Molecular structure of 2-chloromethyl-1H-benzimidazole hydrochloride: Single crystal, spectral, biological studies, and DFT calculations

In the present work, structural studies on 2-chloromethyl-1H-benzimidazole hydrochloride have been performed extensively by X-ray crystallography, 1H NMR, FT-IR, UV/vis, and elemental analysis. The title compound crystallizes in a monoclinic space group P21/c with a = 7.1982 (3) Å, b = 9.4513 (5) Å, c = 14.0485 (7) Å and β = 102.440 (3)° forming an infinite chain structure parallel to “b” axis through the intermolecular hydrogen bond. Optimized geometrical structure, harmonic vibrational frequencies, natural bonding orbital (NBO) and frontier molecular orbitals (FMO) were obtained by DFT/B3LYP method combined with 6-31G(d) basis set. TD-DFT calculations help to assign the electronic transitions. The 1H NMR chemical shifts were computed at the B3LYP/6-311 + G(2d,p) level of theory in different solvents by applying GIAO method using the polarizable continuum model (PCM). The title compound was screened for its antibacterial activity referring to Tetracycline as a standard antibacterial agent.

ORTEP plot of 2-chloromethyl-1H-benzimidazole hydrochloride.Figure optionsDownload as PowerPoint slideHighlights
► The title compound inhibits the metabolic growth of the investigated bacteria to different extents.
► The spectroscopic data of this derivative is affected by intermolecular H-bonding.
► The inclusion of solvation to NMR calculations is essential especially for acidic protons.
► All the vibrational modes were examined and proposed at high level of theory.
► The low value of HOMO–LUMO gap reflects the reactivity of the title compound.