Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807042584/om2153sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807042584/om2153Isup2.hkl |
CCDC reference: 663561
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.
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).
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.
For related literature, see: Al-Bazi & Preiser (1987); Ito et al. (1997); Li et al. (2005); Türktekin et al. (2005).
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.
[PdCl2(C13H18N2S)2] | F(000) = 664 |
Mr = 646.01 | Dx = 1.436 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
a = 14.3559 (11) Å | θ = 1.5–28.3° |
b = 7.7688 (6) Å | µ = 0.96 mm−1 |
c = 14.5566 (11) Å | T = 298 K |
β = 113.073 (1)° | Block, yellow |
V = 1493.6 (2) Å3 | 0.20 × 0.16 × 0.11 mm |
Z = 2 |
Bruker APEXII 1K CCD area-detector diffractometer | 3515 independent reflections |
Radiation source: fine-focus sealed tube | 2649 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.022 |
φ and ω scans | θmax = 28.3°, θmin = 1.5° |
Absorption correction: numerical (SADABS; Sheldrick, 2002) | h = −19→18 |
Tmin = 0.831, Tmax = 0.902 | k = −10→10 |
12251 measured reflections | l = −19→19 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.045 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.139 | H-atom parameters constrained |
S = 1.01 | w = 1/[σ2(Fo2) + (0.0906P)2 + 0.5462P] where P = (Fo2 + 2Fc2)/3 |
3515 reflections | (Δ/σ)max = 0.001 |
161 parameters | Δρmax = 1.33 e Å−3 |
1 restraint | Δρmin = −0.53 e Å−3 |
[PdCl2(C13H18N2S)2] | V = 1493.6 (2) Å3 |
Mr = 646.01 | Z = 2 |
Monoclinic, P21/c | Mo Kα radiation |
a = 14.3559 (11) Å | µ = 0.96 mm−1 |
b = 7.7688 (6) Å | T = 298 K |
c = 14.5566 (11) Å | 0.20 × 0.16 × 0.11 mm |
β = 113.073 (1)° |
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 = 0.902 | Rint = 0.022 |
12251 measured reflections |
R[F2 > 2σ(F2)] = 0.045 | 1 restraint |
wR(F2) = 0.139 | H-atom parameters constrained |
S = 1.01 | Δρmax = 1.33 e Å−3 |
3515 reflections | Δρmin = −0.53 e Å−3 |
161 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 | ||
Pd1 | 0.0000 | 0.5000 | 0.0000 | 0.04347 (15) | |
S1 | 0.13339 (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 | −0.0367 | 0.4326 | 0.3216 | 0.085* | |
Cl1 | 0.02540 (13) | 0.78914 (15) | 0.02260 (10) | 0.1020 (5) | |
C1 | −0.2480 (4) | 0.4513 (7) | 0.2038 (4) | 0.0920 (15) | |
H1 | −0.2502 | 0.4356 | 0.2662 | 0.110* | |
