Law and mechanism analysis of biodegradability of polychlorinated naphthalenes based on principal component analysis, QSAR models, molecular docking and molecular dynamics simulation

Abstract

The quantization parameters, infrared and Raman spectra of 75 polychlorinated naphthalenes (PCNs) and 42 environmentally friendly CN-56 (CN-56: No. 56 PCN molecule; 1, 2, 3, 7, 8-PentaCN) molecules that are easier to degrade were first calculated via the density functional theory (DFT) method, and the structural characteristics of the molecules were analysed to obtain the substituent characteristics. The principal component analysis method was used to systematically analyse and summarize the effects of macroscopic substituent characteristics, microscopic quantitative parameters and spectral information on the biodegradability of PCNs and 42 environmentally friendly CN-56 molecules, and then the quantitative structure-activity relationship (QSAR), molecular docking and molecular dynamics simulation methods were used to further investigate the biodegradation mechanism from the perspective of molecules and protein receptors. The results showed that PCNs and new PCNs extracted 5 and 6 principal components from 21 kinds of original parameter indicators, respectively, which can effectively explain the original variable information. Besides that, electrostatic activity is the primary factor affecting the degradation of PCNs; reducing the para-substitution logarithm or increasing the total number of substituents and introducing electrostatic groups in the ortho or meta position of PCN molecules can design new PCN derivatives with higher degradability; enhancing the irradiation of Raman light or reducing the irradiation of infrared light properly can increase the biodegradation rate of PCN molecules.

Keywords: Biodegradability; Molecular docking; Molecular dynamics simulation; Polychlorinated naphthalenes (PCNs); Principal component analysis (PCA); Quantitative structure-activity relationship (QSAR).