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Comparison of two simulation methods to compute solvation free energies and partition coefficients.

Research paper by Li L Yang, Alauddin A Ahmed, Stanley I SI Sandler

Indexed on: 31 Oct '12Published on: 31 Oct '12Published in: Journal of Computational Chemistry



Abstract

The thermodynamic integration (TI) and expanded ensemble (EE) methods are used here to calculate the hydration free energy in water, the solvation free energy in 1-octanol, and the octanol-water partition coefficient for a six compounds of varying functionality using the optimized potentials for liquid simulations (OPLS) all-atom (AA) force field parameters and atomic charges. Both methods use the molecular dynamics algorithm as a primary component of the simulation protocol, and both have found wide applications in fields such as the calculation of activity coefficients, phase behavior, and partition coefficients. Both methods result in solvation free energies and 1-octanol/water partition coefficients with average absolute deviations (AAD) from experimental data to within 4 kJ/mol and 0.5 log units, respectively. Here, we find that in simulations the OPLS-AA force field parameters (with fixed charges) can reproduce solvation free energies of solutes in 1-octanol with AAD of about half that for the solute hydration free energies using a extended simple point charge (SPC/E) model of water. The computational efficiency of the two simulation methods are compared based on the time (in nanoseconds) required to obtain similar standard deviations in the solvation free energies and 1-octanol/water partition coefficients. By this analysis, the EE method is found to be a factor of nine more efficient than the TI algorithm. For both methods, solvation free energy calculations in 1-octanol consume roughly an order of magnitude more CPU hours than the hydration free energy calculations.