Predicting adsorption of organic compounds onto graphene and black phosphorus by molecular dynamics and machine learning

Abstract

With an increase in production and application of various engineering nanomaterials (ENMs), they will inevitably be released into the environment. Adsorption of various organic chemicals onto ENMs will impact on their environmental behavior and toxicology. It is unrealistic to experimentally determine adsorption equilibrium constants (K) for the vast number of organics and ENMs due to high cost in expenditure and time. Herein, appropriate molecular dynamics (MD) methods were evaluated and selected by comparing experimental K values of seven organics adsorbed onto graphene with the MD-calculated ones. Machine learning (ML) models on K of organics adsorption onto graphene and black phosphorus nanomaterials were constructed based on a benchmark data set from the MD simulations. Lasso models based on Mordred descriptors outperformed ML models built by support vector machine, random forest, k-nearest neighbor, and gradient boosting decision tree, in terms of cross-validation coefficients (Q² > 0.90). The Lasso models also outperformed conventional poly-parameter linear free energy relationship models for predicting logK. Compared with previous models, the Lasso models considered more compounds with different functional groups and thus have broader applicability domains. This study provides a promising way to fill the data gap in logK for chemicals adsorbed onto the ENMs.

Keywords: Adsorption; Graphene; Machine learning; Molecular dynamics; Organic pollutants; Phosphorene.