Dichloridobis[N-(2-pyridylmethyl)­benzamide-κ²N,O]cadmium(II)

In the title compound, [CdCl₂(C₁₃H₁₂N₂O)₂], the Cd^II 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 π–π 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.

Key indicators

• Single-crystal X-ray study
• T = 153 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.025
• wR factor = 0.066
• Data-to-parameter ratio = 17.4

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?

Alert level G
PLAT794_ALERT_5_G Check Predicted Bond Valency for Cd1         (2)       2.04

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

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 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
   0 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

---

S1. Comment

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

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).

S2. Experimental

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.

S3. Refinement

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 U_iso(H) = 1.2U_eq(C).

Computing details

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

	Fig. 1. View of the title compound, with displacement ellipsoids drawn at the 30% probability level [symmetry code: (i) -x + 2, -y, -z + 1].
	Fig. 2. Two-dimensional layers parallel to bc plane in (I).
	Fig. 3. Packing diagram for (I) viewed down the b axis.

Dichloridobis[N-(2-pyridylmethyl)benzamide-κ²N,O]cadmium(II)

Crystal data

[CdCl2(C13H12N2O)2]	F(000) = 612.0
Mr = 607.80	Dx = 1.609 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 5099 reflections
a = 11.800 (2) Å	θ = 3.2–27.5°
b = 8.5536 (17) Å	µ = 1.12 mm^−1
c = 12.909 (3) Å	T = 153 K
β = 105.60 (3)°	Block, colourless
V = 1254.9 (5) Å^3	0.42 × 0.34 × 0.24 mm
Z = 2

Data collection

Rigaku R-AXIS RAPID IP area-detector diffractometer	2876 independent reflections
Radiation source: fine-focus sealed tube	2620 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.033
ω scans	θmax = 27.5°, θmin = 3.2°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −15→15
Tmin = 0.642, Tmax = 0.762	k = −11→11
11378 measured reflections	l = −15→16

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.025	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.066	w = 1/[σ^2(Fo^2) + (0.0358P)^2 + 0.9904P] where P = (Fo^2 + 2Fc^2)/3
S = 1.01	(Δ/σ)max < 0.001
2876 reflections	Δρmax = 0.69 e Å^−3
165 parameters	Δρmin = −0.76 e Å^−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 1997), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0144 (10)

