Calculation of diffusion coefficients of pesticides by employing molecular dynamics simulations

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• Diffusion coefficients of pesticides in water are obtained by MD simulations. • Key methodological features are proposed for calculating diffusion coefficients. • Simulation results show good agreement with available experimental data. • Diffusion coefficients are rationalized in terms of solute–solvent H-bonds and SASA. Extensive use of pesticides causes serious environmental problems that require insightful knowledge from physics and chemistry sciences to be efficiently tackled. In particular, diffusion is a relevant property when evaluating the fluxes of pesticides in the groundwater. This work employed the best practices for the computation of diffusion coefficients from molecular dynamics simulations in the canonical ensemble. The investigation has been complemented with a study of the effect of the simulation time on the calculated diffusion coefficients. The methodology was successfully tested in the water benchmark system and, then, it was applied to obtain the diffusion coefficients of various pesticides (cymoxanil, imidacloprid, pirimicarb and glufosinate ion). The comparison of the calculated diffusion coefficients with recent experimental data reveals errors ranging from ∼ 6 % for the glufosinate ion and ∼ 16 % for cymoxanil. The results have been rationalized in terms of solute–solvent interactions.