supplementary materials


su2529 scheme

Acta Cryst. (2013). E69, m36    [ doi:10.1107/S1600536812049768 ]

(Benzyl isocyanide-[kappa]C1)chlorido(2-chloro-3-dimethylamino-1-phenylprop-1-en-1-yl-[kappa]2C1,N)palladium(II)

A. C. Mafud, M. A. R. Oliviera and M. T. P. Gambardella

Abstract top

In the title compound, [Pd(C11H13ClN)Cl(C8H7N)], which crystallized in the chiral space group P212121, the PdII atom is coordinated by two C atoms, a Csp2 atom of the 2-chloro-3-dimethylamino-1-phenylprop-1-en-1-yl ligand and a Csp atom from the benzyl isocyanide ligand, as well as an N atom of the ligand and a Cl atom, in a square-planar geometry. In the complex, there is a short C-H...Cl hydrogen bond and a C-H...[pi] interaction. In the crystal, molecules are linked via C-H...Cl hydrogen bonds, forming chains along the a-axis direction.

Comment top

The title compound was obtained from the reaction between the dimer [Pd(DMBA)(µX)]2 [where X = Cl, N3, NCO, and DMBA = 7,12-dimethylbenz(a)anthracene] and thiourea, being the product of a cleavage reaction. As a palladium complex it could be of interest with respect to anticancer activity.

In the title compound, Fig. 1, the palladium atom coordinates to two C atoms, a Csp2 and a Csp atom [Pd1—C9 2.006 (5) Å, Pd1—C1 1.928 (6) Å, respectively], the amine N atom [Pd1—N2 2.098 (4) Å] and an atom of chlorine [Pd1—Cl1 2.3929 (2) Å], with a square planar geometry. The distances and angles in the title compound are close to those reported for similar compounds (Moro et al., 2004; Caires et al., 2006; Mafud et al., 2013). In the molecule there is a short C-H···Cl contact and a C-H···π interaction (Table 1).

In the crystal, molecules are linked via C-H···Cl hydrogen bonds (Fig. 2 and Table 1) forming chains along the a axis.

Related literature top

For the crystal structures of similar compounds, see: Moro et al. (2004); Caires et al. (2006); Mafud et al. (2013).

Experimental top

The title compound is the product of a cleavage reaction. It was obtained from the reaction between the dimer [Pd (DMBA)(µX)]2 [where X = Cl, N3, NCO, and DMBA = 7,12-dimethylbenz(a)anthracene] and thiourea, in a 1:2 stoichiometric ratio in chloroform. The solution was stirred during 1 h and then the mixture was left for the solvent to slowly evaporate at room temperature. Large yellow needle-shaped crystals, suitable for X-ray diffraction analysis, were obtained.

Refinement top

The C-bound H-atoms were included in calculated positions and treated as riding atoms: C—H = 0.93, 0.96 and 0.97 Å, for CH, CH3 and CH2 H atoms, respectively, with Uiso(H) = k × Ueq(parent C-atom), were k = 1.5 for CH3 H atoms, and = 1.2 for other H atoms.

Computing details top

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell refinement: CAD-4 EXPRESS (Enraf–Nonius, 1994); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: WinGX (Farrugia, 2012).

