Vibrational spectroscopic analysis, molecular dynamics simulations and molecular docking study of 5-nitro-2-phenoxymethyl benzimidazole

Publication date: 5 February 2017 Source:Journal of Molecular Structure, Volume 1129 Author(s): Vidya V. Menon, Egemen Foto, Y. Sheena Mary, Esin Karatas, C. Yohannan Panicker, Gözde Yalcin, Stevan Armaković, Sanja J. Armaković, C. Van Alsenoy, Ilkay Yildiz FT-IR and FT-Raman spectra of 5-nitro-2-phenoxymethylbenzimidazole were recorded and analyzed theoretically and experimentally. The splitting of NH stretching mode in the IR spectrum with a red shift from the calculated value indicates the weakening of the NH bond. The theoretical calculations give the phenyl ring breathing modes at 999 cm−1 for mono substituted benzene ring and at 1040 cm−1 for tri-substituted benzene ring. The theoretical NMR chemical shifts are in agreement with the experimental chemical shifts. The most reactive sites for electrophilic and nucleophilic attack are predicted from the MEP analysis. HOMO of π nature is delocalized over the entire molecule whereas the LUMO is located over the complete molecule except mono-substituted phenyl ring and oxygen atom. Reactive sites of the title molecule have been located with the help of ALIE surfaces and Fukui functions. In order to determine locations prone to autoxidation and locations interesting for starting of degradation, bond dissociation energies have been calculated for all single acyclic bonds. For the determination of atoms with pronounced interactions with water we have calculated radial distribution functions obtained after mo...
Source: Journal of Molecular Structure - Category: Molecular Biology Source Type: research