C2 | −0.3343 (5) | 0.4676 (8) | 0.1192 (5) | 0.1021 (19) | |
H2 | −0.3967 | 0.4647 | 0.1247 | 0.123* | |
C3 | −0.3320 (5) | 0.4884 (6) | 0.0248 (5) | 0.0931 (18) | |
H3 | −0.3925 | 0.4974 | −0.0309 | 0.112* | |
C4 | −0.2417 (4) | 0.4958 (4) | 0.0129 (4) | 0.0712 (12) | |
H4 | −0.2399 | 0.5098 | −0.0499 | 0.085* | |
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) | |
C7 | 0.0026 (3) | 0.4639 (5) | 0.2064 (3) | 0.0553 (8) | |
C8 | 0.1645 (4) | 0.4744 (5) | 0.3879 (3) | 0.0727 (12) | |
H8A | 0.1334 | 0.5770 | 0.4013 | 0.087* | |
H8B | 0.1383 | 0.3753 | 0.4108 | 0.087* | |
C9 | 0.2782 (5) | 0.4839 (6) | 0.4432 (4) | 0.0892 (16) | |
H9A | 0.3086 | 0.3808 | 0.4295 | 0.107* | |
H9B | 0.3038 | 0.5819 | 0.4190 | 0.107* | |
C10 | 0.3079 (6) | 0.5007 (7) | 0.5525 (5) | 0.112 (2) | |
H10A | 0.2865 | 0.4013 | 0.5796 | 0.135* | |
H10B | 0.2797 | 0.6040 | 0.5688 | 0.135* | |
C11 | 0.4287 (9) | 0.5116 (10) | 0.5928 (8) | 0.177 (5) | |
H11A | 0.4547 | 0.4044 | 0.5782 | 0.212* | |
H11B | 0.4474 | 0.6033 | 0.5580 | 0.212* | |
C12 | 0.4752 (9) | 0.5440 (15) | 0.7007 (8) | 0.204 (5) | |
H12A | 0.4560 | 0.4542 | 0.7362 | 0.245* | |
H12B | 0.4520 | 0.6535 | 0.7159 | 0.245* | |
C13 | 0.5877 (6) | 0.5466 (12) | 0.7325 (7) | 0.171 (4) | |
H13A | 0.6107 | 0.4343 | 0.7236 | 0.257* | |
H13B | 0.6189 | 0.5787 | 0.8016 | 0.257* | |
H13C | 0.6055 | 0.6286 | 0.6928 | 0.257* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Pd1 | 0.0645 (3) | 0.0425 (2) | 0.0360 (2) | 0.00197 (13) | 0.03335 (17) | 0.00119 (11) |
S1 | 0.0703 (6) | 0.1298 (10) | 0.0493 (5) | 0.0124 (6) | 0.0329 (5) | 0.0106 (6) |
N1 | 0.0679 (17) | 0.0520 (16) | 0.0398 (14) | 0.0033 (11) | 0.0344 (13) | 0.0021 (9) |
N2 | 0.088 (2) | 0.096 (2) | 0.0461 (16) | 0.005 (2) | 0.0459 (17) | 0.0100 (16) |
Cl1 | 0.2099 (14) | 0.0490 (6) | 0.1058 (8) | −0.0188 (7) | 0.1254 (9) | −0.0148 (5) |
C1 | 0.095 (4) | 0.129 (4) | 0.081 (3) | −0.002 (3) | 0.066 (3) | 0.003 (3) |
C2 | 0.070 (3) | 0.156 (5) | 0.096 (4) | 0.001 (3) | 0.051 (3) | 0.000 (3) |
C3 | 0.071 (3) | 0.134 (6) | 0.078 (3) | 0.002 (2) | 0.034 (3) | 0.000 (2) |
C4 | 0.075 (3) | 0.093 (4) | 0.054 (2) | 0.0026 (18) | 0.034 (2) | 0.0020 (16) |
C5 | 0.068 (2) | 0.060 (2) | 0.0512 (19) | 0.0016 (14) | 0.0390 (17) | 0.0003 (13) |
C6 | 0.074 (3) | 0.080 (2) | 0.055 (2) | 0.0016 (19) | 0.043 (2) | 0.0031 (18) |
C7 | 0.067 (2) | 0.068 (2) | 0.0417 (17) | 0.0047 (16) | 0.0340 (16) | 0.0074 (14) |
C8 | 0.077 (3) | 0.096 (3) | 0.048 (2) | 0.005 (2) | 0.029 (2) | 0.0096 (18) |