Figures top
[Figure 1] Fig. 1. Perspective view of the molecular structure of the title compound, with the atom numbering. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. The view along the b axis of the crystal packing of the title compound. The C-H···Cl interactions are shown as dashed cyan lines and the H atoms not involved in these interactions have been omitted for clarity.
(Benzyl isocyanide-κC1)chlorido(2-chloro-3-dimethylamino-1-phenylprop- 1-en-1-yl-κ2C1,N)palladium(II) top
Crystal data top
[Pd(C11H13ClN)Cl(C8H7N)]F(000) = 912
Mr = 453.67Dx = 1.572 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 25 reflections
a = 6.2529 (7) Åθ = 11.2–18.2°
b = 11.0931 (10) ŵ = 1.25 mm1
c = 27.640 (2) ÅT = 290 K
V = 1917.2 (3) Å3Prism, yellow
Z = 40.63 × 0.08 × 0.05 mm
Data collection top
Enraf–Nonius TurboCAD-4
diffractometer
2420 reflections with I > 2σ(I)
Radiation source: Enraf Nonius FR590Rint = 0.019
Graphite monochromatorθmax = 29.9°, θmin = 2.9°
non–profiled ω scansh = 81
Absorption correction: ψ scan
(North et al., 1968)
k = 150
Tmin = 0.871, Tmax = 0.928l = 038
3421 measured reflections3 standard reflections every 120 min
3358 independent reflections intensity decay: 1%
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)] = 0.039H-atom parameters constrained
wR(F2) = 0.085 w = 1/[σ2(Fo2) + (0.0337P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max = 0.001
3358 reflectionsΔρmax = 0.67 e Å3
219 parametersΔρmin = 1.07 e Å3
0 restraintsAbsolute structure: Flack (1983), 161 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.10 (5)
Crystal data top
[Pd(C11H13ClN)Cl(C8H7N)]V = 1917.2 (3) Å3
Mr = 453.67Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 6.2529 (7) ŵ = 1.25 mm1
b = 11.0931 (10) ÅT = 290 K
c = 27.640 (2) Å0.63 × 0.08 × 0.05 mm
Data collection top
Enraf–Nonius TurboCAD-4
diffractometer
2420 reflections with I > 2σ(I)
Absorption correction: ψ scan
(North et al., 1968)
Rint = 0.019
Tmin = 0.871, Tmax = 0.928θmax = 29.9°
3421 measured reflections3 standard reflections every 120 min
3358 independent reflections intensity decay: 1%
Refinement top
R[F2 > 2σ(F2)] = 0.039H-atom parameters constrained
wR(F2) = 0.085Δρmax = 0.67 e Å3
S = 1.03Δρmin = 1.07 e Å3
3358 reflectionsAbsolute structure: Flack (1983), 161 Friedel pairs
219 parametersFlack parameter: 0.10 (5)
0 restraints
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
Pd10.69687 (7)0.16519 (4)0.302107 (14)0.03072 (10)
Cl20.1519 (3)0.35671 (17)0.37641 (6)0.0620 (5)
Cl10.9388 (3)0.12673 (13)0.23683 (5)0.0460 (4)
N10.8931 (9)0.0511 (5)0.35548 (17)0.0432 (12)
N20.5455 (8)0.3051 (4)0.26417 (15)0.0336 (11)
C10.8195 (11)0.0332 (5)0.33801 (18)0.0374 (13)
C20.9749 (11)0.1613 (6)0.3763 (2)0.0584 (18)
H2A1.07980.14180.40090.07*
H2B1.04620.20780.35130.07*
C30.7989 (12)0.2368 (5)0.39854 (19)0.0420 (13)
C40.6530 (14)0.1880 (7)0.4296 (2)0.062 (2)
H40.66050.10650.43730.075*
C50.4955 (16)0.2581 (9)0.4496 (3)0.084 (3)
H50.39790.22470.47120.1*
C60.4832 (18)0.3770 (9)0.4377 (3)0.087 (3)
H60.37480.42440.45070.104*
C70.6277 (17)0.4276 (7)0.4068 (3)0.082 (3)
H70.61880.5090.39910.098*
C80.7869 (14)0.3574 (6)0.3870 (2)0.0608 (19)
H80.8860.39130.3660.073*
C90.4927 (9)0.2110 (5)0.35497 (18)0.0325 (13)
