metal-organic compounds
H-benzimidazol-2-yl-κN3)aniline-κN]zinc dinitrate
of aquabis[2-(1aDepartment of Chemistry, Chungnam National University, Daejeon 305-764, Republic of Korea
*Correspondence e-mail: skkang@cnu.ac.kr
The cation of the complex title salt, [Zn(C13H11N3)2(H2O)](NO3)2, lies about a twofold rotation axis, which passes through the ZnII atom and the O atom of the aqua ligand. The ZnII 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.
CCDC reference: 1052527
1. 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).
2. Experimental
2.1. Crystal data
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2.3. Refinement
|
Data collection: SMART (Bruker, 2002); cell 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).
Supporting information
CCDC reference: 1052527
10.1107/S2056989015004636/tk5361sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S2056989015004636/tk5361Isup2.hkl
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 ZnII 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.
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.
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 ZnII 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.
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).
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.
detailsH 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 Uiso(H) = 1.2Ueq(C).
Data collection: SMART (Bruker, 2002); cell
SAINT (Bruker, 2002); data reduction: SAINT (Bruker, 2002); 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).Fig. 1. Molecular structure of the title complex, showing the atom-numbering scheme and 30% probability ellipsoids. [Symmetry code: (i): -x + 1, y, -z + 1/2] | |
Fig. 2. 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). |
[Zn(C13H11N3)2(H2O)](NO3)2 | F(000) = 1288 |
Mr = 625.9 | Dx = 1.542 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 6738 reflections |
a = 16.2892 (9) Å | θ = 2.7–28.0° |
b = 15.0782 (8) Å | µ = 0.97 mm−1 |
c = 11.6840 (6) Å | T = 296 K |
β = 110.0178 (8)° | Block, yellow |
V = 2696.4 (2) Å3 | 0.21 × 0.2 × 0.18 mm |
Z = 4 |
Bruker SMART CCD area-detector diffractometer | 3007 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.020 |
φ and ω scans | θmax = 28.3°, θmin = 1.9° |
Absorption correction: multi-scan (SADABS; Bruker, 2002) | h = −21→21 |
Tmin = 0.546, Tmax = 0.726 | k = −19→20 |
13558 measured reflections | l = −15→11 |
3347 independent reflections |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.027 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.078 | w = 1/[σ2(Fo2) + (0.0439P)2 + 1.0441P] where P = (Fo2 + 2Fc2)/3 |
S = 1.06 | (Δ/σ)max < 0.001 |
3347 reflections | Δρmax = 0.35 e Å−3 |
