Crystal structure of aqua­bis­[2-(1H-benzimidazol-2-yl-κN 3)aniline-κN]zinc dinitrate

Yongtae Kim; Sung Kwon Kang

doi:10.1107/S2056989015004636

. 2015 Mar 14;71(Pt 4):m85–m86. doi: 10.1107/S2056989015004636

Crystal structure of aquabis[2-(1H-benzimidazol-2-yl-κN ³)aniline-κN]zinc dinitrate

Yongtae Kim ^a, Sung Kwon Kang ^a,^*

PMCID: PMC4438813 PMID: 26029414

Abstract

The cation of the complex title salt, [Zn(C₁₃H₁₁N₃)₂(H₂O)](NO₃)₂, lies about a twofold rotation axis, which passes through the Zn^II atom and the O atom of the aqua ligand. The Zn^II atom adopts a distorted trigonal–bipyramidal geometry defined by two N atoms in axial positions [angle = 166.24 (7)°], and two N and one O atom in the equatorial plane [range of angles: 115.17 (7)–122.42 (3)°]. The dihedral angle between the imidazole and aniline rings is 23.86 (5)°. In the crystal, N—H⋯O and O—H⋯O hydrogen bonds link the components into a three-dimensional network.

Keywords: crystal structure, zinc complex, benzimidazole, hydrogen bonding

Related literature

For the synthesis of the title complex and derivatives, see: Esparza-Ruiz et al. (2011 ▸); Eltayeb et al. (2011 ▸). For background to benzimidazoles and their applications, see: Chassaing et al. (2008 ▸); Podunavac-Kuzmonovic et al. (1999 ▸); Sánchez-Guadarrama et al. (2009 ▸); Xue et al. (2011 ▸). graphic file with name e-71-00m85-scheme1.jpg

Experimental

Crystal data

[Zn(C₁₃H₁₁N₃)₂(H₂O)](NO₃)₂
M _r = 625.9
Monoclinic,
a = 16.2892 (9) Å
b = 15.0782 (8) Å
c = 11.6840 (6) Å
β = 110.0178 (8)°
V = 2696.4 (2) Å³
Z = 4
Mo Kα radiation
μ = 0.97 mm⁻¹
T = 296 K
0.21 × 0.20 × 0.18 mm

Data collection

Bruker SMART CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2002 ▸) T _min = 0.546, T _max = 0.726
13558 measured reflections
3347 independent reflections
3007 reflections with I > 2σ(I)
R _int = 0.020

Refinement

R[F ² > 2σ(F ²)] = 0.027
wR(F ²) = 0.078
S = 1.06
3347 reflections
207 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.35 e Å⁻³
Δρ_min = −0.20 e Å⁻³

Data collection: SMART (Bruker, 2002 ▸); cell refinement: SAINT (Bruker, 2002 ▸); data reduction: SAINT; program(s) used to solve structure: SHELXS2013 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015 ▸); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▸); software used to prepare material for publication: WinGX (Farrugia, 2012 ▸).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015004636/tk5361sup1.cif

e-71-00m85-sup1.cif^{(20.4KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015004636/tk5361Isup2.hkl

e-71-00m85-Isup2.hkl^{(183.9KB, hkl)}

Click here for additional data file.^{(1.2MB, tif)}

x y z . DOI: 10.1107/S2056989015004636/tk5361fig1.tif

Molecular structure of the title complex, showing the atom-numbering scheme and 30% probability ellipsoids. [Symmetry code: (i): −x + 1, y, −z + Inline graphic ]

Click here for additional data file.^{(3.3MB, tif)}

. DOI: 10.1107/S2056989015004636/tk5361fig2.tif

Part of the crystal structure of the title complex, showing the 3-D network of molecules linked by intermolecular N—H⋯O and O—H⋯O hydrogen bonds (dashed lines).

CCDC reference: 1052527

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

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
N9H9O21ⁱ	0.74(2)	2.51(2)	3.248(2)	173(2)
N9H9O22ⁱ	0.74(2)	2.37(2)	2.944(2)	134.7(19)
N17H17AO20ⁱⁱ	0.86(2)	2.14(2)	2.9937(17)	169(2)
O18H18O20	0.77(2)	1.92(2)	2.6897(14)	175(2)
O18H18O22	0.77(2)	2.50(2)	3.0345(16)	128(2)

Open in a new tab

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

Acknowledgments

This work was supported by the research fund of Chungnam National University.

supplementary crystallographic information

S1. Structural commentary

The heterocycles azole and benzazole have been of interest in several important functions in biological systems (Esparza-Ruiz et al., 2011; Eltayeb et al., 2011). benzimidazole compounds show a variety of biological properties such as inhibitory activities against enteroviruses and antibacterials (Xue et al., 2011; Chassaing et al., 2008; Sánchez-Guadarrama et al., 2009). Transition metal complexes with benzimidazole derivatives have been studied as models of some important biological molecules (Podunavac-Kuzmonovic et al., 1999). Motivated by these studies, the title complex has been synthesized and characterized by X-ray crystallography.

In the title complex, the Zn^II atom lies on a two-fold axis and is coordinated by one O atom and four N atoms of two bidentate imidazoleaniline ligands, forming a distorted trigonal bipyrdmidal geometry. The axial Zn1—N17 bond distance of 2.2147 (17) Å is longer than the equatorial Zn1—N2 distance of 2.0421 (11) Å. The N17—Zn1—N17ⁱ axial angle is 166.24 (7)°, and the angles of two N and one O atom in the equatorial plane is within the range of 115.17 (7) and 122.42 (3)°. The dihedral angle between the imidazole and aniline rings in the coordinated bidentate ligand is 23.86 (5)°. In the crystal, intermolecular N—H···O and O—H···O hydrogen bonds link the molecules into a three-dimensional network.

S2. Synthesis and crystallization

To a stirred solution of 2-(2-aminophenyl)-1H-benzimidazole (0.188 g, 0.9 mmol) in EtOH (20 ml) was added a solution of zinc nitrate hexahydrate (0.089 g, 0.3 mmol) in EtOH (10 mL) at 60 °. After 24 h of reflux, the color of solution turned yellow. The product was isolated as a pale yellow powder by removing the solvent. Yellow single crystals of the title complex were obtained from its methanol solution by slow evaporation of the solvent at room temperature within several days.

S3. Refinement

H atoms on NH, NH₂, and OH₂ groups were located in a difference Fourier map and refined freely [refined N—H distances = 0.74 (2)–0.87 (2), O—H = 0.77 (2)Å]. Other H atoms were positioned geometrically and refined using riding model, with d(C—H) = 0.93 Å, and with U_iso(H) = 1.2U_eq(C).