Crystal structure and Hirshfeld surface analysis and of 2-ammoniumylmethyl-1H-benzimidazol-3-ium chloride monohydrate

In the crystal, the crystal packing is ordered via synergetic contributions from N—H⋯Cl, O—H⋯Cl and N—H⋯O hydrogen bonds, which together assemble the cations and anions into a three-dimensional framework.


Chemical context
Heterocyclic compounds containing nitrogen such as benzimidazoles and their derivatives have attracted attention because of their medicinal applications as antiulcer, anticancer, antifungal, antimycobacterial and anti-inflammatory agents (El-masry et al., 2000). Besides being important pharmacophores, in particular amine-substituted benzimidazoles are good intermediates for the synthesis of different organic compounds (Maurya et al., 2007). General methods for the preparation of benzimidazoles involve the reaction of o-phenylenediamine and carboxylic acid or its derivatives under harsh dehydrating conditions or with aldehydes followed by oxidation (Peng et al., 2014).

Figure 2
The view of the crystal packing of the title compound. Dashed lines denote the hydrogen bonds.

Figure 3
The Hirshfeld surface of the title compound mapped over d norm , d i and d e .

Figure 1
The molecular structure of the title compound, showing the atom labelling. Displacement ellipsoids are drawn at the 20% probability level.
interactions in the synthesized complex. Red spots on the Hirshfeld surfaces indicate the intermolecular contacts involved in strong hydrogen bonds and interatomic contacts (Gü mü ş et al., 2018;. The red spots in Fig. 4 correspond to the HÁ Á ÁCl contacts resulting from the N-HÁ Á ÁCl and O-HÁ Á ÁCl hydrogen bonds. The Hirshfeld surfaces were mapped using a standard (high) surface resolution with the three-dimensional d norm surfaces mapped over a fixed colour scale of À0.518 (red) to 1.174 (blue) a.u.. Fig. 5 shows the two-dimensional fingerprint plot of all the contacts contributing to the Hirshfeld surface represented in normal mode. Fig. 6 shows the two-dimensional fingerprint plots of the (d i , d e ) points associated with various atoms. HÁ Á ÁH contacts contribute 37.4% to the Hirshfeld surface. The graph for ClÁ Á ÁH/HÁ Á ÁCl shows the contacts between the chlorine atoms inside the Hirshfeld surface and the hydrogen atoms outside the surface and vice versa, and has two symmetrical wings on the left and right sides (35.5%). Further, there are CÁ Á ÁH/HÁ Á ÁC (9.5%), CÁ Á ÁC (6.9%), OÁ Á ÁH/HÁ Á ÁO (4.1%) and NÁ Á ÁH/HÁ Á ÁN (3.4%) contacts.

Synthesis and crystallization
o-Phenylenediamine (10.8 g, 99.87 mmol) and glycine (10.00 g, 133.2 mmol) were dissolved in 5.5 M HCl (150 mL) . The reaction mixture was purged by argon at room temperature and heated up to reflux temperature for 12 h. The reaction was monitored by TLC. After completion of the reaction, the mixture was concentrated to 50 mL and kept at 269 K for 2 d. The crystals were filtered off and washed twice with acetone and dried to give the desired product ( Fig. 7).

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2. C-bound H atoms were positioned geometrically with C-H distances of 0.93-0.97 Å . and refined as riding, with U iso (H) = 1.2U eq (C). N-bound H atoms were located in difference-Fourier maps and refined isotropically. The coordinates of the water H atoms were determined from a difference-Fourier map and refined isotropically subject to a restraint of O-H = 0.82 (4) Å . Fingerprint plot of all the contacts.