C100.4966 (9)0.1640 (6)0.40531 (18)0.0364 (12)
C110.6694 (11)0.1801 (6)0.43592 (19)0.0458 (15)
H110.79110.21930.42470.055*
C120.6627 (11)0.1380 (6)0.4833 (2)0.0514 (17)
H120.77840.15140.50370.062*
C130.4896 (14)0.0777 (6)0.4999 (2)0.0551 (19)
H130.48850.04860.53140.066*
C140.3175 (13)0.0594 (6)0.4709 (2)0.0538 (17)
H140.1980.01860.48250.065*
C150.3225 (12)0.1027 (5)0.4235 (2)0.0463 (15)
H150.20480.08980.40360.056*
C160.3523 (9)0.2918 (5)0.3399 (2)0.0388 (14)
C170.3425 (9)0.3377 (6)0.28883 (18)0.0449 (14)
H17A0.22220.30180.2720.054*
H17B0.32420.42460.28880.054*
C180.6951 (13)0.4088 (5)0.2648 (2)0.0585 (18)
H18A0.63720.47320.24570.088*
H18B0.83050.38450.25170.088*
H18C0.71440.43590.29750.088*
C190.4974 (12)0.2744 (6)0.21329 (19)0.0564 (19)
H19A0.40080.20720.21230.085*
H19B0.62750.25350.19690.085*
H19C0.43270.34250.19760.085*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.02745 (18)0.02875 (17)0.03597 (17)0.0004 (2)0.0021 (2)0.00213 (19)
Cl20.0515 (11)0.0667 (12)0.0677 (10)0.0150 (10)0.0197 (9)0.0015 (9)
Cl10.0411 (9)0.0440 (8)0.0529 (8)0.0055 (7)0.0090 (7)0.0006 (7)
N10.041 (3)0.037 (3)0.052 (3)0.001 (3)0.009 (3)0.008 (2)
N20.028 (2)0.033 (3)0.039 (2)0.001 (2)0.001 (2)0.004 (2)
C10.038 (3)0.037 (3)0.037 (3)0.011 (3)0.005 (3)0.000 (2)
C20.058 (4)0.042 (3)0.075 (4)0.014 (4)0.010 (4)0.017 (4)
C30.048 (4)0.033 (3)0.045 (3)0.001 (4)0.006 (4)0.012 (2)
C40.074 (6)0.049 (4)0.064 (4)0.004 (4)0.012 (4)0.002 (3)
C50.068 (6)0.094 (7)0.088 (6)0.018 (6)0.021 (5)0.027 (6)
C60.083 (8)0.073 (6)0.104 (7)0.016 (6)0.001 (6)0.040 (5)
C70.109 (9)0.047 (4)0.089 (6)0.018 (5)0.017 (6)0.015 (4)
C80.082 (5)0.051 (4)0.049 (3)0.004 (5)0.011 (4)0.002 (3)
C90.029 (3)0.031 (3)0.037 (3)0.005 (2)0.001 (2)0.002 (2)
C100.035 (3)0.035 (3)0.039 (3)0.006 (3)0.000 (2)0.001 (3)
C110.040 (4)0.050 (4)0.047 (3)0.008 (4)0.004 (3)0.001 (3)
C120.052 (4)0.059 (4)0.043 (3)0.006 (4)0.014 (3)0.002 (3)
C130.077 (5)0.054 (4)0.034 (3)0.001 (4)0.010 (4)0.005 (3)
C140.053 (4)0.057 (4)0.052 (3)0.015 (4)0.008 (4)0.012 (3)
C150.037 (4)0.053 (4)0.048 (3)0.012 (4)0.001 (3)0.004 (3)
C160.030 (3)0.040 (3)0.046 (3)0.003 (3)0.002 (3)0.005 (3)
C170.034 (3)0.048 (3)0.053 (3)0.011 (3)0.004 (2)0.003 (3)
C180.051 (4)0.034 (3)0.091 (5)0.006 (4)0.009 (5)0.015 (3)
C190.056 (5)0.068 (5)0.044 (3)0.006 (4)0.010 (3)0.012 (3)
Geometric parameters (Å, º) top
Pd1—C11.928 (6)C8—H80.93
Pd1—C92.006 (5)C9—C161.322 (8)
Pd1—N22.099 (4)C9—C101.486 (7)
Pd1—Cl12.3927 (15)C10—C151.379 (8)
Cl2—C161.762 (6)C10—C111.384 (8)
N1—C11.148 (7)C11—C121.390 (8)
N1—C21.445 (8)C11—H110.93
N2—C191.478 (7)C12—C131.353 (9)
N2—C181.483 (8)C12—H120.93
N2—C171.485 (7)C13—C141.357 (10)
C2—C31.513 (9)C13—H130.93
C2—H2A0.97C14—C151.396 (7)
C2—H2B0.97C14—H140.93
C3—C41.365 (9)C15—H150.93
C3—C81.377 (8)C16—C171.503 (8)
C4—C51.371 (11)C17—H17A0.97
C4—H40.93C17—H17B0.97
C5—C61.363 (11)C18—H18A0.96
C5—H50.93C18—H18B0.96
C6—C71.364 (12)C18—H18C0.96
C6—H60.93C19—H19A0.96
C7—C81.376 (11)C19—H19B0.96
C7—H70.93C19—H19C0.96
C1—Pd1—C994.0 (2)C10—C9—Pd1125.7 (4)
C1—Pd1—N2176.6 (2)C15—C10—C11117.2 (5)
C9—Pd1—N283.7 (2)C15—C10—C9120.1 (5)
C1—Pd1—Cl190.08 (18)C11—C10—C9122.7 (5)
C9—Pd1—Cl1175.44 (16)C10—C11—C12120.6 (6)
N2—Pd1—Cl192.31 (12)C10—C11—H11119.7
C1—N1—C2176.5 (6)C12—C11—H11119.7
