 1, entry 2).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O3—H3⋯Cl1ⁱ	0.97 (4)	2.28 (4)	3.252 (2)	175 (3)
C7—H7A⋯O3ⁱⁱ	0.97	2.40	3.327 (3)	160
C7—H7B⋯O1ⁱⁱⁱ	0.97	2.51	3.436 (3)	159
Symmetry codes: (i) ; (ii) ; (iii) .

Figure 1
Molecular structure of the title compound, with displacement ellipsoids for non-H atoms at the 30% probability level. Non-labelled atoms are generated by the symmetry operation 1 − x, −y, 1 − z.

Figure 2
An overlay calculated with Mercury (Macrae et al., 2020

), comparing the shape of secnidazole as free ligand (red molecule; Novoa de Armas et al., 1997

) and in the title compound (green molecule). The overlay was computed using the five atoms belonging to the imidazole heterocycle. Note the small rotation of ca 14° for the nitro group.

The orientation of the hydroxy group promotes the formation of intermolecular hydrogen bonds and acts as a donor to the chloride ion, which acts as an acceptor (Table 1, entry 1). The crystal structure features centrosymmetric $[R_{2}^{2}]$ (18) ring motifs formed by the interaction between the non-coordinating hydroxy group and the chloride ion of a symmetry-related complex. A periodic framework is created, based on chains running in the [010] direction (Fig. 3). These chains are parallel in the crystal, and interact poorly, through weak C—H⋯O contacts involving the hydroxy and nitro groups as acceptors (Table 1, entries 2 and 3).

Figure 3
Part of the supramolecular framework based on intermolecular O—H⋯Cl hydrogen bonds (dashed purple lines) corresponding to the first entry in Table 1

, as viewed down [100].

Synthesis and crystallization

Two ethanolic solutions of secnim (185 mg, 1 mmol in 15 ml) and CuCl₂·2H₂O (170 mg, 1 mmol, in 15 ml) were prepared at ambient conditions. Acetic acid (5 ml) was added to the CuCl₂·2H₂O solution. The solutions were combined under stirring for 1 h at 333 K. The resulting solution was then filtered and allowed to evaporate at 298 K over 2 days, affording blue single crystals suitable for X-ray crystallography.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	[CuCl₂(C₇H₁₁N₃O₃)₂]
M_r	504.81
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	298
a, b, c (Å)	4.6536 (3), 8.2542 (3), 13.6820 (6)
α, β, γ (°)	78.092 (4), 82.801 (4), 85.469 (4)
V (Å³)	509.42 (4)
Z	1
Radiation type	Mo Kα
μ (mm⁻¹)	1.38
Crystal size (mm)	0.28 × 0.21 × 0.10

Data collection
Diffractometer	SuperNova, Dual, AtlasS2
Absorption correction	Multi-scan (CrysAlis PRO; Rigaku OD, 2022 $[Rigaku OD (2022). CrysAlis PRO. Rigaku Oxford Diffraction Ltd, Yarnton, England.]$ )
T_min, T_max	0.879, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	11147, 2582, 1956
R_int	0.066
(sin θ/λ)_max (Å⁻¹)	0.692

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.041, 0.108, 1.05
No. of reflections	2582
No. of parameters	139
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.70, −0.33
Computer programs: CrysAlis PRO (Rigaku OD, 2022 $[Rigaku OD (2022). CrysAlis PRO. Rigaku Oxford Diffraction Ltd, Yarnton, England.]$ ), SHELXT2018/2 (Sheldrick, 2015a ), SHELXL2019/2 (Sheldrick, 2015b ), XP in SHELXTL-Plus (Sheldrick, 2008 ), Mercury (Macrae et al., 2020 ) and publCIF (Westrip, 2010 ).

