DFT studies on vibrational and electronic spectra, HOMO-LUMO, MEP, HOMA, NBO and molecular docking analysis of benzyl-3-N-(2,4,5-trimethoxyphenylmethylene)hydrazinecarbodithioate

Mohammad Abdul Mumit; Tarun Kumar Pal; Md Ashraful Alam; Md Al-Amin-Al-Azadul Islam; Subrata Paul; Md Chanmiya Sheikh

doi:10.1016/j.molstruc.2020.128715

DFT studies on vibrational and electronic spectra, HOMO-LUMO, MEP, HOMA, NBO and molecular docking analysis of benzyl-3-N-(2,4,5-trimethoxyphenylmethylene)hydrazinecarbodithioate

J Mol Struct. 2020 Nov 15:1220:128715. doi: 10.1016/j.molstruc.2020.128715. Epub 2020 Jun 20.

Authors

Mohammad Abdul Mumit¹, Tarun Kumar Pal¹, Md Ashraful Alam¹, Md Al-Amin-Al-Azadul Islam¹, Subrata Paul², Md Chanmiya Sheikh³

Affiliations

¹ Department of Chemistry, Rajshahi University of Engineering & Technology, Rajshahi, 6204, Bangladesh.
² Department of Pharmacy, Rajshahi University, Rajshahi, 6205, Bangladesh.
³ Faculty of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan.

Abstract

Benzyl-3-N-(2,4,5-trimethoxyphenylmethylene)hydrazinecarbodithioate (compound 1) is a bidentate and nitrogen-sulfur containing Schiff base, which has been synthesized by the condensation reaction of S-benzylndithiocarbazate and 2,4,5-trimethoxybenzaldehyde. The theoretical calculations of the mentioned compound have been carried out using the more popular density functional theory method, Becke-3-Parameter-Lee-Yang-Parr (B3LYP) in 6-31G+(d,p) basis set. The computational results of the compound were compared with the obtained experimental value. Moreover, the highest occupied molecular orbital, the lowest unoccupied molecular orbital, molecular electrostatic potential, chemical reactivity parameters and natural bond orbital of the optimized structure have been evaluated at the same level of theory. Furthermore, the UV-Vis spectrum of the compound has been carried out for the better understanding of electronic absorption spectra with the help of the time-dependent density functional theory at room temperature. Besides, the molecular docking simulation of the mentioned molecule with target protein was also investigated. In addition, in silico studies were performed to predict absorption, distribution, metabolism, excretion and toxicity profiles of the designed compound. The results indicated that the theoretical data have well correlated with the observed values. The narrow frontier orbital gap indicated that the eventual charge transfer interaction occurs within the studied molecule and showed high chemical reactivity. The global reactivity values showed that the compound is soft molecule, electrophilic species and has strong binding ability with biomolecules. The molecular electrostatic potential structure indicated that the negative and positive potential sites are around electronegative atoms and hydrogen atoms of studied compound, respectively. The natural bond orbital data revealed that the compound contains 97.42% Lewis and 2.58% non-Lewis structure. The intra and inter-molecular charge transfers process occur within the studied compound. The studied compound showed more binding energy (-6.0 kcal/mol) with target protein than hydroxychloroquine (-5.6 kcal/mol). The absorption, distribution, metabolism, excretion and toxicity investigation predicted that the compound has good drug like character.

Keywords: ADMET; DFT; HOMA; Molecular docking; NBO.