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Acta Cryst. (2007). E63, m3068    [ doi:10.1107/S1600536807058357 ]

Diaquabis[N-(2-pyridylmethyl)benzamide-[kappa]2O,N]zinc(II) dinitrate

X.-R. Zhang, B.-P. Qi, F. Li and S. Bi

Abstract top

In the title compound, [Zn(C13H12N2O)2(H2O)2](NO3)2, the ZnII ion is located on an inversion center. Each Zn center is six-coordinated by two O atoms and two N atoms from two benzamide ligands, and two O atoms from two water molecules, in a distorted octahedral geometry with normal values of Zn-N [2.1977 (19) Å] and Zn-O [2.0853 (17) and 2.1081 (18) Å] coordinating bonds. Intermolecular N-H...O and O-H...O hydrogen bonds link cations and anions into layers parallel to the bc plane.

Comment top

Some benzamide molecules with the aminopyridine structure exhibit anti-ulcerogenic, sedative or anti-inflammatory properties (Arora et al., 2005; Nielsen et al., 2004). In order to search for aminopyridine derivatives with higher pharmacological properties, the title complex, (I), was synthesized and its structure is presented here.

The ZnII atoms, which are located on inversion centers, is six-coordinated by two O atoms and two N atoms from two benzamide ligands, and two O atoms from two water molecules (Fig. 1). The geometry around the Zn atom is distorted octahedral with the normal values of Zn—N [2.1977 (19) Å] and Zn—O [2.0853 (17), 2.1081 (18) Å] coordinating bonds. Two nitrate anions lie outside the coordination sphere, balancing the charge. The character due to donation of the non-bonding electron pair on the nitrogen (Fekner et al., 2004). The benzamide chelate is not planar and the two aromatic rings make a dihedral angle of 60.06 (1)°. There is an intramolecular C1—H1A···O1 hydrogen bond, which forms a six-number ring.

In the crystal strucure, intermolecular N—H···O and O—H···O hydrogen bonds (Table 1) link cations and anions into the layers parallell to bc plane (Fig. 2). The packing is further stabilized by C—H···π (C6—H6A···Cg1iii) interactions with the distance of H6A···Cg1iii 2.85 Å, where Cg1 denotes the centroid of N1/C1—C5 pyridine ring [symmetry code: (iii) −x + 1, y + 1/2, −z + 1/2].

Related literature top

For details of pharmacological properties of aminopyridine derivatives, see: Arora et al. (2005); Nielsen et al. (2004). For general background, see: Fekner et al. (2004).

Experimental top

To a cold solution of 2-(2-aminomethyl)pyridine (2 ml, 19 mmol) and triethylamine (2.63 ml, 19 mmol) in dry CH2Cl2 (25 ml) was added dropwise a solution of benzyl chloride (2 ml, 17.2 mmol) in dry CH2Cl2 (15 ml). Stirring was continued at room temperature for 1 h, then at 333 K for 5 h. After filtering, the filtrate was washed with water, dried over anhydrous Na2SO4, and then evaporated to give N-(pyridin-2-ylmethyl)benzamide as a yellow oil. To a solution of ligand (0.34 g, 1.6 mmol) in ethyl acetate (15 ml) was added slowly a solution of Zn(NO3)2·6H2O (0.24 g, 0.80 mmol) in ethyl acetate (10 ml). The mixture was stirred for 2 h until a white solid appeared. Light yellow crystals suitable for an X-ray diffraction study were obtained by slow evaporation of an ethyl acetate solution.

Refinement top

All H atoms were located in difference Fourier map, placed in idealized positions [O—H 0.82 Å, C—H 0.93–0.97 Å] and refined as riding, with Uiso(H) = 1.2 Ueq of the parent atom.

Computing details top

Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT (Siemens, 1996); program(s) used to solve structure: SHELXTL (Sheldrick, 1997); program(s) used to refine structure: SHELXTL (Sheldrick, 1997); molecular graphics: SHELXTL (Sheldrick, 1997); software used to prepare material for publication: SHELXTL (Sheldrick, 1997), PARST (Nardelli, 1995) and PLATON (Spek, 2003).

