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Acta Cryst. (2007). E63, m2474    [ doi:10.1107/S1600536807042584 ]

Dichlorido[bis(2-hexylsulfanyl)-1H-benzimidazole-[kappa]N3]palladium(II)

Z.-J. Huang, L. Du, M.-J. Xie and J. Chen

Abstract top

The title compound, [PdCl2(C13H18N2S)2], was obtained from 2-hexylsulfanyl-1H-benzimidazole and (NH4)2PdCl4 in ethanol. The crystal structure reveals that the molecule resides on a crystallographic centre of symmetry, with the Pd atom at the centre of the square-planar complex. Molecules are linked by N-H...Cl hydrogen bonds.

Comment top

Sulfides are known to be highly selective for extraction of Pd(II), and have been widely used in the extraction of this species (Al-Bazi & Preiser, 1987). So far, most sufides reported for this purpose are dialkyl sufides. The title compound is a new heterocyclic sufide Pd(II) complex containing benzimidazole rings. The complex molecules have the trans configuration with two Cl atoms and two 2-hexylsulfanyl-1H-benzimidazole molecules, which act as neutral unidentate ligands through the N atom of the benzimidazole rings. This is quite different from general dialkyl sufides of Pd(II) complexes in which sufides are coordinated with palladium via the S atoms of the ligand. The molecular structure is shown in Fig. 1. The Pd(II) is at the inversion center of the square-planar complex. This is similar to bis[2-(2-benzoxazolyl)phenol-N]dichloropalladium(II) (Ito et al., 1997) and bis(iso-Amyl benzothiazolyl sulfoxide)dichloropalladium(II) (Li et al., 2005). The entire benzimidazole ligand system is roughly planar. The N1/N2/C1—C7 benzimidazole is planar, with a maximum deviation of N1 from the mean plane of 0.010 (2) Å. Molecules are linked by N—H···Cl hydrogen bonds (dashed lines) between N atoms of the of the benzimidazole rings and Cl atoms of adjacent molecules (Table 2). These hydrogen bond interactions give rise to a three-dimensional network. The crystal packing of the complex is shown in Fig. 2.

Related literature top

For related literature, see: Al-Bazi & Preiser (1987); Ito et al. (1997); Li et al. (2005); Türktekin et al. (2005).

Experimental top

2-Mercaptobenzimidazole, acetone, water and KOH were put in a round-bottom flask with a mechanical stirrer and condenser and the mixture was heated for about 30 min. 1-bromo-hexane was then added gradually with stirring through a dropping funnel and the reaction mixture was refluxed for 6 h. The residual solid was filtered after cooling down and the acetone was removed by distillation. The organic phase was diluted with ether, washed with water two times and dried with anhydrous Na2SO4. The ether was evaporated and 2-hexylsulfanyl-1H-benzimidazole was obtained. A solution of (NH4)2PdCl4 (28.4 mg, 0.1 mmol) in EtOH/H2O(1:1,10 ml) was added to a solution of 2-hexylsulfanyl-1H-benzimidazole (46.8 mg, 0.2 mmol) in EtOH/H2O (1:1, 20 ml). The mixture was stirred for 50 min. The resulting solution was filtered and the filtrate was left to stand at room temperature. Yellow single crystals were obtained upon slow evaporation of the solvent.

Refinement top

The H atoms on the C atoms were located in a difference Fourier map and refined as riding on their parent atoms with Uiso(H)=1.2Ueq(C), Uiso(H)=1.5Ueq(C13) and with C—H distances of 0.93–0.97 Å. H atoms on N atoms were included in calculated positions, constrained to an ideal geometry with N—H distance of 0.86 Å and with Uiso(H)=1.2Ueq(N). The atoms C11 and C12 are disordered. We used the SHELXL97 command "DFIX" to restrain C11 and C12 to an ideal geometry with distance 1.468 Å. A similar structure is observed in the compound [CoCl2(C11H14N2O)2] (Türktekin et al., 2005).

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97) (Sheldrick, 1997); molecular graphics: SHELXTL (Sheldrick, 2000); software used to prepare material for publication: SHELXL97.

