Diaqua­bis[N-(2-pyridylmeth­yl)­benzamide-κ²O,N]zinc(II) dinitrate

In the title compound, [Zn(C₁₃H₁₂N₂O)₂(H₂O)₂](NO₃)₂, the Zn^II 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.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.036
• wR factor = 0.101
• Data-to-parameter ratio = 14.5

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT415_ALERT_2_B Short Inter D-H..H-X       H1WB   ..  H4A     ..       1.91 Ang.
PLAT420_ALERT_2_B D-H Without Acceptor       O1W    -   H1WB   ...          ?

Alert level C
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .......          ?
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for        C10
PLAT244_ALERT_4_C Low   'Solvent' Ueq as Compared to Neighbors for         N3
PLAT710_ALERT_4_C Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... #          5
            N1  -ZN1 -N1  -C1    150.85  0.16   3.665   1.555   1.555   1.555
PLAT710_ALERT_4_C Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... #         10
            N1  -ZN1 -N1  -C5    -30.60  0.30   3.665   1.555   1.555   1.555
PLAT710_ALERT_4_C Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... #         11
            O1  -ZN1 -O1  -C7     12.00  0.00   3.665   1.555   1.555   1.555
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........          2

Alert level G
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature .        293 K
PLAT794_ALERT_5_G Check Predicted Bond Valency for Zn1         (2)       1.93

   0 ALERT level A = In general: serious problem
   2 ALERT level B = Potentially serious problem
   7 ALERT level C = Check and explain
   3 ALERT level G = General alerts; check

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   6 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

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S1. Comment

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 Zn^II 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

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).

S2. Experimental

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.

S3. Refinement

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 U_iso(H) = 1.2 U_eq of the parent atom.

Computing details

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

	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].
	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

Crystal data

[Zn(C13H12N2O)2(H2O)2](NO3)2	F(000) = 672
Mr = 649.93	Dx = 1.483 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
a = 11.054 (2) Å	Cell parameters from 3058 reflections
b = 8.9058 (18) Å	θ = 2.7–25.6°
c = 15.306 (3) Å	µ = 0.91 mm^−1
β = 105.037 (3)°	T = 293 K
V = 1455.1 (5) Å^3	Prism, colourless
Z = 2	0.30 × 0.19 × 0.08 mm

