Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807031054/cv2267sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807031054/cv2267Isup2.hkl |
CCDC reference: 657528
Key indicators
- Single-crystal X-ray study
- T = 153 K
- Mean (C-C) = 0.003 Å
- R factor = 0.025
- wR factor = 0.066
- Data-to-parameter ratio = 17.4
checkCIF/PLATON results
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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
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.
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).
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].
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).
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.
[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) Å3 | 0.42 × 0.34 × 0.24 mm |
Z = 2 |
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 on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.025 | H 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 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+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0144 (10) |
[CdCl2(C13H12N2O)2] | V = 1254.9 (5) Å3 |
Mr = 607.80 | Z = 2 |
Monoclinic, P21/c | Mo Kα radiation |
a = 11.800 (2) Å | µ = 1.12 mm−1 |
b = 8.5536 (17) Å | T = 153 K |
c = 12.909 (3) Å | 0.42 × 0.34 × 0.24 mm |
β = 105.60 (3)° |
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 = 0.762 | Rint = 0.033 |
11378 measured reflections |
R[F2 > 2σ(F2)] = 0.025 | 0 restraints |
wR(F2) = 0.066 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.01 | Δρmax = 0.69 e Å−3 |
2876 reflections | Δρmin = −0.76 e Å−3 |
165 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. |
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. |
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* |
U11 | U22 | U33 | U12 | U13 | U23 | |
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) |
Cd1—N1i | 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—O1i | 2.3878 (17) | C10—H10A | 0.9300 |
Cd1—Cl1i | 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 | ||
N1i—Cd1—N1 | 180.0 | C9—C8—H8A | 118.8 |
N1i—Cd1—O1 | 86.26 (5) | N1—C12—C11 | 122.07 (18) |
N1—Cd1—O1 | 93.74 (5) | N1—C12—C13 | 117.14 (16) |
N1i—Cd1—O1i | 93.74 (5) | C11—C12—C13 | 120.66 (17) |
N1—Cd1—O1i | 86.26 (5) | C10—C11—C12 | 118.84 (18) |
O1—Cd1—O1i | 180.000 (1) | C10—C11—H11A | 120.6 |
N1i—Cd1—Cl1i | 90.96 (4) | C12—C11—H11A | 120.6 |
N1—Cd1—Cl1i | 89.04 (4) | C11—C10—C9 | 119.22 (17) |
O1—Cd1—Cl1i | 84.61 (3) | C11—C10—H10A | 120.4 |
O1i—Cd1—Cl1i | 95.39 (3) | C9—C10—H10A | 120.4 |
N1i—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 |
O1i—Cd1—Cl1 | 84.61 (3) | C1—C6—H6A | 119.9 |
Cl1i—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. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2B···Cl1ii | 0.83 (3) | 2.39 (3) | 3.1705 (18) | 158 (2) |
Symmetry code: (ii) −x+2, y+1/2, −z+3/2. |
Experimental details
Crystal data | |
Chemical formula | [CdCl2(C13H12N2O)2] |
Mr | 607.80 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 153 |
a, b, c (Å) | 11.800 (2), 8.5536 (17), 12.909 (3) |
β (°) | 105.60 (3) |
V (Å3) | 1254.9 (5) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 1.12 |
Crystal size (mm) | 0.42 × 0.34 × 0.24 |
Data collection | |
Diffractometer | Rigaku R-AXIS RAPID IP area-detector |
Absorption correction | Multi-scan (ABSCOR; Higashi, 1995) |
Tmin, Tmax | 0.642, 0.762 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 11378, 2876, 2620 |
Rint | 0.033 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.025, 0.066, 1.01 |
No. of reflections | 2876 |
No. of parameters | 165 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.69, −0.76 |
Computer programs: RAPID-AUTO (Rigaku, 2001), RAPID-AUTO, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 1999), SHELXTL.
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2B···Cl1i | 0.83 (3) | 2.39 (3) | 3.1705 (18) | 158 (2) |
Symmetry code: (i) −x+2, y+1/2, −z+3/2. |
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].