Structural data

CCDC reference: 2350906

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314624003766/bx4028sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314624003766/bx4028Isup2.hkl

checkCIF report

Computing details top

trans-Dichloridobis(secnidazole-κN³)copper(II) top

Crystal data top

[CuCl₂(C₇H₁₁N₃O₃)₂]	Z = 1
M_r = 504.81	F(000) = 259
Triclinic, P1	D_x = 1.646 Mg m⁻³
a = 4.6536 (3) Å	Mo Kα radiation, λ = 0.71073 Å
b = 8.2542 (3) Å	Cell parameters from 4331 reflections
c = 13.6820 (6) Å	θ = 4.3–28.4°
α = 78.092 (4)°	µ = 1.38 mm⁻¹
β = 82.801 (4)°	T = 298 K
γ = 85.469 (4)°	Plate, blue
V = 509.42 (4) Å³	0.28 × 0.21 × 0.10 mm

Data collection top

SuperNova, Dual, AtlasS2 diffractometer	2582 independent reflections
Radiation source: micro-focus sealed X-ray tube, SuperNova (Mo) X-ray Source	1956 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.066
Detector resolution: 5.1970 pixels mm^-1	θ_max = 29.5°, θ_min = 3.2°
ω scans	h = −6→5
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2022)	k = −11→11
T_min = 0.879, T_max = 1.000	l = −18→18
11147 measured reflections

Refinement top

Refinement on F²	Primary atom site location: dual
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.041	Hydrogen site location: mixed
wR(F²) = 0.108	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	w = 1/[σ²(F_o²) + (0.0399P)² + 0.261P] where P = (F_o² + 2F_c²)/3
2582 reflections	(Δ/σ)_max < 0.001
139 parameters	Δρ_max = 0.70 e Å⁻³
0 restraints	Δρ_min = −0.33 e Å⁻³
0 constraints

Special details top

Refinement. Methine, methylene and methyl H atoms were refined using a riding model and calculated displacement parameters, while hydroxy H atom (H3) was refined with free coordinates and isotropic displacement parameter.