Data collection

Simens SMART 1000 CCD area-detector diffractometer	2849 independent reflections
Radiation source: fine-focus sealed tube	2313 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.019
Detector resolution: 8.33 pixels mm^-1	θmax = 26.1°, θmin = 1.9°
ω scans	h = −13→13
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	k = −7→10
Tmin = 0.772, Tmax = 0.931	l = −18→18
7832 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.101	H-atom parameters constrained
S = 1.03	w = 1/[σ^2(Fo^2) + (0.0516P)^2 + 0.6788P] where P = (Fo^2 + 2Fc^2)/3
2849 reflections	(Δ/σ)max < 0.001
196 parameters	Δρmax = 0.34 e Å^−3
0 restraints	Δρmin = −0.43 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
Zn1	0.5000	0.5000	0.0000	0.03717 (14)
N1	0.59165 (18)	0.5211 (2)	0.14516 (12)	0.0389 (4)
O1	0.31996 (16)	0.50820 (19)	0.01892 (11)	0.0513 (4)
O1W	0.49296 (15)	0.2660 (2)	0.01872 (12)	0.0559 (5)
H1WA	0.5626	0.2298	0.0235	0.067*
H1WB	0.4714	0.2486	0.0651	0.067*
C5	0.5456 (2)	0.5925 (3)	0.20741 (15)	0.0424 (5)
C4	0.6129 (3)	0.6010 (3)	0.29739 (16)	0.0570 (7)
H4A	0.5787	0.6497	0.3392	0.068*
N2	0.31605 (19)	0.5545 (3)	0.16206 (14)	0.0507 (5)
H2A	0.2841	0.5330	0.2061	0.061*
C1	0.7055 (2)	0.4593 (3)	0.17359 (16)	0.0485 (6)
H1A	0.7380	0.4090	0.1315	0.058*
C6	0.4180 (2)	0.6636 (3)	0.17684 (17)	0.0507 (6)
H6A	0.4082	0.7355	0.2221	0.061*
H6B	0.4123	0.7180	0.1210	0.061*
C8	0.1587 (2)	0.3897 (3)	0.06956 (17)	0.0477 (6)
C7	0.2714 (2)	0.4878 (3)	0.08311 (16)	0.0432 (5)
N3	0.3019 (2)	0.4922 (2)	0.38825 (16)	0.0549 (6)
C2	0.7769 (3)	0.4663 (3)	0.26170 (18)	0.0601 (7)
H2B	0.8562	0.4231	0.2781	0.072*
C12	−0.0099 (3)	0.2758 (4)	0.1182 (3)	0.0782 (9)
H12A	−0.0520	0.2610	0.1628	0.094*
C13	0.0940 (2)	0.3680 (3)	0.1351 (2)	0.0650 (8)
H13A	0.1208	0.4159	0.1907	0.078*
O3	0.2683 (3)	0.5981 (3)	0.33914 (19)	0.1082 (10)
C3	0.7297 (3)	0.5377 (4)	0.32484 (18)	0.0633 (8)
H3A	0.7758	0.5433	0.3849	0.076*
C9	0.1180 (3)	0.3175 (4)	−0.0121 (2)	0.0702 (8)
H9A	0.1605	0.3305	−0.0567	0.084*