Figures top
[Figure 1] Fig. 1. The structure of the compound (I) showing 50% probability displacement ellipsoids and the atom numbering scheme [symmetry codes: (A) −x + 1, −y + 1, −z].
[Figure 2] Fig. 2. A portion of the crystal packing of (I). Hydrogen bonds are indicated by dashed lines.
Diaquabis[N-(2-pyridylmethyl)benzamide-κ2O,N]zinc(II) dinitrate top
Crystal data top
[Zn(C13H12N2O)2(H2O)2](NO3)2F000 = 672
Mr = 649.93Dx = 1.483 Mg m−3
Monoclinic, P21/cMo Kα radiation
λ = 0.71073 Å
a = 11.054 (2) ÅCell parameters from 3058 reflections
b = 8.9058 (18) Åθ = 2.7–25.6º
c = 15.306 (3) ŵ = 0.91 mm−1
β = 105.037 (3)ºT = 293 (2) K
V = 1455.1 (5) Å3Prism, colourless
Z = 20.30 × 0.19 × 0.08 mm
Data collection top
Simens SMART 1000 CCD area-detector
diffractometer		2849 independent reflections
Radiation source: fine-focus sealed tube2313 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.019
Detector resolution: 8.33 pixels mm-1θmax = 26.1º
T = 293(2) Kθmin = 1.9º
ω scansh = −13→13
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		k = −7→10
Tmin = 0.772, Tmax = 0.931l = −18→18
7832 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.036H-atom parameters constrained
wR(F2) = 0.101  w = 1/[σ2(Fo2) + (0.0516P)2 + 0.6788P]
where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max < 0.001
2849 reflectionsΔρmax = 0.34 e Å−3
196 parametersΔρmin = −0.43 e Å−3
Primary atom site location: structure-invariant direct methodsExtinction correction: none
Crystal data top
[Zn(C13H12N2O)2(H2O)2](NO3)2V = 1455.1 (5) Å3
Mr = 649.93Z = 2
Monoclinic, P21/cMo Kα
a = 11.054 (2) ŵ = 0.91 mm−1
b = 8.9058 (18) ÅT = 293 (2) K
c = 15.306 (3) Å0.30 × 0.19 × 0.08 mm
β = 105.037 (3)º
Data collection top
Simens SMART 1000 CCD area-detector
diffractometer		2849 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		2313 reflections with I > 2σ(I)
Tmin = 0.772, Tmax = 0.931Rint = 0.019
7832 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.036196 parameters
wR(F2) = 0.101H-atom parameters constrained
S = 1.03Δρmax = 0.34 e Å−3
2849 reflectionsΔρmin = −0.43 e Å−3
Special details top