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
Cd1	1.0000	0.0000	0.5000	0.01528 (9)
Cl1	0.93804 (4)	−0.28494 (5)	0.50928 (3)	0.02087 (12)
N1	0.88328 (14)	0.07711 (18)	0.61167 (12)	0.0176 (3)
N2	1.11051 (14)	0.0398 (2)	0.79049 (13)	0.0183 (3)
C9	0.71170 (17)	0.2170 (2)	0.62332 (16)	0.0245 (4)
H9A	0.6497	0.2834	0.5914	0.029*
C13	1.00864 (16)	−0.0644 (2)	0.76345 (14)	0.0180 (4)
H13A	1.0008	−0.1162	0.8280	0.022*
H13B	1.0199	−0.1439	0.7135	0.022*
C8	0.79178 (17)	0.1707 (2)	0.56796 (15)	0.0218 (4)
H8A	0.7816	0.2058	0.4979	0.026*
C12	0.89841 (17)	0.0275 (2)	0.71330 (15)	0.0164 (3)
C11	0.82046 (17)	0.0666 (2)	0.77302 (15)	0.0208 (4)
H11A	0.8317	0.0289	0.8426	0.025*
C10	0.72589 (17)	0.1625 (3)	0.72706 (17)	0.0257 (4)
H10A	0.6725	0.1900	0.7654	0.031*
H2B	1.116 (2)	0.097 (3)	0.843 (2)	0.022 (6)*
O1	1.17479 (13)	−0.01963 (15)	0.64476 (11)	0.0197 (3)
C6	1.34268 (17)	0.2209 (2)	0.69617 (16)	0.0240 (4)
H6A	1.3150	0.1940	0.6240	0.029*
C5	1.43790 (18)	0.3211 (3)	0.72918 (19)	0.0311 (5)
H5A	1.4734	0.3619	0.6789	0.037*
C3	1.42620 (19)	0.3022 (3)	0.91142 (19)	0.0335 (5)
H3A	1.4541	0.3297	0.9835	0.040*
C7	1.18598 (16)	0.0533 (2)	0.73064 (14)	0.0174 (3)
C1	1.28839 (16)	0.1604 (2)	0.77084 (15)	0.0200 (4)
C4	1.48055 (19)	0.3610 (3)	0.8368 (2)	0.0337 (5)
H4A	1.5453	0.4269	0.8588	0.040*
C2	1.33055 (18)	0.2026 (3)	0.87908 (16)	0.0265 (4)
H2A	1.2943	0.1637	0.9294	0.032*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cd1	0.02031 (12)	0.01474 (12)	0.01195 (12)	0.00114 (6)	0.00633 (7)	−0.00019 (6)
Cl1	0.0316 (2)	0.0164 (2)	0.0165 (2)	−0.00131 (17)	0.00967 (17)	0.00081 (16)
N1	0.0205 (7)	0.0162 (7)	0.0173 (7)	0.0004 (6)	0.0071 (6)	−0.0016 (6)
N2	0.0201 (8)	0.0204 (7)	0.0142 (7)	0.0013 (6)	0.0042 (6)	−0.0038 (7)
C9	0.0184 (9)	0.0256 (10)	0.0281 (10)	0.0027 (8)	0.0039 (7)	−0.0051 (8)
C13	0.0233 (9)	0.0157 (9)	0.0161 (8)	0.0007 (7)	0.0073 (7)	0.0011 (7)
C8	0.0230 (9)	0.0221 (9)	0.0195 (8)	0.0016 (8)	0.0045 (7)	−0.0009 (8)
C12	0.0191 (8)	0.0146 (8)	0.0162 (8)	−0.0041 (7)	0.0059 (7)	−0.0030 (7)
C11	0.0225 (9)	0.0237 (10)	0.0186 (8)	−0.0056 (8)	0.0096 (7)	−0.0038 (8)
C10	0.0202 (9)	0.0305 (11)	0.0298 (10)	−0.0030 (8)	0.0123 (8)	−0.0091 (9)
O1	0.0237 (7)	0.0218 (7)	0.0140 (6)	0.0028 (5)	0.0056 (5)	−0.0017 (5)
C6	0.0225 (9)	0.0260 (10)	0.0249 (9)	0.0052 (8)	0.0087 (7)	−0.0001 (8)
C5	0.0235 (10)	0.0315 (11)	0.0417 (12)	0.0021 (8)	0.0149 (9)	0.0018 (10)
C3	0.0261 (10)	0.0389 (12)	0.0314 (11)	−0.0028 (9)	0.0008 (8)	−0.0083 (10)
C7	0.0198 (8)	0.0174 (9)	0.0141 (8)	0.0053 (7)	0.0031 (6)	0.0020 (7)
C1	0.0180 (8)	0.0203 (9)	0.0213 (9)	0.0047 (7)	0.0045 (7)	−0.0010 (7)
C4	0.0207 (9)	0.0312 (11)	0.0485 (13)	−0.0027 (9)	0.0081 (9)	−0.0071 (10)
C2	0.0241 (9)	0.0329 (11)	0.0216 (9)	−0.0002 (9)	0.0043 (7)	−0.0026 (8)

Geometric parameters (Å, º)

