DMSO Transport across Water/Hexane Interface by Molecular Dynamics Simulation

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections

The computation of distribution coefficients between polar and apolar phases requires both an accurate characterization of transfer free energies between phases and proper accounting of ionization and protomerization. We present a protocol for accurately predicting partition coefficients between two immiscible phases, and then apply it to 53 drug-like molecules in the SAMPL5 blind prediction challenge. Our results combine implicit solvent QM calculations with classical MD simulations using the non-Boltzmann Bennett free energy estimator. The OLYP/DZP/SMD method yields predictions that have a small deviation from experiment (RMSD = 2.3 [Formula: see text] D units), relative to other participants in the challenge. Our free energy corrections based on QM protomer and [Formula: see text] calculations increase the correlation between predicted and experimental distribution coefficients, for all methods used. Unfortunately, these corrections are overly hydrophilic, and fail to account for additional effects such as aggregation, water dragging and the presence of polar impurities in the apolar phase. We show that, although expensive, QM-NBB free energy calculations offer an accurate and robust method that is superior to standard MM and QM techniques alone.

Experimental and molecular dynamic simulation study of perfluorooctane sulfonate adsorption on soil and sediment components

Soil and sediment play a crucial role in the fate and transport of perfluorooctane sulfonate (PFOS) in the environment. However, the molecular mechanisms of major soil/sediment components on PFOS adsorption remain unclear. This study experimentally isolated three major components in soil/sediment: humin/kerogen, humic/fulvic acid (HA/FA), and inorganic component after removing organics, and explored their contributions to PFOS adsorption using batch adsorption experiments and molecular dynamic simulations. The results suggest that the humin/kerogen component dominated the PFOS adsorption due to its aliphatic features where hydrophobic effect and phase transfer are the primary adsorption mechanism. Compared with the humin/kerogen, the HA/FA component contributed less to the PFOS adsorption because of its hydrophilic and polar characteristics. The electrostatic repulsion between the polar groups of HA/FA and PFOS anions was attributable to the reduced PFOS adsorption. When the soil organic matter was extracted, the inorganic component also plays a non-negligible role because PFOS molecules might form surface complexes on SiO2 surface. The findings obtained in this study illustrate the contribution of organic matters in soils and sediments to PFOS adsorption and provided new perspective to understanding the adsorption process of PFOS on micro-interface in the environment.