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.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Zn10.50000.50000.00000.03717 (14)
N10.59165 (18)0.5211 (2)0.14516 (12)0.0389 (4)
O10.31996 (16)0.50820 (19)0.01892 (11)0.0513 (4)
O1W0.49296 (15)0.2660 (2)0.01872 (12)0.0559 (5)
H1WA0.56260.22980.02350.067*
H1WB0.47140.24860.06510.067*
C50.5456 (2)0.5925 (3)0.20741 (15)0.0424 (5)
C40.6129 (3)0.6010 (3)0.29739 (16)0.0570 (7)
H4A0.57870.64970.33920.068*
N20.31605 (19)0.5545 (3)0.16206 (14)0.0507 (5)
H2A0.28410.53300.20610.061*
C10.7055 (2)0.4593 (3)0.17359 (16)0.0485 (6)
H1A0.73800.40900.13150.058*
C60.4180 (2)0.6636 (3)0.17684 (17)0.0507 (6)
H6A0.40820.73550.22210.061*
H6B0.41230.71800.12100.061*
C80.1587 (2)0.3897 (3)0.06956 (17)0.0477 (6)
C70.2714 (2)0.4878 (3)0.08311 (16)0.0432 (5)
N30.3019 (2)0.4922 (2)0.38825 (16)0.0549 (6)
C20.7769 (3)0.4663 (3)0.26170 (18)0.0601 (7)
H2B0.85620.42310.27810.072*
C12−0.0099 (3)0.2758 (4)0.1182 (3)0.0782 (9)
H12A−0.05200.26100.16280.094*
C130.0940 (2)0.3680 (3)0.1351 (2)0.0650 (8)
H13A0.12080.41590.19070.078*
O30.2683 (3)0.5981 (3)0.33914 (19)0.1082 (10)
C30.7297 (3)0.5377 (4)0.32484 (18)0.0633 (8)
H3A0.77580.54330.38490.076*
C90.1180 (3)0.3175 (4)−0.0121 (2)0.0702 (8)
H9A0.16050.3305−0.05670.084*
O20.3366 (3)0.5101 (3)0.47054 (17)0.1026 (10)
C11−0.0506 (3)0.2070 (4)0.0371 (3)0.0862 (11)
H11A−0.12200.14730.02530.103*
O40.3071 (4)0.3698 (3)0.3566 (2)0.1251 (11)
C100.0136 (3)0.2255 (5)−0.0280 (3)0.0949 (12)
H10A−0.01330.1758−0.08310.114*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Zn10.0382 (2)0.0444 (2)0.0298 (2)−0.00112 (15)0.01025 (14)0.00098 (15)
N10.0431 (10)0.0437 (11)0.0311 (9)−0.0027 (8)0.0119 (8)−0.0016 (8)
O10.0410 (9)0.0788 (13)0.0366 (9)−0.0026 (8)0.0147 (7)−0.0025 (8)
O1W0.0628 (11)0.0495 (10)0.0563 (11)−0.0011 (8)0.0172 (9)0.0093 (8)
C50.0519 (13)0.0405 (12)0.0381 (12)−0.0098 (10)0.0175 (10)−0.0053 (10)
C40.0722 (18)0.0623 (17)0.0391 (13)−0.0146 (14)0.0191 (12)−0.0146 (12)
N20.0493 (12)0.0671 (13)0.0426 (11)−0.0068 (10)0.0241 (9)−0.0072 (10)
C10.0485 (14)0.0596 (15)0.0368 (12)0.0062 (11)0.0102 (10)0.0017 (11)
C60.0545 (14)0.0513 (14)0.0504 (14)−0.0026 (12)0.0212 (11)−0.0135 (11)
C80.0370 (11)0.0530 (14)0.0527 (14)0.0046 (10)0.0110 (10)0.0048 (11)
C70.0374 (11)0.0533 (14)0.0408 (12)0.0074 (10)0.0136 (10)0.0016 (10)
N30.0655 (14)0.0513 (13)0.0534 (14)0.0030 (10)0.0253 (11)0.0008 (11)
C20.0557 (16)0.0741 (19)0.0432 (14)0.0062 (13)−0.0004 (12)0.0042 (13)
C120.0532 (16)0.082 (2)0.109 (3)−0.0063 (16)0.0385 (18)0.001 (2)
C130.0516 (15)0.0738 (19)0.0772 (19)−0.0072 (14)0.0306 (14)−0.0094 (15)
O30.185 (3)0.0732 (16)0.0937 (18)0.0554 (18)0.0855 (19)0.0338 (14)
C30.0707 (19)0.0769 (19)0.0346 (13)−0.0110 (15)−0.0003 (13)−0.0049 (13)
C90.0664 (18)0.084 (2)0.0568 (17)−0.0173 (16)0.0100 (14)−0.0020 (15)
O20.0866 (18)0.167 (3)0.0527 (14)0.0014 (15)0.0158 (13)−0.0032 (14)
C110.0543 (18)0.082 (2)0.117 (3)−0.0193 (17)0.0126 (19)0.009 (2)
O40.203 (3)0.0602 (16)0.118 (2)0.0137 (18)0.052 (2)−0.0138 (15)
C100.089 (2)0.107 (3)0.075 (2)−0.039 (2)−0.0028 (19)−0.010 (2)
Geometric parameters (Å, °) top
Zn1—O1i2.0853 (17)C6—H6A0.9700
Zn1—O12.0853 (17)C6—H6B0.9700
Zn1—O1W2.1081 (18)C8—C91.373 (4)
Zn1—O1Wi2.1081 (18)C8—C131.388 (4)
Zn1—N1i2.1977 (19)C8—C71.492 (3)
Zn1—N12.1977 (19)N3—O41.201 (3)
N1—C11.338 (3)N3—O31.203 (3)