Figures top
[Figure 1] Fig. 1. The molecular structure of the title complex. Displacement ellipsoids are drawn at the 30% probability level, and H atoms are shown as spheres of arbitrary radii.
[Figure 2] Fig. 2. The crystal packing of the title complex. Dashed lines represent hydrogen bonds.
Dichlorido[bis(2-hexylsulfanyl)-1H-benzimidazole- κN3]palladium(II) top
Crystal data top
[PdCl2(C13H18N2S)2]F000 = 664
Mr = 646.01Dx = 1.436 Mg m−3
Monoclinic, P21/cMo Kα radiation
λ = 0.71073 Å
a = 14.3559 (11) Åθ = 1.5–28.3º
b = 7.7688 (6) ŵ = 0.96 mm−1
c = 14.5566 (11) ÅT = 298 (2) K
β = 113.0730 (10)ºBlock, yellow
V = 1493.6 (2) Å30.20 × 0.16 × 0.11 mm
Z = 2
Data collection top
Bruker APEXII 1K CCD area-detector
diffractometer		3515 independent reflections
Radiation source: fine-focus sealed tube2649 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.022
T = 298(2) Kθmax = 28.3º
φ and ω scansθmin = 1.5º
Absorption correction: numerical
(SADABS; Sheldrick, 2002)		h = −19→18
Tmin = 0.831, Tmax = 0.902k = −10→10
12251 measured reflectionsl = −19→19
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)] = 0.045H-atom parameters constrained
wR(F2) = 0.139  w = 1/[σ2(Fo2) + (0.0906P)2 + 0.5462P]
where P = (Fo2 + 2Fc2)/3
S = 1.01(Δ/σ)max = 0.001
3515 reflectionsΔρmax = 1.33 e Å−3
161 parametersΔρmin = −0.53 e Å−3
1 restraintExtinction correction: none
Primary atom site location: structure-invariant direct methods
Crystal data top
[PdCl2(C13H18N2S)2]V = 1493.6 (2) Å3
Mr = 646.01Z = 2
Monoclinic, P21/cMo Kα
a = 14.3559 (11) ŵ = 0.96 mm−1
b = 7.7688 (6) ÅT = 298 (2) K
c = 14.5566 (11) Å0.20 × 0.16 × 0.11 mm
β = 113.0730 (10)º
Data collection top
Bruker APEXII 1K CCD area-detector
diffractometer		3515 independent reflections
Absorption correction: numerical
(SADABS; Sheldrick, 2002)		2649 reflections with I > 2σ(I)
Tmin = 0.831, Tmax = 0.902Rint = 0.022
12251 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0451 restraint
wR(F2) = 0.139H-atom parameters constrained
S = 1.01Δρmax = 1.33 e Å−3
3515 reflectionsΔρmin = −0.53 e Å−3
161 parameters
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
Pd10.00000.50000.00000.04347 (15)
S10.13339 (9)0.4562 (2)0.25428 (8)0.0802 (4)
N1−0.0520 (3)0.4856 (3)0.1094 (2)0.0491 (7)
N2−0.0570 (3)0.4476 (5)0.2582 (2)0.0706 (9)
H2A−0.03670.43260.32160.085*
Cl10.02540 (13)0.78914 (15)0.02260 (10)0.1020 (5)
C1−0.2480 (4)0.4513 (7)0.2038 (4)0.0920 (15)
H1−0.25020.43560.26620.110*
C2−0.3343 (5)0.4676 (8)0.1192 (5)0.1021 (19)
H2−0.39670.46470.12470.123*
C3−0.3320 (5)0.4884 (6)0.0248 (5)0.0931 (18)