207 parameters | Δρmin = −0.20 e Å−3 |
[Zn(C13H11N3)2(H2O)](NO3)2 | V = 2696.4 (2) Å3 |
Mr = 625.9 | Z = 4 |
Monoclinic, C2/c | Mo Kα radiation |
a = 16.2892 (9) Å | µ = 0.97 mm−1 |
b = 15.0782 (8) Å | T = 296 K |
c = 11.6840 (6) Å | 0.21 × 0.2 × 0.18 mm |
β = 110.0178 (8)° |
Bruker SMART CCD area-detector diffractometer | 3347 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2002) | 3007 reflections with I > 2σ(I) |
Tmin = 0.546, Tmax = 0.726 | Rint = 0.020 |
13558 measured reflections |
R[F2 > 2σ(F2)] = 0.027 | 0 restraints |
wR(F2) = 0.078 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.35 e Å−3 |
3347 reflections | Δρmin = −0.20 e Å−3 |
207 parameters |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
Zn1 | 0.5 | 0.15270 (2) | 0.25 | 0.03249 (9) | |
N2 | 0.59261 (7) | 0.22530 (8) | 0.37818 (10) | 0.0317 (2) | |
C3 | 0.61501 (9) | 0.22740 (10) | 0.50420 (12) | 0.0331 (3) | |
C4 | 0.60111 (11) | 0.16542 (11) | 0.58370 (15) | 0.0436 (4) | |
H4 | 0.5726 | 0.1121 | 0.5556 | 0.052* | |
C5 | 0.63145 (12) | 0.18640 (14) | 0.70620 (15) | 0.0522 (4) | |
H5 | 0.6242 | 0.1458 | 0.7619 | 0.063* | |
C6 | 0.67293 (11) | 0.26740 (13) | 0.74848 (14) | 0.0499 (4) | |
H6 | 0.6914 | 0.2797 | 0.8314 | 0.06* | |
C7 | 0.68716 (10) | 0.32919 (11) | 0.67076 (14) | 0.0413 (3) | |
H7 | 0.7143 | 0.3831 | 0.6989 | 0.05* | |
C8 | 0.65875 (9) | 0.30678 (10) | 0.54755 (12) | 0.0338 (3) | |
N9 | 0.66310 (9) | 0.35081 (9) | 0.44630 (12) | 0.0348 (3) | |
H9 | 0.6898 (13) | 0.3906 (14) | 0.4450 (18) | 0.045 (5)* | |
C10 | 0.62329 (8) | 0.29990 (9) | 0.34760 (12) | 0.0309 (3) | |
C11 | 0.61314 (9) | 0.32625 (10) | 0.22259 (13) | 0.0346 (3) | |
C12 | 0.61377 (12) | 0.41579 (12) | 0.19286 (16) | 0.0496 (4) | |
H12 | 0.6228 | 0.4586 | 0.2533 | 0.059* | |
C13 | 0.60111 (15) | 0.44164 (14) | 0.07450 (18) | 0.0645 (6) | |
H13 | 0.601 | 0.5015 | 0.0551 | 0.077* | |
C14 | 0.58865 (16) | 0.37784 (16) | −0.01468 (18) | 0.0660 (6) | |
H14 | 0.5801 | 0.395 | −0.0944 | 0.079* | |
C15 | 0.58871 (13) | 0.28936 (13) | 0.01287 (15) | 0.0524 (4) | |
H15 | 0.5804 | 0.2473 | −0.0483 | 0.063* | |
C16 | 0.60098 (9) | 0.26197 (11) | 0.13089 (13) | 0.0372 (3) | |
N17 | 0.59641 (9) | 0.17030 (9) | 0.15649 (13) | 0.0397 (3) | |
H17A | 0.5924 (14) | 0.1410 (14) | 0.092 (2) | 0.053 (6)* | |
H17B | 0.6415 (14) | 0.1544 (11) | 0.2191 (19) | 0.040 (5)* | |
O18 | 0.5 | 0.02352 (11) | 0.25 | 0.0668 (7) | |
H18 | 0.5330 (14) | −0.0001 (16) | 0.3054 (19) | 0.066 (7)* | |
N19 | 0.67858 (9) | −0.01854 (9) | 0.48037 (12) | 0.0434 (3) | |
O20 | 0.60669 (8) | −0.05918 (8) | 0.44950 (11) | 0.0528 (3) | |
O21 | 0.73467 (10) | −0.03031 (13) | 0.58020 (13) | 0.0808 (5) | |
