1-Methyl-2-methylsulfanyl-6-nitro-1H-benzimidazole

The molecule of the title compound, C9H9N3O2S, is built up from fused five- and six-membered rings connected to methylsulfanyl and nitro groups, respectively. The mean plane through the fused ring system is inclined slightly relative to the plane passing through the nitro group [dihedral angle = 3.6 (2)°]. In the crystal, molecules are linked by C—H⋯O hydrogen bonds and π–π interactions between imidazole rings [inter-centroid distance = 3.667 (3) Å], forming a three-dimensional network.

The molecule of the title compound, C 9 H 9 N 3 O 2 S, is built up from fused five-and six-membered rings connected to methylsulfanyl and nitro groups, respectively. The mean plane through the fused ring system is inclined slightly relative to the plane passing through the nitro group [dihedral angle = 3.6 (2) ]. In the crystal, molecules are linked by C-HÁ Á ÁO hydrogen bonds andinteractions between imidazole rings [inter-centroid distance = 3.667 (3) Å ], forming a threedimensional network.
The molecule of the title compound, C 9 H 9 N 3 O 2 S, is formed by a fused five-and six-membered rings as shown in Fig.1.
The mean plane through the fused ring system (N1,N2,C1 to C7) is slightly inclined relative to the mean plane passing through the nitro group with a dihedral angle of 3.6 (2)°. In the crystal, molecules are linked by C-H···O hydrogen bonds and π-π interactions between indazole rings [inter-centroid distance = 3.667 (3) Å], forming a three-dimensional network as shown in Fig.2 and Table 1.

Synthesis and crystallization
To a solution of 5-nitro-1H-benzimidazole-2-thiol (5.12 mmol) in DMSO (15 ml) was added potassium carbonate (5.2 mmol). After 15 min. at 298 K, methyl iodide (7.68 mmol) was added drop wise. Upon disappearance of the starting material, as indicated by TLC, the resulting mixture was evaporated. The crude material was dissolved with EtOAc (60 ml), washed with water and brine, dried over MgSO 4 and the solvent was evaporated in vacuo. The resulting residue was purified by column chromatography (EtOAc/hexane 3/7). The title compound was recrystallized from acetone at room temperature giving colourless crystals (M.pt: 475 K, yield: 47%).

Refinement
H atoms were located in a difference map and treated as riding with C-H = 0.96 Å and C-H = 0.93 Å for methyl-and aromatic-H, respectively. All hydrogen with U iso (H) = 1.5 U eq for methyl-H and U iso (H) = 1.2 U eq for aromatic-H.  Plot of the molecule of the title compound with the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented as small circles.

Figure 2
Partial crystal packing for the title compound showing molecules linked by π-π interactions and hydrogen bonds (dashed lines). 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.