N1—C51.350 (3)N3—O21.228 (3)
O1—C71.249 (3)C2—C31.368 (4)
O1W—H1WA0.8200C2—H2B0.9300
O1W—H1WB0.8201C12—C111.353 (5)
C5—C41.387 (3)C12—C131.380 (4)
C5—C61.505 (3)C12—H12A0.9300
C4—C31.371 (4)C13—H13A0.9300
C4—H4A0.9300C3—H3A0.9300
N2—C71.322 (3)C9—C101.385 (4)
N2—C61.460 (3)C9—H9A0.9300
N2—H2A0.8600C11—C101.374 (5)
C1—C21.376 (4)C11—H11A0.9300
C1—H1A0.9300C10—H10A0.9300
O1i—Zn1—O1180.00 (13)N2—C6—H6A109.0
O1i—Zn1—O1W93.12 (7)C5—C6—H6A109.0
O1—Zn1—O1W86.88 (7)N2—C6—H6B109.0
O1i—Zn1—O1Wi86.88 (7)C5—C6—H6B109.0
O1—Zn1—O1Wi93.12 (7)H6A—C6—H6B107.8
O1W—Zn1—O1Wi180.000 (15)C9—C8—C13119.0 (2)
O1i—Zn1—N1i93.60 (7)C9—C8—C7117.7 (2)
O1—Zn1—N1i86.40 (7)C13—C8—C7123.3 (2)
O1W—Zn1—N1i91.67 (7)O1—C7—N2121.3 (2)
O1Wi—Zn1—N1i88.33 (7)O1—C7—C8119.3 (2)
O1i—Zn1—N186.40 (7)N2—C7—C8119.4 (2)
O1—Zn1—N193.60 (7)O4—N3—O3119.9 (3)
O1W—Zn1—N188.33 (7)O4—N3—O2119.8 (3)
O1Wi—Zn1—N191.67 (7)O3—N3—O2120.2 (3)
N1i—Zn1—N1180.00 (4)C3—C2—C1119.1 (3)
C1—N1—C5117.3 (2)C3—C2—H2B120.5
C1—N1—Zn1116.20 (15)C1—C2—H2B120.5
C5—N1—Zn1126.46 (16)C11—C12—C13120.2 (3)
C7—O1—Zn1136.42 (16)C11—C12—H12A119.9
Zn1—O1W—H1WA109.5C13—C12—H12A119.9
Zn1—O1W—H1WB109.5C12—C13—C8120.5 (3)
H1WA—O1W—H1WB109.0C12—C13—H13A119.8
N1—C5—C4121.5 (2)C8—C13—H13A119.8
N1—C5—C6118.2 (2)C2—C3—C4118.4 (2)
C4—C5—C6120.2 (2)C2—C3—H3A120.8
C3—C4—C5120.1 (2)C4—C3—H3A120.8
C3—C4—H4A119.9C8—C9—C10119.8 (3)
C5—C4—H4A119.9C8—C9—H9A120.1
C7—N2—C6122.0 (2)C10—C9—H9A120.1
C7—N2—H2A119.0C12—C11—C10120.0 (3)
C6—N2—H2A119.0C12—C11—H11A120.0
N1—C1—C2123.5 (2)C10—C11—H11A120.0
N1—C1—H1A118.2C11—C10—C9120.5 (3)
C2—C1—H1A118.2C11—C10—H10A119.8
N2—C6—C5113.0 (2)C9—C10—H10A119.8
O1i—Zn1—N1—C1−27.82 (17)C7—N2—C6—C5−88.9 (3)
O1—Zn1—N1—C1152.18 (17)N1—C5—C6—N276.4 (3)
O1W—Zn1—N1—C165.42 (17)C4—C5—C6—N2−103.6 (3)
O1Wi—Zn1—N1—C1−114.58 (17)Zn1—O1—C7—N250.2 (3)
N1i—Zn1—N1—C1150.85 (16)Zn1—O1—C7—C8−131.5 (2)
O1i—Zn1—N1—C5150.74 (18)C6—N2—C7—O14.6 (4)
O1—Zn1—N1—C5−29.26 (18)C6—N2—C7—C8−173.7 (2)
O1W—Zn1—N1—C5−116.02 (18)C9—C8—C7—O14.3 (3)
O1Wi—Zn1—N1—C563.98 (18)C13—C8—C7—O1−175.9 (2)
N1i—Zn1—N1—C5−30.6 (3)C9—C8—C7—N2−177.4 (3)
O1i—Zn1—O1—C7121 (100)C13—C8—C7—N22.4 (4)
O1W—Zn1—O1—C768.7 (2)N1—C1—C2—C31.1 (5)
O1Wi—Zn1—O1—C7−111.3 (2)C11—C12—C13—C8−0.8 (5)
N1i—Zn1—O1—C7160.6 (2)C9—C8—C13—C12−0.3 (4)
N1—Zn1—O1—C7−19.4 (2)C7—C8—C13—C12179.9 (3)
C1—N1—C5—C4−0.3 (3)C1—C2—C3—C4−0.6 (5)
Zn1—N1—C5—C4−178.86 (18)C5—C4—C3—C2−0.3 (4)
C1—N1—C5—C6179.7 (2)C13—C8—C9—C100.3 (5)
Zn1—N1—C5—C61.1 (3)C7—C8—C9—C10−179.9 (3)
N1—C5—C4—C30.8 (4)C13—C12—C11—C101.8 (6)
C6—C5—C4—C3−179.2 (2)C12—C11—C10—C9−1.8 (6)
C5—N1—C1—C2−0.6 (4)C8—C9—C10—C110.7 (6)
Zn1—N1—C1—C2178.1 (2)
Symmetry codes: (i) −x+1, −y+1, −z.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1W—H1WA···O2ii0.822.242.934 (4)142
N2—H2A···O30.862.172.919 (4)146
C1—H1A···O1i0.932.342.901 (3)118
Symmetry codes: (ii) −x+1, y−1/2, −z+1/2; (i) −x+1, −y+1, −z.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1W—H1WA···O2i0.822.242.934 (4)142
N2—H2A···O30.862.172.919 (4)146
C1—H1A···O1ii0.932.342.901 (3)118
Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) −x+1, −y+1, −z.
Acknowledgements top

This project was supported by the Natural Science Foundation of Shandong Province (grant Nos. Z2006B01 and Y2006B07).

references
References top

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