Molecular Dynamics-Based Free-Energy Prediction of Pesticide Adsorption on Graphenic and Amorphous Silica Surfaces

Abstract The removal of agrochemical contaminants from water and soil is a major challenge in environmental remediation. Adsorption-based treatments are widely used for contaminant removal due to their efficiency, scalability, and relatively low cost, making the understanding at the molecular level of pesticide–surface interactions essential for improving remediation strategies. Here, molecular dynamics (MD) simulations with adaptive biasing force (ABF) were used to evaluate the adsorption free energies of several well-known agrochemicals, including glyphosate, atrazine, chlorpyrifos, aminomethylphosphonic acid (AMPA), glufosinate, rotenone, and paraquat, on graphene, graphene oxide, and hydroxylated silica surfaces. These materials represent model systems for the carbonaceous and mineral components commonly found in environmental matrices. MD simulations reveal systematically stronger adsorption on graphene-based materials (≈ −3 to −13 kcal/mol), driven primarily by dispersion and π-surface interactions, resulting in particularly high affinity for aromatic and compounds with low polarity such as atrazine, chlorpyrifos, and rotenone. In contrast, adsorption on hydroxylated silica is substantially weaker (≈ −1 to −3 kcal/mol) and reflects competition between hydrogen bonding, electrostatic interactions with surface silanol groups, and interfacial hydration. Polar molecules, such as glyphosate, glufosinate, and AMPA, interact mainly through hydration-mediated mechanisms, while other compounds, such as paraquat, exhibit intermediate behavior due to their planar aromatic structure. Overall, these findings provide a thermodynamic rationale at the molecular level for the role of soil organic carbon in limiting pesticide leaching and suggest that carbon amendments designed with complementary mineral phases may enhance the retention capacity of natural substrates.