Cd1—N1^i	2.3404 (15)	C12—C11	1.391 (3)
Cd1—N1	2.3404 (15)	C11—C10	1.384 (3)
Cd1—O1	2.3878 (17)	C11—H11A	0.9300
Cd1—O1^i	2.3878 (17)	C10—H10A	0.9300
Cd1—Cl1^i	2.5566 (6)	O1—C7	1.248 (2)
Cd1—Cl1	2.5566 (6)	C6—C5	1.386 (3)
N1—C8	1.340 (3)	C6—C1	1.393 (3)
N1—C12	1.344 (2)	C6—H6A	0.9300
N2—C7	1.332 (2)	C5—C4	1.387 (3)
N2—C13	1.461 (2)	C5—H5A	0.9300
N2—H2B	0.83 (3)	C3—C2	1.386 (3)
C9—C10	1.385 (3)	C3—C4	1.387 (3)
C9—C8	1.387 (3)	C3—H3A	0.9300
C9—H9A	0.9300	C7—C1	1.494 (3)
C13—C12	1.508 (3)	C1—C2	1.399 (3)
C13—H13A	0.9700	C4—H4A	0.9300
C13—H13B	0.9700	C2—H2A	0.9300
C8—H8A	0.9300
N1^i—Cd1—N1	180.0	C9—C8—H8A	118.8
N1^i—Cd1—O1	86.26 (5)	N1—C12—C11	122.07 (18)
N1—Cd1—O1	93.74 (5)	N1—C12—C13	117.14 (16)
N1^i—Cd1—O1^i	93.74 (5)	C11—C12—C13	120.66 (17)
N1—Cd1—O1^i	86.26 (5)	C10—C11—C12	118.84 (18)
O1—Cd1—O1^i	180.000 (1)	C10—C11—H11A	120.6
N1^i—Cd1—Cl1^i	90.96 (4)	C12—C11—H11A	120.6
N1—Cd1—Cl1^i	89.04 (4)	C11—C10—C9	119.22 (17)
O1—Cd1—Cl1^i	84.61 (3)	C11—C10—H10A	120.4
O1^i—Cd1—Cl1^i	95.39 (3)	C9—C10—H10A	120.4
N1^i—Cd1—Cl1	89.04 (4)	C7—O1—Cd1	121.53 (12)
N1—Cd1—Cl1	90.96 (4)	C5—C6—C1	120.18 (19)
O1—Cd1—Cl1	95.39 (3)	C5—C6—H6A	119.9
O1^i—Cd1—Cl1	84.61 (3)	C1—C6—H6A	119.9
Cl1^i—Cd1—Cl1	180.0	C6—C5—C4	120.4 (2)
C8—N1—C12	118.68 (16)	C6—C5—H5A	119.8
C8—N1—Cd1	116.73 (12)	C4—C5—H5A	119.8
C12—N1—Cd1	124.50 (12)	C2—C3—C4	120.3 (2)
C7—N2—C13	123.35 (16)	C2—C3—H3A	119.8
C7—N2—H2B	120.5 (17)	C4—C3—H3A	119.8
C13—N2—H2B	116.0 (16)	O1—C7—N2	122.99 (18)
C10—C9—C8	118.67 (18)	O1—C7—C1	119.86 (16)
C10—C9—H9A	120.7	N2—C7—C1	117.15 (16)
C8—C9—H9A	120.7	C6—C1—C2	119.30 (18)
N2—C13—C12	110.11 (15)	C6—C1—C7	117.84 (17)
N2—C13—H13A	109.6	C2—C1—C7	122.85 (17)
C12—C13—H13A	109.6	C5—C4—C3	119.7 (2)
N2—C13—H13B	109.6	C5—C4—H4A	120.2
C12—C13—H13B	109.6	C3—C4—H4A	120.2
H13A—C13—H13B	108.2	C3—C2—C1	120.1 (2)
N1—C8—C9	122.48 (18)	C3—C2—H2A	120.0
N1—C8—H8A	118.8	C1—C2—H2A	120.0

Symmetry code: (i) −x+2, −y, −z+1.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2B···Cl1^ii	0.83 (3)	2.39 (3)	3.1705 (18)	158 (2)

Symmetry code: (ii) −x+2, y+1/2, −z+3/2.