O22 | 0.69082 (10) | 0.03590 (10) | 0.40974 (15) | 0.0712 (4) |
U11 | U22 | U33 | U12 | U13 | U23 | |
Zn1 | 0.03883 (14) | 0.02325 (12) | 0.03001 (13) | 0 | 0.00485 (9) | 0 |
N2 | 0.0331 (5) | 0.0301 (6) | 0.0296 (5) | −0.0014 (4) | 0.0078 (4) | −0.0025 (4) |
C3 | 0.0311 (6) | 0.0359 (7) | 0.0303 (6) | 0.0021 (5) | 0.0081 (5) | −0.0015 (5) |
C4 | 0.0476 (9) | 0.0412 (8) | 0.0396 (8) | −0.0031 (6) | 0.0120 (7) | 0.0035 (6) |
C5 | 0.0563 (10) | 0.0629 (11) | 0.0368 (8) | −0.0011 (8) | 0.0153 (7) | 0.0108 (8) |
C6 | 0.0474 (9) | 0.0708 (12) | 0.0292 (7) | −0.0006 (8) | 0.0102 (6) | −0.0037 (7) |
C7 | 0.0373 (7) | 0.0496 (9) | 0.0343 (7) | −0.0013 (6) | 0.0090 (6) | −0.0097 (6) |
C8 | 0.0288 (6) | 0.0392 (7) | 0.0320 (7) | 0.0017 (5) | 0.0087 (5) | −0.0040 (5) |
N9 | 0.0362 (6) | 0.0332 (6) | 0.0344 (6) | −0.0076 (5) | 0.0114 (5) | −0.0069 (5) |
C10 | 0.0281 (6) | 0.0316 (7) | 0.0326 (6) | 0.0000 (5) | 0.0102 (5) | −0.0045 (5) |
C11 | 0.0344 (7) | 0.0377 (7) | 0.0328 (7) | −0.0055 (5) | 0.0130 (5) | −0.0027 (5) |
C12 | 0.0633 (11) | 0.0425 (9) | 0.0426 (8) | −0.0154 (8) | 0.0177 (8) | −0.0028 (7) |
C13 | 0.0902 (15) | 0.0509 (11) | 0.0520 (11) | −0.0227 (10) | 0.0240 (10) | 0.0093 (8) |
C14 | 0.0855 (15) | 0.0755 (14) | 0.0402 (9) | −0.0255 (12) | 0.0256 (9) | 0.0052 (9) |
C15 | 0.0620 (11) | 0.0649 (11) | 0.0364 (8) | −0.0171 (9) | 0.0246 (7) | −0.0087 (8) |
C16 | 0.0336 (7) | 0.0448 (8) | 0.0364 (7) | −0.0050 (6) | 0.0162 (6) | −0.0060 (6) |
N17 | 0.0429 (7) | 0.0391 (7) | 0.0367 (7) | 0.0044 (5) | 0.0129 (6) | −0.0102 (5) |
O18 | 0.0787 (14) | 0.0254 (8) | 0.0592 (12) | 0 | −0.0243 (10) | 0 |
N19 | 0.0440 (7) | 0.0394 (7) | 0.0416 (7) | −0.0037 (5) | 0.0079 (5) | −0.0051 (5) |
O20 | 0.0555 (7) | 0.0511 (7) | 0.0437 (6) | −0.0187 (6) | 0.0066 (5) | 0.0105 (5) |
O21 | 0.0619 (9) | 0.1084 (14) | 0.0499 (8) | 0.0073 (8) | −0.0093 (7) | −0.0063 (8) |
O22 | 0.0671 (9) | 0.0601 (9) | 0.0866 (11) | −0.0203 (7) | 0.0266 (8) | 0.0165 (7) |
Zn1—O18 | 1.9479 (17) | N9—H9 | 0.74 (2) |
Zn1—N2i | 2.0421 (11) | C10—C11 | 1.467 (2) |
Zn1—N2 | 2.0421 (11) | C11—C12 | 1.395 (2) |
Zn1—N17i | 2.2147 (14) | C11—C16 | 1.408 (2) |
Zn1—N17 | 2.2147 (14) | C12—C13 | 1.383 (3) |
N2—C10 | 1.3285 (18) | C12—H12 | 0.93 |
N2—C3 | 1.3908 (17) | C13—C14 | 1.381 (3) |
C3—C4 | 1.390 (2) | C13—H13 | 0.93 |
C3—C8 | 1.396 (2) | C14—C15 | 1.372 (3) |
C4—C5 | 1.382 (2) | C14—H14 | 0.93 |
C4—H4 | 0.93 | C15—C16 | 1.387 (2) |
C5—C6 | 1.401 (3) | C15—H15 | 0.93 |
C5—H5 | 0.93 | C16—N17 | 1.422 (2) |
C6—C7 | 1.375 (2) | N17—H17A | 0.86 (2) |
C6—H6 | 0.93 | N17—H17B | 0.87 (2) |
C7—C8 | 1.395 (2) | O18—H18 | 0.77 (2) |
C7—H7 | 0.93 | N19—O21 | 1.2235 (18) |
C8—N9 | 1.379 (2) | N19—O22 | 1.228 (2) |
