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Arsenic (As) contamination of soils is a critical environmental and geochemical concern, with its mobility and bioavailability largely controlled by molecular-scale interactions with soil minerals. This study investigates the adsorption behavior of arsenate [As(V)] and arsenious acid [As(III)] on major clay minerals to elucidate fundamental controls on As retention in soil and sediment systems. Molecular modeling approaches were employed to investigate these interactions. Density functional theory (DFT) calculations were performed on cluster models of illite, chlorite, montmorillonite, and kaolinite to evaluate adsorption configurations and binding energies of arsenate and arsenious acid. In addition, semiempirical (PM6) and classical force-field (UFF) methods were used to examine the influence of vermicompost-derived organic matter on arsenate-mineral interactions. Multiple adsorption configurations, including atop atom, bridge, three-fold filled, and three-fold hollow sites, were evaluated, and binding energies were calculated with correction for basis set superposition error. The results indicate that three-fold hollow sites are the most favorable, with As(V) binding energies of 60–65 kcal mol−1 on illite, chlorite, and montmorillonite, reaching 75 kcal mol−1 on kaolinite at a surface distance of 2.7 Å. In contrast, As(III) shows weaker and energetically flatter adsorption, with binding energies of 28–54 kcal mol−1 and larger equilibrium distances of 3.2–4.0 Å. Modeling of vermicompost addition suggests a substantial reduction in arsenate binding on most clay minerals, except illite, indicating competitive or disruptive interactions at mineral surfaces. These findings provide quantitative, atomistic insight into mineral- and amendment-specific controls on As stabilization and mobility in soil and sediment systems.