H3−0.39250.4974−0.03090.112*
C4−0.2417 (4)0.4958 (4)0.0129 (4)0.0712 (12)
H4−0.23990.5098−0.04990.085*
C5−0.1532 (3)0.4818 (4)0.0980 (3)0.0549 (9)
C6−0.1562 (3)0.4595 (5)0.1915 (3)0.0643 (10)
C70.0026 (3)0.4639 (5)0.2064 (3)0.0553 (8)
C80.1645 (4)0.4744 (5)0.3879 (3)0.0727 (12)
H8A0.13340.57700.40130.087*
H8B0.13830.37530.41080.087*
C90.2782 (5)0.4839 (6)0.4432 (4)0.0892 (16)
H9A0.30860.38080.42950.107*
H9B0.30380.58190.41900.107*
C100.3079 (6)0.5007 (7)0.5525 (5)0.112 (2)
H10A0.28650.40130.57960.135*
H10B0.27970.60400.56880.135*
C110.4287 (9)0.5116 (10)0.5928 (8)0.177 (5)
H11A0.45470.40440.57820.212*
H11B0.44740.60330.55800.212*
C120.4752 (9)0.5440 (15)0.7007 (8)0.204 (5)
H12A0.45600.45420.73620.245*
H12B0.45200.65350.71590.245*
C130.5877 (6)0.5466 (12)0.7325 (7)0.171 (4)
H13A0.61070.43430.72360.257*
H13B0.61890.57870.80160.257*
H13C0.60550.62860.69280.257*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.0645 (3)0.0425 (2)0.0360 (2)0.00197 (13)0.03335 (17)0.00119 (11)
S10.0703 (6)0.1298 (10)0.0493 (5)0.0124 (6)0.0329 (5)0.0106 (6)
N10.0679 (17)0.0520 (16)0.0398 (14)0.0033 (11)0.0344 (13)0.0021 (9)
N20.088 (2)0.096 (2)0.0461 (16)0.005 (2)0.0459 (17)0.0100 (16)
Cl10.2099 (14)0.0490 (6)0.1058 (8)−0.0188 (7)0.1254 (9)−0.0148 (5)
C10.095 (4)0.129 (4)0.081 (3)−0.002 (3)0.066 (3)0.003 (3)
C20.070 (3)0.156 (5)0.096 (4)0.001 (3)0.051 (3)0.000 (3)
C30.071 (3)0.134 (6)0.078 (3)0.002 (2)0.034 (3)0.000 (2)
C40.075 (3)0.093 (4)0.054 (2)0.0026 (18)0.034 (2)0.0020 (16)
C50.068 (2)0.060 (2)0.0512 (19)0.0016 (14)0.0390 (17)0.0003 (13)
C60.074 (3)0.080 (2)0.055 (2)0.0016 (19)0.043 (2)0.0031 (18)
C70.067 (2)0.068 (2)0.0417 (17)0.0047 (16)0.0340 (16)0.0074 (14)
C80.077 (3)0.096 (3)0.048 (2)0.005 (2)0.029 (2)0.0096 (18)
C90.083 (3)0.119 (5)0.068 (3)0.003 (2)0.031 (3)0.008 (2)
C100.101 (4)0.149 (7)0.066 (3)0.003 (3)0.009 (3)−0.003 (2)
C110.147 (9)0.221 (15)0.146 (10)0.013 (5)0.039 (8)−0.001 (5)
C120.146 (9)0.320 (15)0.133 (9)−0.002 (8)0.040 (7)−0.008 (8)
C130.082 (4)0.322 (12)0.104 (5)0.005 (5)0.030 (4)0.033 (6)
Geometric parameters (Å, °) top
Pd1—N1i2.009 (3)C5—C61.390 (5)
Pd1—N12.009 (3)C8—C91.512 (8)
Pd1—Cl12.2788 (12)C8—H8A0.9700
Pd1—Cl1i2.2788 (12)C8—H8B0.9700
S1—C71.729 (4)C9—C101.482 (9)
S1—C81.823 (4)C9—H9A0.9700
N1—C71.331 (5)C9—H9B0.9700
N1—C51.396 (5)C10—C111.600 (13)
N2—C71.350 (4)C10—H10A0.9700
N2—C61.377 (6)C10—H10B0.9700
N2—H2A0.8600C11—C121.468 (9)
C1—C21.369 (9)C11—H11A0.9700
C1—C61.398 (6)C11—H11B0.9700
C1—H10.9300C12—C131.495 (14)
C2—C31.396 (9)C12—H12A0.9700
C2—H20.9300C12—H12B0.9700