N9—C10 | 1.3518 (18) | N19—O20 | 1.2601 (17) |
O18—Zn1—N2i | 122.42 (3) | C8—N9—H9 | 127.4 (15) |
O18—Zn1—N2 | 122.42 (3) | N2—C10—N9 | 111.48 (12) |
N2i—Zn1—N2 | 115.17 (7) | N2—C10—C11 | 124.91 (12) |
O18—Zn1—N17i | 96.88 (4) | N9—C10—C11 | 123.58 (13) |
N2i—Zn1—N17i | 80.04 (5) | C12—C11—C16 | 119.21 (14) |
N2—Zn1—N17i | 92.55 (5) | C12—C11—C10 | 120.13 (14) |
O18—Zn1—N17 | 96.88 (4) | C16—C11—C10 | 120.65 (14) |
N2i—Zn1—N17 | 92.55 (5) | C13—C12—C11 | 120.70 (17) |
N2—Zn1—N17 | 80.04 (5) | C13—C12—H12 | 119.6 |
N17i—Zn1—N17 | 166.24 (7) | C11—C12—H12 | 119.6 |
C10—N2—C3 | 106.20 (11) | C14—C13—C12 | 119.43 (18) |
C10—N2—Zn1 | 120.54 (9) | C14—C13—H13 | 120.3 |
C3—N2—Zn1 | 130.45 (10) | C12—C13—H13 | 120.3 |
C4—C3—N2 | 130.43 (14) | C15—C14—C13 | 120.80 (17) |
C4—C3—C8 | 120.91 (13) | C15—C14—H14 | 119.6 |
N2—C3—C8 | 108.66 (12) | C13—C14—H14 | 119.6 |
C5—C4—C3 | 117.13 (16) | C14—C15—C16 | 120.73 (17) |
C5—C4—H4 | 121.4 | C14—C15—H15 | 119.6 |
C3—C4—H4 | 121.4 | C16—C15—H15 | 119.6 |
C4—C5—C6 | 121.54 (16) | C15—C16—C11 | 119.12 (15) |
C4—C5—H5 | 119.2 | C15—C16—N17 | 119.91 (15) |
C6—C5—H5 | 119.2 | C11—C16—N17 | 120.88 (14) |
C7—C6—C5 | 121.85 (15) | C16—N17—Zn1 | 108.50 (9) |
C7—C6—H6 | 119.1 | C16—N17—H17A | 107.9 (14) |
C5—C6—H6 | 119.1 | Zn1—N17—H17A | 121.4 (14) |
C6—C7—C8 | 116.50 (15) | C16—N17—H17B | 110.7 (11) |
C6—C7—H7 | 121.7 | Zn1—N17—H17B | 95.1 (13) |
C8—C7—H7 | 121.7 | H17A—N17—H17B | 112.7 (18) |
N9—C8—C7 | 132.26 (14) | Zn1—O18—H18 | 117.5 (18) |
N9—C8—C3 | 105.73 (12) | O21—N19—O22 | 119.85 (16) |
C7—C8—C3 | 122.00 (14) | O21—N19—O20 | 121.32 (16) |
C10—N9—C8 | 107.93 (12) | O22—N19—O20 | 118.78 (14) |
C10—N9—H9 | 123.6 (15) |
Symmetry code: (i) −x+1, y, −z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N9—H9···O21ii | 0.74 (2) | 2.51 (2) | 3.248 (2) | 173 (2) |
N9—H9···O22ii | 0.74 (2) | 2.37 (2) | 2.944 (2) | 134.7 (19) |
N17—H17A···O20iii | 0.86 (2) | 2.14 (2) | 2.9937 (17) | 169 (2) |
O18—H18···O20 | 0.77 (2) | 1.92 (2) | 2.6897 (14) | 175 (2) |
O18—H18···O22 | 0.77 (2) | 2.50 (2) | 3.0345 (16) | 128 (2) |
Symmetry codes: (ii) −x+3/2, −y+1/2, −z+1; (iii) x, −y, z−1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N9—H9···O21i | 0.74 (2) | 2.51 (2) | 3.248 (2) | 173 (2) |
N9—H9···O22i | 0.74 (2) | 2.37 (2) | 2.944 (2) | 134.7 (19) |
N17—H17A···O20ii | 0.86 (2) | 2.14 (2) | 2.9937 (17) | 169 (2) |
O18—H18···O20 | 0.77 (2) | 1.92 (2) | 2.6897 (14) | 175 (2) |
O18—H18···O22 | 0.77 (2) | 2.50 (2) | 3.0345 (16) | 128 (2) |
Symmetry codes: (i) −x+3/2, −y+1/2, −z+1; (ii) x, −y, z−1/2. |
Acknowledgements
This work was supported by the research fund of Chungnam National University.
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