O2	0.3366 (3)	0.5101 (3)	0.47054 (17)	0.1026 (10)
C11	−0.0506 (3)	0.2070 (4)	0.0371 (3)	0.0862 (11)
H11A	−0.1220	0.1473	0.0253	0.103*
O4	0.3071 (4)	0.3698 (3)	0.3566 (2)	0.1251 (11)
C10	0.0136 (3)	0.2255 (5)	−0.0280 (3)	0.0949 (12)
H10A	−0.0133	0.1758	−0.0831	0.114*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Zn1	0.0382 (2)	0.0444 (2)	0.0298 (2)	−0.00112 (15)	0.01025 (14)	0.00098 (15)
N1	0.0431 (10)	0.0437 (11)	0.0311 (9)	−0.0027 (8)	0.0119 (8)	−0.0016 (8)
O1	0.0410 (9)	0.0788 (13)	0.0366 (9)	−0.0026 (8)	0.0147 (7)	−0.0025 (8)
O1W	0.0628 (11)	0.0495 (10)	0.0563 (11)	−0.0011 (8)	0.0172 (9)	0.0093 (8)
C5	0.0519 (13)	0.0405 (12)	0.0381 (12)	−0.0098 (10)	0.0175 (10)	−0.0053 (10)
C4	0.0722 (18)	0.0623 (17)	0.0391 (13)	−0.0146 (14)	0.0191 (12)	−0.0146 (12)
N2	0.0493 (12)	0.0671 (13)	0.0426 (11)	−0.0068 (10)	0.0241 (9)	−0.0072 (10)
C1	0.0485 (14)	0.0596 (15)	0.0368 (12)	0.0062 (11)	0.0102 (10)	0.0017 (11)
C6	0.0545 (14)	0.0513 (14)	0.0504 (14)	−0.0026 (12)	0.0212 (11)	−0.0135 (11)
C8	0.0370 (11)	0.0530 (14)	0.0527 (14)	0.0046 (10)	0.0110 (10)	0.0048 (11)
C7	0.0374 (11)	0.0533 (14)	0.0408 (12)	0.0074 (10)	0.0136 (10)	0.0016 (10)
N3	0.0655 (14)	0.0513 (13)	0.0534 (14)	0.0030 (10)	0.0253 (11)	0.0008 (11)
C2	0.0557 (16)	0.0741 (19)	0.0432 (14)	0.0062 (13)	−0.0004 (12)	0.0042 (13)
C12	0.0532 (16)	0.082 (2)	0.109 (3)	−0.0063 (16)	0.0385 (18)	0.001 (2)
C13	0.0516 (15)	0.0738 (19)	0.0772 (19)	−0.0072 (14)	0.0306 (14)	−0.0094 (15)
O3	0.185 (3)	0.0732 (16)	0.0937 (18)	0.0554 (18)	0.0855 (19)	0.0338 (14)
C3	0.0707 (19)	0.0769 (19)	0.0346 (13)	−0.0110 (15)	−0.0003 (13)	−0.0049 (13)
C9	0.0664 (18)	0.084 (2)	0.0568 (17)	−0.0173 (16)	0.0100 (14)	−0.0020 (15)
O2	0.0866 (18)	0.167 (3)	0.0527 (14)	0.0014 (15)	0.0158 (13)	−0.0032 (14)
C11	0.0543 (18)	0.082 (2)	0.117 (3)	−0.0193 (17)	0.0126 (19)	0.009 (2)
O4	0.203 (3)	0.0602 (16)	0.118 (2)	0.0137 (18)	0.052 (2)	−0.0138 (15)
C10	0.089 (2)	0.107 (3)	0.075 (2)	−0.039 (2)	−0.0028 (19)	−0.010 (2)

