A DFT study of the chemical bonding properties, aromaticity indexes and molecular docking study of some phenylureas herbicides

Abstract

Herbicides have implied disastrous consequences towards the environment and human health. This practice urges scientists to investigate the physical, chemical and biological properties of these substances, hence avoiding the use of the most harmful pesticides. For this purpose, the molecular structure and chemical bonding properties of phenylurea herbicides namely: Fenuron (L1), Monuron (L2), Diuron (L3) and Chlorotoluron (L4), were calculated in water using density functional theory (DFT). The energy decomposition analysis (EDA) and the extended transition state natural orbitals for chemical Valence (ETS-NOCV) reveal the dominant ionic character in Carbon-Nitrogen bond between dimethylurea fragment and benzene ring. Besides, the interaction of these herbicides with the Human Serum Albumin (HSA) was undertaken by molecular modeling. The calculation of HOMA and FLU indexes indicate that the electronic delocalization is stronger in Diuron than the other compounds, mainly caused by the two chloro substituents effects on benzene. Good correlations are found between the calculated parameters such as structural parameters, Mulliken atomic charge, topological and bonding properties and aromaticity indexes. The Vinardo molecular docking results suggest that, the binding energies of the complexes formed between HSA target and investigated compounds have the following order: L3 (-27.57 kJ/mol) < L2 (-25.56 kJ/mol) < L4 (-24.94 kJ/mol) < L1 (-24.10 kJ/mol), which confirmed that the Fenuron is the less harmful option between the studied herbicides especially against HSA.

In Vitro and In Silico Studies on Benzimidazole‐Based Compounds

“…The DFT calculations were carried out using the Gaussian 16 program, and the geometries of benzimidazole derivatives were optimized using a B3LYP/6-311G + + (2d, 2p) [21,22] which is a commonly used level of theory for organic [23,24] and benzimidazole compounds. [25,26] Other calculations were performed using ADF (Amsterdam density functional), [27] with the hybrid-type B3LYP (Becke's three-parameter hybrid ex-change functional coupled with the Lee-Yang-Parr non-local correlation functional).…”