C9 | 0.083 (3) | 0.119 (5) | 0.068 (3) | 0.003 (2) | 0.031 (3) | 0.008 (2) |
C10 | 0.101 (4) | 0.149 (7) | 0.066 (3) | 0.003 (3) | 0.009 (3) | −0.003 (2) |
C11 | 0.147 (9) | 0.221 (15) | 0.146 (10) | 0.013 (5) | 0.039 (8) | −0.001 (5) |
C12 | 0.146 (9) | 0.320 (15) | 0.133 (9) | −0.002 (8) | 0.040 (7) | −0.008 (8) |
C13 | 0.082 (4) | 0.322 (12) | 0.104 (5) | 0.005 (5) | 0.030 (4) | 0.033 (6) |
Pd1—N1i | 2.009 (3) | C5—C6 | 1.390 (5) |
Pd1—N1 | 2.009 (3) | C8—C9 | 1.512 (8) |
Pd1—Cl1 | 2.2788 (12) | C8—H8A | 0.9700 |
Pd1—Cl1i | 2.2788 (12) | C8—H8B | 0.9700 |
S1—C7 | 1.729 (4) | C9—C10 | 1.482 (9) |
S1—C8 | 1.823 (4) | C9—H9A | 0.9700 |
N1—C7 | 1.331 (5) | C9—H9B | 0.9700 |
N1—C5 | 1.396 (5) | C10—C11 | 1.600 (13) |
N2—C7 | 1.350 (4) | C10—H10A | 0.9700 |
N2—C6 | 1.377 (6) | C10—H10B | 0.9700 |
N2—H2A | 0.8600 | C11—C12 | 1.468 (9) |
C1—C2 | 1.369 (9) | C11—H11A | 0.9700 |
C1—C6 | 1.398 (6) | C11—H11B | 0.9700 |
C1—H1 | 0.9300 | C12—C13 | 1.495 (14) |
C2—C3 | 1.396 (9) | C12—H12A | 0.9700 |
C2—H2 | 0.9300 | C12—H12B | 0.9700 |
C3—C4 | 1.375 (7) | C13—H13A | 0.9600 |
C3—H3 | 0.9300 | C13—H13B | 0.9600 |
C4—C5 | 1.388 (6) | C13—H13C | 0.9600 |
C4—H4 | 0.9300 | ||
N1i—Pd1—N1 | 180.00 (16) | C9—C8—H8A | 109.8 |
N1i—Pd1—Cl1 | 88.35 (7) | S1—C8—H8A | 109.8 |
N1—Pd1—Cl1 | 91.65 (7) | C9—C8—H8B | 109.8 |
N1i—Pd1—Cl1i | 91.65 (7) | S1—C8—H8B | 109.8 |
N1—Pd1—Cl1i | 88.35 (7) | H8A—C8—H8B | 108.2 |
Cl1—Pd1—Cl1i | 180.0 | C10—C9—C8 | 111.8 (6) |
C7—S1—C8 | 101.6 (2) | C10—C9—H9A | 109.2 |
C7—N1—C5 | 106.0 (3) | C8—C9—H9A | 109.2 |
C7—N1—Pd1 | 126.9 (3) | C10—C9—H9B | 109.2 |
C5—N1—Pd1 | 126.8 (3) | C8—C9—H9B | 109.2 |
C7—N2—C6 | 107.9 (3) | H9A—C9—H9B | 107.9 |
C7—N2—H2A | 126.1 | C9—C10—C11 | 102.3 (7) |
C6—N2—H2A | 126.1 | C9—C10—H10A | 111.3 |
C2—C1—C6 | 116.6 (5) | C11—C10—H10A | 111.3 |
C2—C1—H1 | 121.7 | C9—C10—H10B | 111.3 |
C6—C1—H1 | 121.7 | C11—C10—H10B | 111.3 |
C1—C2—C3 | 122.2 (5) | H10A—C10—H10B | 109.2 |
C1—C2—H2 | 118.9 | C12—C11—C10 | 112.0 (10) |
C3—C2—H2 | 118.9 | C12—C11—H11A | 109.2 |
C4—C3—C2 | 121.1 (6) | C10—C11—H11A | 109.2 |
C4—C3—H3 | 119.4 | C12—C11—H11B | 109.2 |
C2—C3—H3 | 119.4 | C10—C11—H11B | 109.2 |
C3—C4—C5 | 117.5 (5) | H11A—C11—H11B | 107.9 |
C3—C4—H4 | 121.2 | C11—C12—C13 | 108.5 (11) |
C5—C4—H4 | 121.2 | C11—C12—H12A | 110.0 |
C4—C5—C6 | 121.0 (4) | C13—C12—H12A | 110.0 |
C4—C5—N1 | 130.5 (4) | C11—C12—H12B | 110.0 |
C6—C5—N1 | 108.5 (4) | C13—C12—H12B | 110.0 |