Geometric parameters (Å, º)

Zn1—O1^i	2.0853 (17)	C6—H6A	0.9700
Zn1—O1	2.0853 (17)	C6—H6B	0.9700
Zn1—O1W	2.1081 (18)	C8—C9	1.373 (4)
Zn1—O1W^i	2.1081 (18)	C8—C13	1.388 (4)
Zn1—N1^i	2.1977 (19)	C8—C7	1.492 (3)
Zn1—N1	2.1977 (19)	N3—O4	1.201 (3)
N1—C1	1.338 (3)	N3—O3	1.203 (3)
N1—C5	1.350 (3)	N3—O2	1.228 (3)
O1—C7	1.249 (3)	C2—C3	1.368 (4)
O1W—H1WA	0.8200	C2—H2B	0.9300
O1W—H1WB	0.8201	C12—C11	1.353 (5)
C5—C4	1.387 (3)	C12—C13	1.380 (4)
C5—C6	1.505 (3)	C12—H12A	0.9300
C4—C3	1.371 (4)	C13—H13A	0.9300
C4—H4A	0.9300	C3—H3A	0.9300
N2—C7	1.322 (3)	C9—C10	1.385 (4)
N2—C6	1.460 (3)	C9—H9A	0.9300
N2—H2A	0.8600	C11—C10	1.374 (5)
C1—C2	1.376 (4)	C11—H11A	0.9300
C1—H1A	0.9300	C10—H10A	0.9300
O1^i—Zn1—O1	180.00 (13)	N2—C6—H6A	109.0
O1^i—Zn1—O1W	93.12 (7)	C5—C6—H6A	109.0
O1—Zn1—O1W	86.88 (7)	N2—C6—H6B	109.0
O1^i—Zn1—O1W^i	86.88 (7)	C5—C6—H6B	109.0
O1—Zn1—O1W^i	93.12 (7)	H6A—C6—H6B	107.8
O1W—Zn1—O1W^i	180.000 (15)	C9—C8—C13	119.0 (2)
O1^i—Zn1—N1^i	93.60 (7)	C9—C8—C7	117.7 (2)
O1—Zn1—N1^i	86.40 (7)	C13—C8—C7	123.3 (2)
O1W—Zn1—N1^i	91.67 (7)	O1—C7—N2	121.3 (2)
O1W^i—Zn1—N1^i	88.33 (7)	O1—C7—C8	119.3 (2)
O1^i—Zn1—N1	86.40 (7)	N2—C7—C8	119.4 (2)
O1—Zn1—N1	93.60 (7)	O4—N3—O3	119.9 (3)
O1W—Zn1—N1	88.33 (7)	O4—N3—O2	119.8 (3)
O1W^i—Zn1—N1	91.67 (7)	O3—N3—O2	120.2 (3)
N1^i—Zn1—N1	180.00 (4)	C3—C2—C1	119.1 (3)
C1—N1—C5	117.3 (2)	C3—C2—H2B	120.5
C1—N1—Zn1	116.20 (15)	C1—C2—H2B	120.5
C5—N1—Zn1	126.46 (16)	C11—C12—C13	120.2 (3)
C7—O1—Zn1	136.42 (16)	C11—C12—H12A	119.9
Zn1—O1W—H1WA	109.5	C13—C12—H12A	119.9
Zn1—O1W—H1WB	109.5	C12—C13—C8	120.5 (3)
H1WA—O1W—H1WB	109.0	C12—C13—H13A	119.8
N1—C5—C4	121.5 (2)	C8—C13—H13A	119.8
N1—C5—C6	118.2 (2)	C2—C3—C4	118.4 (2)
C4—C5—C6	120.2 (2)	C2—C3—H3A	120.8
C3—C4—C5	120.1 (2)	C4—C3—H3A	120.8
C3—C4—H4A	119.9	C8—C9—C10	119.8 (3)
C5—C4—H4A	119.9	C8—C9—H9A	120.1
C7—N2—C6	122.0 (2)	C10—C9—H9A	120.1
C7—N2—H2A	119.0	C12—C11—C10	120.0 (3)
C6—N2—H2A	119.0	C12—C11—H11A	120.0
N1—C1—C2	123.5 (2)	C10—C11—H11A	120.0
N1—C1—H1A	118.2	C11—C10—C9	120.5 (3)
C2—C1—H1A	118.2	C11—C10—H10A	119.8
N2—C6—C5	113.0 (2)	C9—C10—H10A	119.8
O1^i—Zn1—N1—C1	−27.82 (17)	C7—N2—C6—C5	−88.9 (3)
O1—Zn1—N1—C1	152.18 (17)	N1—C5—C6—N2	76.4 (3)
O1W—Zn1—N1—C1	65.42 (17)	C4—C5—C6—N2	−103.6 (3)
O1W^i—Zn1—N1—C1	−114.58 (17)	Zn1—O1—C7—N2	50.2 (3)
N1^i—Zn1—N1—C1	150.85 (16)	Zn1—O1—C7—C8	−131.5 (2)
O1^i—Zn1—N1—C5	150.74 (18)	C6—N2—C7—O1	4.6 (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—O1	4.3 (3)
O1W^i—Zn1—N1—C5	63.98 (18)	C13—C8—C7—O1	−175.9 (2)
N1^i—Zn1—N1—C5	−30.6 (3)	C9—C8—C7—N2	−177.4 (3)
O1^i—Zn1—O1—C7	121 (100)	C13—C8—C7—N2	2.4 (4)
O1W—Zn1—O1—C7	68.7 (2)	N1—C1—C2—C3	1.1 (5)
O1W^i—Zn1—O1—C7	−111.3 (2)	C11—C12—C13—C8	−0.8 (5)
N1^i—Zn1—O1—C7	160.6 (2)	C9—C8—C13—C12	−0.3 (4)
N1—Zn1—O1—C7	−19.4 (2)	C7—C8—C13—C12	179.9 (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—C6	179.7 (2)	C13—C8—C9—C10	0.3 (5)
Zn1—N1—C5—C6	1.1 (3)	C7—C8—C9—C10	−179.9 (3)
N1—C5—C4—C3	0.8 (4)	C13—C12—C11—C10	1.8 (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—C11	0.7 (6)
Zn1—N1—C1—C2	178.1 (2)

Symmetry code: (i) −x+1, −y+1, −z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1W—H1WA···O2^ii	0.82	2.24	2.934 (4)	142
N2—H2A···O3	0.86	2.17	2.919 (4)	146
C1—H1A···O1^i	0.93	2.34	2.901 (3)	118

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