6-Chloro-2-(thiophen-2-yl)-1-[(thiophen-2-yl)methyl]-1H-benzimidazole

The title compound, C16H11ClN2S2, co-crystallizes with a small amount of the 5-chloro- isomer. The ratio of 6-chloro- to 5-chloro- isomers is 0.969 (2):0.031 (2). One thiophen-2-yl substitutent displays rotational disorder with 80.6 (4)% of the molecules exhibiting the major orientation. In the crystal, weak C—H⋯N and C—H⋯S hydrogen-bonding interactions result in chains of molecules parallel to [001].


Comment
The bond distances and angles in the title compound ( Fig. 1) agree very well with the corresponding bond distances and angles reported in closely related compounds (Geiger et al., 2012;Geiger & Destefano, 2012). Crystallization of the title compound occurs with 3.1 (2)% of the sites occupied by the 5-chloro isomer. The 2-thiophene substituent is rotationally disordered with the major component having a refined occupancy of 81.0 (4)%. The benzimidazole moiety is planar (r. m. s. deviation = 0.0079 Å) with the largest deviation being for C1, which is 0.014 (3)  Experimental 1,2-Diamine-4-chlorobenzene (6.3 mmol, 0.90 g) was dissolved in 30 ml ethanol under nitrogen. Two equivalents of 2thiophenecarboxaldehyde (1.3 ml) was added dropwise. After three days, the solvent was removed under reduced pressure and the crude product was chromatographed (silica gel) using a mixture of 30% hexane in ethyl acetate. The first fraction produced hexagonal shaped crystals (1) and the second fraction produced needle-shaped crystals (2) on slow evaporation. Crystals from the first fraction were used for X-ray diffraction experiments. The overall yield was 59%.

Refinement
All hydrogen atoms were observed in difference fourier maps. The H atoms were refined using a riding model with a C-H distance of 0.99 Å for the methylene carbon atoms and 0.95 Å for the phenyl and thiophene carbon atoms. All C-H hydrogen atom thermal parameters were set using the approximation U iso = 1.2U eq . The Cl and H atoms of the major and minor co-crystallization components were modeled as a disorder involving two parts, each containing a chlorine atom and a hydrogen atom. The major component refined to a site occupancy of 0.969 (2).
In addition, the 2-thiophene substituent is rotationally disordered. A model was developed in which the minor component of the thiophene ring was defined using the metrics of the major component as a guide. The disordered fivemember rings were constrained to planarity using FLAT. Corresponding bond distances of the minor component and major component were set equal using SAME and corresponding thermal parameters were held the same using EADP.
All atoms were refined anisotropically with hydrogen atoms in calculated positions using a riding model. With these constraints, the site occupancy of the major component refined to 0.806 (4).

Figure 1
Perspective view of the title compound. Thermal parameters are drawn at the 50% probability level. Only major contributors to the disorder model are shown.  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 F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > σ(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.