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Acta Cryst. (2007). E63, m2058    [ doi:10.1107/S1600536807031054 ]

Dichloridobis[N-(2-pyridylmethyl)benzamide-[kappa]2N,O]cadmium(II)

S.-F. Zhang, X.-G. Yang, Z. Liu, F.-L. Xu and B.-R. Hou

Abstract top

In the title compound, [CdCl2(C13H12N2O)2], the CdII ion is situated on an inversion centre, coordinated by two O atoms [Cd-O = 2.3878 (17) Å] and two N atoms [Cd-N = 2.3404 (15) Å] from two N-(2-pyridylmethyl)benzamide ligands, and two Cl atoms [Cd-Cl = 2.5566 (6) Å], in a distorted octahedral geometry. In the crystal structure, intermolecular N-H...Cl hydrogen bonds [N...Cl = 3.1705 (18) Å] and [pi]-[pi] interactions, with a distance of 3.868 (3) Å between the centroids of the phenyl and pyridyl rings of neighbouring molecules, lead to the formation of two-dimensional layers parallel to the bc plane.

Comment top

It is known that some 2-pyridylmethyl benzamide derivatives as N– or O-donors exhibit excellent coordination capability to form supramolecular frameworks. Self-assembly by H-bonding, π–π stacking, and van der Waals interactions is also an important process in the formation of noncovalent supramolecular frameworks (MacDonald et al., 2000; Noverson et al., 2002). The title compound, (I), was separated by employing 2-pyridylmethyl benzamide as ligand. Here we present its crystal structure.

The Cd(II) atom is coordinated by two O atoms and two N atoms from two benzamide ligands, and bonded to two Cl atoms with the Cd–O distance of 2.388 Å, Cd–N distance of 2.340 Å, and Cd–Cl distance of 2.557 Å, respectively (Fig. 1). The phenyl ring and pyridyl ring in the 2-pyridylmethyl benzamide molecule are rigid, and possess of typical bond lengths and angles. The amide C–N bond is known to possess a partial double-bond character due to donation of the non-bonding electron pair on the nitrogen (Fekner et al., 2004).

In the crystal structure, the N atoms on the pyridyl rings act as donors to form N–H···Cl hydrogen bonds (Table 1), which link the [(C13H12N2O)2CdCl2] molecules into two-dimensional layers with four-membered ring {Cd4} extending along the bc plane (Fig. 2). The packing of adjacent layers is also stabilized by intermolecular π–π stacking interactions (Fig. 3), with relatively short distance Cg1···Cg2i 3.868 (3) Å, where Cg1 and Cg2 are centroids of C1–C6 and N1/C8–C12 rings, respectively [symmetry code: (i) -x + 2, y + 1/2, -z + 3/2].

Related literature top

For a related crystal structure, see: Zhang et al. (2006). For general background, see: MacDonald et al. (2000); Noverson et al. (2002); 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 anhydrous CH2Cl2 (25 ml) was added dropwise a solution of benzyl chloride (2 ml, 17.2 mmol) in anhydrous 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 the oil (0.16 g, 0.75 mmol) in ethyl acetate (10 ml), 0.114 g (0.5 mmol) CdCl2 powder was slowly added. After stirring for four hours, the solution was filtered to remove the precipitate and placed in a desiccator filled with phosphorus pentaoxide. Colourless crystals were obtained about one month later.

Refinement top

The H2B atom (attached to N2) was located on a difference Fourier map and isotropically refined. The C-bound H-atoms were geometrically positioned (C—H 0.93–0.97 Å) and refined using a riding model, with Uiso(H) = 1.2Ueq(C).

Computing details top

Data collection: RAPID-AUTO (Rigaku, 2001); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 1999); software used to prepare material for publication: SHELXTL.