C19—N2—C18108.6 (5)C13—C12—C11120.7 (6)
C19—N2—C17108.6 (5)C13—C12—H12119.7
C18—N2—C17110.1 (5)C11—C12—H12119.7
C19—N2—Pd1113.4 (4)C12—C13—C14120.6 (6)
C18—N2—Pd1106.5 (4)C12—C13—H13119.7
C17—N2—Pd1109.7 (3)C14—C13—H13119.7
N1—C1—Pd1173.8 (5)C13—C14—C15119.0 (7)
N1—C2—C3111.9 (5)C13—C14—H14120.5
N1—C2—H2A109.2C15—C14—H14120.5
C3—C2—H2A109.2C10—C15—C14122.0 (7)
N1—C2—H2B109.2C10—C15—H15119
C3—C2—H2B109.2C14—C15—H15119
H2A—C2—H2B107.9C9—C16—C17123.6 (5)
C4—C3—C8119.6 (7)C9—C16—Cl2124.7 (5)
C4—C3—C2121.5 (6)C17—C16—Cl2111.7 (4)
C8—C3—C2118.9 (7)N2—C17—C16108.3 (5)
C3—C4—C5120.6 (7)N2—C17—H17A110
C3—C4—H4119.7C16—C17—H17A110
C5—C4—H4119.7N2—C17—H17B110
C6—C5—C4119.4 (9)C16—C17—H17B110
C6—C5—H5120.3H17A—C17—H17B108.4
C4—C5—H5120.3N2—C18—H18A109.5
C5—C6—C7120.8 (9)N2—C18—H18B109.5
C5—C6—H6119.6H18A—C18—H18B109.5
C7—C6—H6119.6N2—C18—H18C109.5
C6—C7—C8119.7 (8)H18A—C18—H18C109.5
C6—C7—H7120.2H18B—C18—H18C109.5
C8—C7—H7120.2N2—C19—H19A109.5
C7—C8—C3119.8 (8)N2—C19—H19B109.5
C7—C8—H8120.1H19A—C19—H19B109.5
C3—C8—H8120.1N2—C19—H19C109.5
C16—C9—C10122.9 (5)H19A—C19—H19C109.5
C16—C9—Pd1111.4 (4)H19B—C19—H19C109.5
C1—Pd1—N2—C1990 (3)Cl1—Pd1—C9—C1635 (2)
C9—Pd1—N2—C19136.9 (4)C1—Pd1—C9—C1010.9 (5)
Cl1—Pd1—N2—C1945.2 (4)N2—Pd1—C9—C10171.6 (5)
C1—Pd1—N2—C18151 (3)Cl1—Pd1—C9—C10144.0 (18)
C9—Pd1—N2—C18103.8 (4)C16—C9—C10—C1561.4 (8)
Cl1—Pd1—N2—C1874.1 (4)Pd1—C9—C10—C15119.9 (6)
C1—Pd1—N2—C1732 (3)C16—C9—C10—C11117.9 (7)
C9—Pd1—N2—C1715.3 (4)Pd1—C9—C10—C1160.8 (8)
Cl1—Pd1—N2—C17166.8 (3)C15—C10—C11—C121.5 (9)
C2—N1—C1—Pd156 (14)C9—C10—C11—C12177.8 (6)
C9—Pd1—C1—N1142 (5)C10—C11—C12—C131.8 (10)
N2—Pd1—C1—N195 (6)C11—C12—C13—C141.3 (11)
Cl1—Pd1—C1—N140 (5)C12—C13—C14—C150.6 (11)
C1—N1—C2—C342 (11)C11—C10—C15—C140.8 (10)
N1—C2—C3—C449.3 (9)C9—C10—C15—C14178.6 (6)
N1—C2—C3—C8130.8 (6)C13—C14—C15—C100.3 (10)
C8—C3—C4—C50.3 (11)C10—C9—C16—C17178.3 (6)
C2—C3—C4—C5179.6 (7)Pd1—C9—C16—C172.9 (7)
C3—C4—C5—C61.0 (13)C10—C9—C16—Cl20.5 (8)
C4—C5—C6—C71.2 (15)Pd1—C9—C16—Cl2178.3 (3)
C5—C6—C7—C80.7 (14)C19—N2—C17—C16143.6 (5)
C6—C7—C8—C30.1 (12)C18—N2—C17—C1697.6 (6)
C4—C3—C8—C70.2 (11)Pd1—N2—C17—C1619.2 (6)
C2—C3—C8—C7179.8 (6)C9—C16—C17—N215.7 (8)
C1—Pd1—C9—C16170.3 (4)Cl2—C16—C17—N2165.4 (4)
N2—Pd1—C9—C167.2 (4)
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the C10–C15 ring.
D—H···AD—HH···AD···AD—H···A
C19—H19B···Cl10.962.653.275 (8)123
C17—H17A···Cl1i0.972.803.729 (6)160
C4—H4···Cg10.932.763.622 (8)155
Symmetry code: (i) x1, y, z.
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the C10–C15 ring.
D—H···AD—HH···AD···AD—H···A
C19—H19B···Cl10.962.653.275 (8)123
C17—H17A···Cl1i0.972.803.729 (6)160
C4—H4···Cg10.932.763.622 (8)155
Symmetry code: (i) x1, y, z.
Acknowledgements top

We are extremely grateful to the late Professor Antonio Carlos Favero Caires for supplying us with the sample used, and to the CNPq National Council for Technological and Scientific Development for supporting this study.

references
References top

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Mafud, A. C., Oliviera, M. A. R. & Gambardella, M. T. P. (2013). Acta Cryst. E69, m15.

Moro, A. C., Mauro, A. E. & Ananias, S. R. (2004). Eclet. Quim. 29, 57–61.

North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.