Crystal structure of 3-(2-hydroxyethyl)-2-methylsulfanyl-6-nitro-3H-benzimidazol-1-ium chloride monohydrate

The title hydrated salt, C10H12N3O3S+·Cl−·H2O, forms centrosymmetric (20) dimers through intermolecular C—H⋯O hydrogen bonds. These dimers are stacked via N—H⋯O and O—H⋯Cl hydrogen bonds involving the water molecules and chloride anions. Offset π–π interactions are also present.

In the cation of the title hydrated molecular salt, C 10 H 12 N 3 O 3 S + ÁCl À ÁH 2 O, the benzimidazolium ring system is almost planar (r.m.s. deviation = 0.006 Å ) and the nitro group is inclined at an angle of 4.86 (9) to this plane. In the crystal, C-HÁ Á ÁO hydrogen bonds form centrosymmetric R 2 2 (20) dimers and these are further aggregated through N-HÁ Á ÁO and O-HÁ Á ÁCl hydrogen bonds involving the water molecules and chloride anions. Aromaticstacking interactions are also found between two parallel benzene rings or the benzene and imidazolium rings, with centroid-centroid distances of 3.5246 (9) and 3.7756 (9) Å , respectively. Analysis of the bond lengths and comparison with related compounds show that the nitro substituent is not involved in conjugation with the adjacent -system and hence has no effect on the charge distribution of the heterocyclic ring.

Chemical context
Numerous compounds with benzimidazole ring systems display versatile pharmacological activities such as anti-viral, anti-helmintic, spasmolitic, anti-hypertensive and vasodilator properties (Akkurt et al., 2006). Many benzimidazole derivatives also have anti-microbial and anti-fungal activities (Kü çü kbay et al., 2003(Kü çü kbay et al., , 2004Puratchikody et al., 2008;Alasmary et al., 2015). The synthesis of new benzimidazole derivatives is therefore of considerable current interest. As part of our studies in this area, the title protonated benzimidazole compound (I) has been synthesized and its molecular structure is presented here.

Structural commentary
The molecular structure of the title compound is shown in Fig. 1. The nine-membered benzimidazolium ring system (N4/ C11/N9/C13/C16/C7/C15/C18/C10) is essentially planar, the maximum deviation from planarity being 0.013 (1) Å for atom N4. In addition, atoms N12, C17 and S2 of the nitro, hydroxyethyl and methylsulfanyl substituents lie close to the benzimidazolium ring plane with a maximum deviation of ISSN 2056-9890 À0.059 (1) Å for atom S2. The least-squares plane of the nitro group (C7/N12/O6/O8) lies close to the benzimidazolium ring system, making a dihedral angle of 4.86 (9) . In the structure, the bond lengths and angles of the benzimidazolium ring are generally in good agreement with those observed in related structures (Morozov et al., 2004;Verdan et al., 2009;Chen et al., 2010;Yuasa et al., 2010;Gao et al., 2013;Samsonov et al., 2013;Liu et al., 2014). In addition, the C7-N12 bond length, 1.4667 (19) Å shows that the nitro group is not involved in conjugation with the adjacent -system and hence has no effect on the charge distribution of the heterocyclic ring.

Supramolecular features
In the crystal, C14-H14BÁ Á ÁO8 hydrogen bonds (Table 1) link the organic fragments into centrosymmetric dimers with R 2 2 (20) ring motifs along the [100] direction (Fig. 2). These dimers are further connected along the [100] and [010] directions by N-HÁ Á ÁO and O-HÁ Á ÁCl hydrogen bonds, respectively, generating R 6 4 (22) rings. In the latter ring motifs, both the water molecule and the oxygen atom of the hy-droxyethyl substituent act as donors with the chloride anion as acceptor. The O3 atom of the water molecule serves as acceptor for the H9 atom of the imidazolium NH group (Fig. 3). The pattern formed by the water molecules connecting the chloride anions, and forming an R 4 2 (8) ring, is reminiscent of a parallelogram (Fig. 3). The supramolecular aggregation is completed bystacking interactions between two parallel benzene rings and between the benzene and imidazolium rings: Cg2Á Á ÁCg2(1 À x, Ày, Àz) = 3.5246 (9) The molecular structure of (I), showing the atomic labelling scheme and displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitrary radius. Table 1 Hydrogen-bond geometry (Å , ). Symmetry codes: (i) Àx; Ày; Àz þ 1; (ii) Àx; Ày; Àz; (iii) x þ 1; y; z.

Figure 2
The crystal packing of (I), showing the supramolecular aggregation resulting from the three-dimensional hydrogen-bonded network. Dashed lines indicate hydrogen bonds. H atoms not involved in hydrogen bonding have been omitted for clarity.

Synthesis and crystallization
2-Chloroethanol (1.3 ml, 19.2 mmol) and potassium carbonate (1.32 g, 9.6 mmol) were added to 2-methylthio-5-nitro-1Hbenzimidazole (1.15 g, 4.8 mmol) in dimethyl sulfoxide (DMSO) (10 ml). The reaction mixture was agitated for 5 h at room temperature. 50 ml of water was then added to the reaction mixture, and the products were extracted with dichloromethane (3 Â 50 ml). The combined organic extracts were washed with ammonium chloride solution (10 g of ammonium chloride in 100 ml of water), dried over Na 2 SO 4 , filtered and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel (elution: methanol/ethyl acetate, 20:80, v/v). The resulting powder was dissolved in dichloromethane and after three days, yellow crystals suitable for single-crystal X-ray diffraction analysis were obtained in 72% yield with a melting point of 425 K.

Special details
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2σ(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.  (7) 0.0891 (11) 0.0073 (7) 0.0620 (10) 0.0007 (7)  O6 0.0788 (10) 0.0336 (6) 0.0715 (9) −0.0019 (6) 0.0152 (7) 0.0062 (6)  C7 0.0393 (7) 0.0307 (6)