Figures top
[Figure 1] Fig. 1. View of the title compound, with displacement ellipsoids drawn at the 30% probability level [symmetry code: (i) -x + 2, -y, -z + 1].
[Figure 2] Fig. 2. Two-dimensional layers parallel to bc plane in (I).
[Figure 3] Fig. 3. Packing diagram for (I) viewed down the b axis.
Dichloridobis[N-(2-pyridylmethyl)benzamide-κ2N,O]cadmium(II) top
Crystal data top
[CdCl2(C13H12N2O)2]F(000) = 612.0
Mr = 607.80Dx = 1.609 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 5099 reflections
a = 11.800 (2) Åθ = 3.2–27.5°
b = 8.5536 (17) ŵ = 1.12 mm−1
c = 12.909 (3) ÅT = 153 K
β = 105.60 (3)°Block, colourless
V = 1254.9 (5) Å30.42 × 0.34 × 0.24 mm
Z = 2
Data collection top
Rigaku R-AXIS RAPID IP area-detector
diffractometer		2876 independent reflections
Radiation source: fine-focus sealed tube2620 reflections with I > 2σ(I)
graphiteRint = 0.033
ω scansθmax = 27.5°, θmin = 3.2°
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)		h = −15→15
Tmin = 0.642, Tmax = 0.762k = −11→11
11378 measured reflectionsl = −15→16
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)] = 0.025H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.066 w = 1/[σ2(Fo2) + (0.0358P)2 + 0.9904P]
where P = (Fo2 + 2Fc2)/3
S = 1.01(Δ/σ)max < 0.001
2876 reflectionsΔρmax = 0.69 e Å−3
165 parametersΔρmin = −0.75 e Å−3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0144 (10)
Crystal data top
[CdCl2(C13H12N2O)2]V = 1254.9 (5) Å3
Mr = 607.80Z = 2
Monoclinic, P21/cMo Kα radiation
a = 11.800 (2) ŵ = 1.12 mm−1
b = 8.5536 (17) ÅT = 153 K
c = 12.909 (3) Å0.42 × 0.34 × 0.24 mm
β = 105.60 (3)°
Data collection top
Rigaku R-AXIS RAPID IP area-detector
diffractometer		2876 independent reflections
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)		2620 reflections with I > 2σ(I)
Tmin = 0.642, Tmax = 0.762Rint = 0.033
11378 measured reflectionsθmax = 27.5°
Refinement top
R[F2 > 2σ(F2)] = 0.025H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.066Δρmax = 0.69 e Å−3
S = 1.01Δρmin = −0.75 e Å−3
2876 reflectionsAbsolute structure: ?
165 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
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
Cd11.00000.00000.50000.01528 (9)
Cl10.93804 (4)−0.28494 (5)0.50928 (3)0.02087 (12)
N10.88328 (14)0.07711 (18)0.61167 (12)0.0176 (3)
N21.11051 (14)0.0398 (2)0.79049 (13)0.0183 (3)
C90.71170 (17)0.2170 (2)0.62332 (16)0.0245 (4)
H9A0.64970.28340.59140.029*
C131.00864 (16)−0.0644 (2)0.76345 (14)0.0180 (4)
H13A1.0008−0.11620.82800.022*
H13B1.0199−0.14390.71350.022*
C80.79178 (17)0.1707 (2)0.56796 (15)0.0218 (4)
H8A0.78160.20580.49790.026*
C120.89841 (17)0.0275 (2)0.71330 (15)0.0164 (3)
C110.82046 (17)0.0666 (2)0.77302 (15)0.0208 (4)
H11A0.83170.02890.84260.025*
C100.72589 (17)0.1625 (3)0.72706 (17)0.0257 (4)
H10A0.67250.19000.76540.031*
H2B1.116 (2)0.097 (3)0.843 (2)0.022 (6)*
O11.17479 (13)−0.01963 (15)0.64476 (11)0.0197 (3)
C61.34268 (17)0.2209 (2)0.69617 (16)0.0240 (4)
H6A1.31500.19400.62400.029*
C51.43790 (18)0.3211 (3)0.72918 (19)0.0311 (5)
H5A1.47340.36190.67890.037*
C31.42620 (19)0.3022 (3)0.91142 (19)0.0335 (5)
H3A1.45410.32970.98350.040*
C71.18598 (16)0.0533 (2)0.73064 (14)0.0174 (3)
C11.28839 (16)0.1604 (2)0.77084 (15)0.0200 (4)
C41.48055 (19)0.3610 (3)0.8368 (2)0.0337 (5)
H4A1.54530.42690.85880.040*
C21.33055 (18)0.2026 (3)0.87908 (16)0.0265 (4)
H2A1.29430.16370.92940.032*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cd10.02031 (12)0.01474 (12)0.01195 (12)0.00114 (6)0.00633 (7)−0.00019 (6)