N2—C6—C5 | 106.1 (3) | H12A—C12—H12B | 108.4 |
N2—C6—C1 | 132.3 (4) | C12—C13—H13A | 109.5 |
C5—C6—C1 | 121.6 (4) | C12—C13—H13B | 109.5 |
N1—C7—N2 | 111.4 (3) | H13A—C13—H13B | 109.5 |
N1—C7—S1 | 121.8 (3) | C12—C13—H13C | 109.5 |
N2—C7—S1 | 126.7 (3) | H13A—C13—H13C | 109.5 |
C9—C8—S1 | 109.5 (4) | H13B—C13—H13C | 109.5 |
N1i—Pd1—N1—C7 | 141 (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—C7 | 92.9 (3) | N1—C5—C6—C1 | 179.8 (4) |
N1i—Pd1—N1—C5 | −33 (100) | C2—C1—C6—N2 | −179.7 (5) |
Cl1—Pd1—N1—C5 | 98.7 (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—C3 | 1.1 (9) | Pd1—N1—C7—N2 | −175.6 (2) |
C1—C2—C3—C4 | −0.9 (9) | C5—N1—C7—S1 | 178.8 (2) |
C2—C3—C4—C5 | 0.0 (6) | Pd1—N1—C7—S1 | 3.7 (4) |
C3—C4—C5—C6 | 0.5 (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—N1 | 167.7 (3) |
Pd1—N1—C5—C4 | −3.9 (5) | C8—S1—C7—N2 | −13.1 (4) |
C7—N1—C5—C6 | 0.8 (4) | C7—S1—C8—C9 | −175.7 (3) |
Pd1—N1—C5—C6 | 176.0 (2) | S1—C8—C9—C10 | 179.4 (3) |
C7—N2—C6—C5 | 0.6 (5) | C8—C9—C10—C11 | −179.0 (4) |
C7—N2—C6—C1 | 179.8 (5) | C9—C10—C11—C12 | 175.1 (7) |
C4—C5—C6—N2 | 179.0 (3) | C10—C11—C12—C13 | 178.2 (7) |
Symmetry code: (i) −x, −y+1, −z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···Cl1ii | 0.86 | 2.47 | 3.282 (3) | 157 |
Symmetry code: (ii) −x, y−1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | [PdCl2(C13H18N2S)2] |
Mr | 646.01 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 298 |
a, b, c (Å) | 14.3559 (11), 7.7688 (6), 14.5566 (11) |
β (°) | 113.073 (1) |
V (Å3) | 1493.6 (2) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.96 |
Crystal size (mm) | 0.20 × 0.16 × 0.11 |
Data collection | |
Diffractometer | Bruker APEXII 1K CCD area-detector |
Absorption correction | Numerical (SADABS; Sheldrick, 2002) |
Tmin, Tmax | 0.831, 0.902 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 12251, 3515, 2649 |
Rint | 0.022 |
(sin θ/λ)max (Å−1) | 0.666 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.045, 0.139, 1.01 |
No. of reflections | 3515 |
No. of parameters | 161 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 1.33, −0.53 |
Computer programs: APEX2 (Bruker, 2004), SAINT (Bruker, 2004), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97) (Sheldrick, 1997), SHELXTL (Sheldrick, 2000), SHELXL97.
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···Cl1i | 0.86 | 2.47 | 3.282 (3) | 156.6 |
Symmetry code: (i) −x, y−1/2, −z+1/2. |
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.