Dichlorido[bis­(2-hexyl­sulfanyl)-1H-benzimidazole-κN³]palladium(II)

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.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](C-C) = 0.010 Å
• R factor = 0.045
• wR factor = 0.139
• Data-to-parameter ratio = 21.8

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT110_ALERT_2_B ADDSYM Detects Potential Lattice Centering or Halving .   ?
PLAT220_ALERT_2_B Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       3.72 Ratio
PLAT242_ALERT_2_B Check Low       Ueq as Compared to Neighbors for        Pd1

Alert level C
PLAT048_ALERT_1_C MoietyFormula Not Given ........................          ?
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density ....       2.52
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .......          ?
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.02 Ratio
PLAT230_ALERT_2_C Hirshfeld Test Diff for    C12    -   C13     ..       5.18 su
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for         S1
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for        C11
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for        C12
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        C10
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       2.08
PLAT342_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...         10
PLAT710_ALERT_4_C Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... #          1
            N1  -PD1 -N1  -C7     14.00  0.00   3.565   1.555   1.555   1.555
PLAT710_ALERT_4_C Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... #          4
            N1  -PD1 -N1  -C5      3.00  0.00   3.565   1.555   1.555   1.555

Alert level G
PLAT794_ALERT_5_G Check Predicted Bond Valency for Pd1         (2)       2.24
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          1

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

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
  10 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   3 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

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S1. Comment

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

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

S2. Experimental

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.

S3. Refinement

The H atoms on the C atoms were located in a difference Fourier map and refined as riding on their parent atoms with U_iso(H)=1.2U_eq(C), U_iso(H)=1.5U_eq(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 U_iso(H)=1.2U_eq(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

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

	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.
	Fig. 2. The crystal packing of the title complex. Dashed lines represent hydrogen bonds.

Dichlorido[bis(2-hexylsulfanyl)-1H-benzimidazole- κN³]palladium(II)

Crystal data

[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) Å^3	0.20 × 0.16 × 0.11 mm
Z = 2

Data collection

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

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.045	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.139	H-atom parameters constrained
S = 1.01	w = 1/[σ^2(Fo^2) + (0.0906P)^2 + 0.5462P] where P = (Fo^2 + 2Fc^2)/3
3515 reflections	(Δ/σ)max = 0.001
161 parameters	Δρmax = 1.33 e Å^−3
1 restraint	Δρmin = −0.53 e Å^−3

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
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*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

Geometric parameters (Å, º)

Pd1—N1^i	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—Cl1^i	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
N1^i—Pd1—N1	180.00 (16)	C9—C8—H8A	109.8
N1^i—Pd1—Cl1	88.35 (7)	S1—C8—H8A	109.8
N1—Pd1—Cl1	91.65 (7)	C9—C8—H8B	109.8
N1^i—Pd1—Cl1^i	91.65 (7)	S1—C8—H8B	109.8
N1—Pd1—Cl1^i	88.35 (7)	H8A—C8—H8B	108.2
Cl1—Pd1—Cl1^i	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
N1^i—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)
Cl1^i—Pd1—N1—C7	92.9 (3)	N1—C5—C6—C1	179.8 (4)
N1^i—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)
Cl1^i—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.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···Cl1^ii	0.86	2.47	3.282 (3)	157

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