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

	x	y	z	U_iso*/U_eq
Cu1	0.500000	0.000000	0.500000	0.04075 (17)
Cl1	0.26976 (17)	−0.14756 (8)	0.41467 (5)	0.0491 (2)
O1	0.7606 (6)	0.3821 (3)	0.04775 (15)	0.0687 (7)
O2	1.0650 (7)	0.1867 (4)	0.0998 (2)	0.1057 (12)
O3	0.7513 (5)	0.6770 (3)	0.27030 (16)	0.0542 (5)
N1	0.5217 (4)	0.3783 (2)	0.24801 (14)	0.0310 (4)
N2	0.8580 (6)	0.2806 (3)	0.11389 (17)	0.0495 (6)
N3	0.5786 (5)	0.1665 (2)	0.37287 (15)	0.0381 (5)
C2	0.4408 (5)	0.3135 (3)	0.34601 (17)	0.0324 (5)
C4	0.7580 (7)	0.1368 (3)	0.29152 (19)	0.0446 (7)
H4	0.882134	0.043325	0.289156	0.054*
C5	0.7251 (6)	0.2663 (3)	0.21463 (18)	0.0371 (6)
C6	0.2311 (6)	0.3957 (4)	0.4130 (2)	0.0488 (7)
H6A	0.308953	0.495324	0.422023	0.073*
H6B	0.195815	0.322391	0.477062	0.073*
H6C	0.052384	0.422977	0.383621	0.073*
C7	0.4181 (5)	0.5424 (3)	0.19434 (19)	0.0367 (6)
H7A	0.243775	0.579365	0.232279	0.044*
H7B	0.367519	0.531933	0.129350	0.044*
C8	0.6415 (6)	0.6722 (3)	0.17891 (19)	0.0408 (6)
H8	0.804035	0.640327	0.132601	0.049*
C9	0.5105 (8)	0.8384 (4)	0.1286 (2)	0.0617 (9)
H9A	0.350851	0.873264	0.172485	0.093*
H9B	0.442936	0.827624	0.066869	0.093*
H9C	0.655143	0.919358	0.114551	0.093*
H3	0.598 (9)	0.730 (5)	0.310 (3)	0.084 (12)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cu1	0.0753 (4)	0.0250 (2)	0.0210 (2)	−0.0102 (2)	−0.0118 (2)	0.00433 (16)
Cl1	0.0764 (5)	0.0412 (4)	0.0320 (3)	−0.0149 (3)	−0.0117 (3)	−0.0050 (3)
O1	0.1028 (18)	0.0693 (15)	0.0242 (10)	0.0088 (13)	0.0001 (11)	0.0037 (10)
O2	0.133 (3)	0.096 (2)	0.0610 (17)	0.056 (2)	0.0316 (16)	−0.0013 (15)
O3	0.0585 (13)	0.0574 (13)	0.0476 (12)	0.0023 (10)	−0.0117 (10)	−0.0113 (10)
N1	0.0391 (11)	0.0283 (10)	0.0222 (10)	−0.0017 (8)	−0.0046 (8)	0.0037 (8)
N2	0.0718 (17)	0.0423 (13)	0.0300 (12)	0.0029 (12)	0.0036 (11)	−0.0051 (10)
N3	0.0633 (14)	0.0253 (10)	0.0229 (10)	−0.0046 (9)	−0.0065 (9)	0.0030 (8)
C2	0.0423 (13)	0.0289 (12)	0.0237 (11)	−0.0070 (10)	−0.0049 (9)	0.0024 (9)
C4	0.0704 (19)	0.0309 (13)	0.0300 (14)	0.0092 (12)	−0.0083 (12)	−0.0032 (11)
C5	0.0540 (15)	0.0312 (12)	0.0230 (12)	0.0018 (11)	−0.0028 (10)	−0.0006 (10)
C6	0.0539 (17)	0.0496 (16)	0.0347 (15)	−0.0017 (13)	0.0105 (12)	0.0007 (12)
C7	0.0405 (13)	0.0358 (13)	0.0273 (12)	0.0044 (10)	−0.0069 (10)	0.0082 (10)
C8	0.0559 (16)	0.0334 (13)	0.0297 (13)	0.0002 (12)	−0.0048 (11)	0.0006 (10)
C9	0.097 (3)	0.0335 (15)	0.0472 (18)	0.0074 (15)	−0.0099 (17)	0.0058 (13)

Geometric parameters (Å, º) top

Cu1—N3	1.9953 (19)	C2—C6	1.477 (4)
Cu1—N3ⁱ	1.9953 (19)	C4—C5	1.350 (3)
Cu1—Cl1	2.2586 (6)	C4—H4	0.9300
Cu1—Cl1ⁱ	2.2586 (6)	C6—H6A	0.9600
O1—N2	1.207 (3)	C6—H6B	0.9600
O2—N2	1.210 (3)	C6—H6C	0.9600
O3—C8	1.417 (3)	C7—C8	1.517 (4)
O3—H3	0.97 (4)	C7—H7A	0.9700
N1—C2	1.355 (3)	C7—H7B	0.9700
N1—C5	1.373 (3)	C8—C9	1.520 (4)
N1—C7	1.478 (3)	C8—H8	0.9800
N2—C5	1.424 (3)	C9—H9A	0.9600
N3—C2	1.331 (3)	C9—H9B	0.9600
N3—C4	1.358 (3)	C9—H9C	0.9600