Cl10.0316 (2)0.0164 (2)0.0165 (2)−0.00131 (17)0.00967 (17)0.00081 (16)
N10.0205 (7)0.0162 (7)0.0173 (7)0.0004 (6)0.0071 (6)−0.0016 (6)
N20.0201 (8)0.0204 (7)0.0142 (7)0.0013 (6)0.0042 (6)−0.0038 (7)
C90.0184 (9)0.0256 (10)0.0281 (10)0.0027 (8)0.0039 (7)−0.0051 (8)
C130.0233 (9)0.0157 (9)0.0161 (8)0.0007 (7)0.0073 (7)0.0011 (7)
C80.0230 (9)0.0221 (9)0.0195 (8)0.0016 (8)0.0045 (7)−0.0009 (8)
C120.0191 (8)0.0146 (8)0.0162 (8)−0.0041 (7)0.0059 (7)−0.0030 (7)
C110.0225 (9)0.0237 (10)0.0186 (8)−0.0056 (8)0.0096 (7)−0.0038 (8)
C100.0202 (9)0.0305 (11)0.0298 (10)−0.0030 (8)0.0123 (8)−0.0091 (9)
O10.0237 (7)0.0218 (7)0.0140 (6)0.0028 (5)0.0056 (5)−0.0017 (5)
C60.0225 (9)0.0260 (10)0.0249 (9)0.0052 (8)0.0087 (7)−0.0001 (8)
C50.0235 (10)0.0315 (11)0.0417 (12)0.0021 (8)0.0149 (9)0.0018 (10)
C30.0261 (10)0.0389 (12)0.0314 (11)−0.0028 (9)0.0008 (8)−0.0083 (10)
C70.0198 (8)0.0174 (9)0.0141 (8)0.0053 (7)0.0031 (6)0.0020 (7)
C10.0180 (8)0.0203 (9)0.0213 (9)0.0047 (7)0.0045 (7)−0.0010 (7)
C40.0207 (9)0.0312 (11)0.0485 (13)−0.0027 (9)0.0081 (9)−0.0071 (10)
C20.0241 (9)0.0329 (11)0.0216 (9)−0.0002 (9)0.0043 (7)−0.0026 (8)
Geometric parameters (Å, °) top
Cd1—N1i2.3404 (15)C12—C111.391 (3)
Cd1—N12.3404 (15)C11—C101.384 (3)
Cd1—O12.3878 (17)C11—H11A0.9300
Cd1—O1i2.3878 (17)C10—H10A0.9300
Cd1—Cl1i2.5566 (6)O1—C71.248 (2)
Cd1—Cl12.5566 (6)C6—C51.386 (3)
N1—C81.340 (3)C6—C11.393 (3)
N1—C121.344 (2)C6—H6A0.9300
N2—C71.332 (2)C5—C41.387 (3)
N2—C131.461 (2)C5—H5A0.9300
N2—H2B0.83 (3)C3—C21.386 (3)
C9—C101.385 (3)C3—C41.387 (3)
C9—C81.387 (3)C3—H3A0.9300
C9—H9A0.9300C7—C11.494 (3)
C13—C121.508 (3)C1—C21.399 (3)
C13—H13A0.9700C4—H4A0.9300
C13—H13B0.9700C2—H2A0.9300
C8—H8A0.9300
N1i—Cd1—N1180.0C9—C8—H8A118.8
N1i—Cd1—O186.26 (5)N1—C12—C11122.07 (18)
N1—Cd1—O193.74 (5)N1—C12—C13117.14 (16)
N1i—Cd1—O1i93.74 (5)C11—C12—C13120.66 (17)
N1—Cd1—O1i86.26 (5)C10—C11—C12118.84 (18)
O1—Cd1—O1i180.000 (1)C10—C11—H11A120.6
N1i—Cd1—Cl1i90.96 (4)C12—C11—H11A120.6
N1—Cd1—Cl1i89.04 (4)C11—C10—C9119.22 (17)
O1—Cd1—Cl1i84.61 (3)C11—C10—H10A120.4
O1i—Cd1—Cl1i95.39 (3)C9—C10—H10A120.4
N1i—Cd1—Cl189.04 (4)C7—O1—Cd1121.53 (12)
N1—Cd1—Cl190.96 (4)C5—C6—C1120.18 (19)
O1—Cd1—Cl195.39 (3)C5—C6—H6A119.9
O1i—Cd1—Cl184.61 (3)C1—C6—H6A119.9
Cl1i—Cd1—Cl1180.0C6—C5—C4120.4 (2)
C8—N1—C12118.68 (16)C6—C5—H5A119.8
C8—N1—Cd1116.73 (12)C4—C5—H5A119.8
C12—N1—Cd1124.50 (12)C2—C3—C4120.3 (2)
C7—N2—C13123.35 (16)C2—C3—H3A119.8
C7—N2—H2B120.5 (17)C4—C3—H3A119.8
C13—N2—H2B116.0 (16)O1—C7—N2122.99 (18)
C10—C9—C8118.67 (18)O1—C7—C1119.86 (16)
C10—C9—H9A120.7N2—C7—C1117.15 (16)
C8—C9—H9A120.7C6—C1—C2119.30 (18)
N2—C13—C12110.11 (15)C6—C1—C7117.84 (17)
N2—C13—H13A109.6C2—C1—C7122.85 (17)
C12—C13—H13A109.6C5—C4—C3119.7 (2)
N2—C13—H13B109.6C5—C4—H4A120.2
C12—C13—H13B109.6C3—C4—H4A120.2
H13A—C13—H13B108.2C3—C2—C1120.1 (2)
N1—C8—C9122.48 (18)C3—C2—H2A120.0
N1—C8—H8A118.8C1—C2—H2A120.0
Symmetry codes: (i) −x+2, −y, −z+1.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H2B···Cl1ii0.83 (3)2.39 (3)3.1705 (18)158 (2)
Symmetry codes: (ii) −x+2, y+1/2, −z+3/2.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H2B···Cl1i0.83 (3)2.39 (3)3.1705 (18)158 (2)
Symmetry codes: (i) −x+2, y+1/2, −z+3/2.
Acknowledgements top

The authors thank the International Cooperation Bureau of the Chinese Academy of Sciences (project No. GJHZ0527).

references
References top

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