C3—C41.375 (7)C13—H13A0.9600
C3—H30.9300C13—H13B0.9600
C4—C51.388 (6)C13—H13C0.9600
C4—H40.9300
N1i—Pd1—N1180.00 (16)C9—C8—H8A109.8
N1i—Pd1—Cl188.35 (7)S1—C8—H8A109.8
N1—Pd1—Cl191.65 (7)C9—C8—H8B109.8
N1i—Pd1—Cl1i91.65 (7)S1—C8—H8B109.8
N1—Pd1—Cl1i88.35 (7)H8A—C8—H8B108.2
Cl1—Pd1—Cl1i180.0C10—C9—C8111.8 (6)
C7—S1—C8101.6 (2)C10—C9—H9A109.2
C7—N1—C5106.0 (3)C8—C9—H9A109.2
C7—N1—Pd1126.9 (3)C10—C9—H9B109.2
C5—N1—Pd1126.8 (3)C8—C9—H9B109.2
C7—N2—C6107.9 (3)H9A—C9—H9B107.9
C7—N2—H2A126.1C9—C10—C11102.3 (7)
C6—N2—H2A126.1C9—C10—H10A111.3
C2—C1—C6116.6 (5)C11—C10—H10A111.3
C2—C1—H1121.7C9—C10—H10B111.3
C6—C1—H1121.7C11—C10—H10B111.3
C1—C2—C3122.2 (5)H10A—C10—H10B109.2
C1—C2—H2118.9C12—C11—C10112.0 (10)
C3—C2—H2118.9C12—C11—H11A109.2
C4—C3—C2121.1 (6)C10—C11—H11A109.2
C4—C3—H3119.4C12—C11—H11B109.2
C2—C3—H3119.4C10—C11—H11B109.2
C3—C4—C5117.5 (5)H11A—C11—H11B107.9
C3—C4—H4121.2C11—C12—C13108.5 (11)
C5—C4—H4121.2C11—C12—H12A110.0
C4—C5—C6121.0 (4)C13—C12—H12A110.0
C4—C5—N1130.5 (4)C11—C12—H12B110.0
C6—C5—N1108.5 (4)C13—C12—H12B110.0
N2—C6—C5106.1 (3)H12A—C12—H12B108.4
N2—C6—C1132.3 (4)C12—C13—H13A109.5
C5—C6—C1121.6 (4)C12—C13—H13B109.5
N1—C7—N2111.4 (3)H13A—C13—H13B109.5
N1—C7—S1121.8 (3)C12—C13—H13C109.5
N2—C7—S1126.7 (3)H13A—C13—H13C109.5
C9—C8—S1109.5 (4)H13B—C13—H13C109.5
N1i—Pd1—N1—C7141 (100)N1—C5—C6—N2−0.9 (4)
Cl1—Pd1—N1—C7−87.1 (3)C4—C5—C6—C1−0.3 (6)
Cl1i—Pd1—N1—C792.9 (3)N1—C5—C6—C1179.8 (4)
N1i—Pd1—N1—C5−33 (100)C2—C1—C6—N2−179.7 (5)
Cl1—Pd1—N1—C598.7 (2)C2—C1—C6—C5−0.5 (8)
Cl1i—Pd1—N1—C5−81.3 (2)C5—N1—C7—N2−0.5 (4)
C6—C1—C2—C31.1 (9)Pd1—N1—C7—N2−175.6 (2)
C1—C2—C3—C4−0.9 (9)C5—N1—C7—S1178.8 (2)
C2—C3—C4—C50.0 (6)Pd1—N1—C7—S13.7 (4)
C3—C4—C5—C60.5 (5)C6—N2—C7—N1−0.1 (5)
C3—C4—C5—N1−179.6 (3)C6—N2—C7—S1−179.3 (3)
C7—N1—C5—C4−179.1 (3)C8—S1—C7—N1167.7 (3)
Pd1—N1—C5—C4−3.9 (5)C8—S1—C7—N2−13.1 (4)
C7—N1—C5—C60.8 (4)C7—S1—C8—C9−175.7 (3)
Pd1—N1—C5—C6176.0 (2)S1—C8—C9—C10179.4 (3)
C7—N2—C6—C50.6 (5)C8—C9—C10—C11−179.0 (4)
C7—N2—C6—C1179.8 (5)C9—C10—C11—C12175.1 (7)
C4—C5—C6—N2179.0 (3)C10—C11—C12—C13178.2 (7)
Symmetry codes: (i) −x, −y+1, −z.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···Cl1ii0.862.473.282 (3)157
Symmetry codes: (ii) −x, y−1/2, −z+1/2.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···Cl1i0.862.473.282 (3)157
Symmetry codes: (i) −x, y−1/2, −z+1/2.
Acknowledgements top

This work was supported financially by Yunnan Natural Science Foundation (grant Nos. 2005E0003Z and 5Z0103A).

references
References top

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