N3—Cu1—N3ⁱ	180.0	C2—C6—H6A	109.5
N3—Cu1—Cl1	88.73 (6)	C2—C6—H6B	109.5
N3ⁱ—Cu1—Cl1	91.27 (6)	H6A—C6—H6B	109.5
N3—Cu1—Cl1ⁱ	91.27 (6)	C2—C6—H6C	109.5
N3ⁱ—Cu1—Cl1ⁱ	88.73 (6)	H6A—C6—H6C	109.5
Cl1—Cu1—Cl1ⁱ	180.00 (4)	H6B—C6—H6C	109.5
C8—O3—H3	106 (2)	N1—C7—C8	112.9 (2)
C2—N1—C5	105.98 (19)	N1—C7—H7A	109.0
C2—N1—C7	124.6 (2)	C8—C7—H7A	109.0
C5—N1—C7	129.3 (2)	N1—C7—H7B	109.0
O1—N2—O2	123.5 (3)	C8—C7—H7B	109.0
O1—N2—C5	119.7 (2)	H7A—C7—H7B	107.8
O2—N2—C5	116.8 (2)	O3—C8—C7	111.3 (2)
C2—N3—C4	107.4 (2)	O3—C8—C9	113.4 (2)
C2—N3—Cu1	127.62 (18)	C7—C8—C9	109.2 (2)
C4—N3—Cu1	124.32 (17)	O3—C8—H8	107.6
N3—C2—N1	110.2 (2)	C7—C8—H8	107.6
N3—C2—C6	125.2 (2)	C9—C8—H8	107.6
N1—C2—C6	124.6 (2)	C8—C9—H9A	109.5
C5—C4—N3	108.2 (2)	C8—C9—H9B	109.5
C5—C4—H4	125.9	H9A—C9—H9B	109.5
N3—C4—H4	125.9	C8—C9—H9C	109.5
C4—C5—N1	108.2 (2)	H9A—C9—H9C	109.5
C4—C5—N2	126.7 (2)	H9B—C9—H9C	109.5
N1—C5—N2	125.0 (2)

C4—N3—C2—N1	1.5 (3)	C2—N1—C5—C4	1.2 (3)
Cu1—N3—C2—N1	−169.46 (16)	C7—N1—C5—C4	177.2 (2)
C4—N3—C2—C6	−178.1 (3)	C2—N1—C5—N2	176.6 (3)
Cu1—N3—C2—C6	10.9 (4)	C7—N1—C5—N2	−7.4 (4)
C5—N1—C2—N3	−1.7 (3)	O1—N2—C5—C4	162.4 (3)
C7—N1—C2—N3	−178.0 (2)	O2—N2—C5—C4	−16.9 (5)
C5—N1—C2—C6	177.9 (2)	O1—N2—C5—N1	−12.1 (4)
C7—N1—C2—C6	1.6 (4)	O2—N2—C5—N1	168.5 (3)
C2—N3—C4—C5	−0.8 (3)	C2—N1—C7—C8	103.5 (3)
Cu1—N3—C4—C5	170.60 (19)	C5—N1—C7—C8	−71.9 (3)
N3—C4—C5—N1	−0.3 (3)	N1—C7—C8—O3	−51.0 (3)
N3—C4—C5—N2	−175.6 (3)	N1—C7—C8—C9	−176.9 (2)

Symmetry code: (i) −x+1, −y, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3···Cl1ⁱⁱ	0.97 (4)	2.28 (4)	3.252 (2)	175 (3)
C4—H4···Cl1ⁱⁱⁱ	0.93	2.81	3.537 (3)	136
C6—H6A···Cl1ⁱⁱ	0.96	2.92	3.793 (3)	152
C6—H6B···Cl1^iv	0.96	2.79	3.546 (3)	136
C7—H7A···O3^v	0.97	2.40	3.327 (3)	160
C7—H7B···O1^vi	0.97	2.51	3.436 (3)	159

Symmetry codes: (ii) x, y+1, z; (iii) x+1, y, z; (iv) −x, −y, −z+1; (v) x−1, y, z; (vi) −x+1, −y+1, −z.

Funding information

Funding for this research was provided by: Consejo Nacional de Ciencia y Tecnología (scholarship No. 928228; grant No. INFRA-2014-224405); VIEP-BUAP, Vicerrectoría de Investigación y Estudios de Posgrado (grant No. Proyecto 00030 de grupos de investigación interdisciplinaria 2023).

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