Synthesis, characterization, crystal structure and theoretical study of a compound with benzodiazole ring: Antimicrobial activity and DNA binding

• Benzodiazole ring compound (HL) was synthesized and characterized.
• Single crystal XRD and computational studies were performed for the compound.
• The compound was tested for its antimicrobial activity.
• DNA binding ability of the compound was determined using CT DNA.

2-(Thiophen-2-yl)-1-((thiophen-2-yl)methyl)-1H-1,3-benzodiazole (HL) is synthesized and characterized by elemental analysis, UV–Vis, FT-IR, 1H, 13C NMR, mass spectra, scanning electron microscope (SEM) and single crystal X-ray diffraction. The crystal structure is stabilized by intermolecular CH⋯N and CH⋯π interactions. The molecular structure is also optimized at the B3LYP/6-31G level using density functional theory (DFT). The structural parameters from the theory are nearer to those of crystal, the calculated total energy of coordination is −1522.814 a.u. The energy of HOMO–LUMO and the energy gap are −0.20718, −0.04314, 0.16404 a.u, respectively. All data obtained from the spectral studies support the structural properties of the compound HL. The benzimidazole ring is essentially planar. The in vitro biological screening effects of the synthesized compound is tested against four bacterial and four fungal strains by well diffusion method. Antioxidant property and DNA binding behaviour of the compound has been investigated using spectrophotometric method.

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