A New Formulation for the Concerted Alchemical Calculation of van der Waals and Coulomb Components of Solvation Free Energies

Abstract: Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach, the linear basis function (LBF) methodology [Naden, L. N.; et al. J. Chem. Theory Comput. 2014, 10 (3), 1128; 2015, 11 (6), 2536] has emerged as a suitable alternative. It overcomes the end-point singularity of the scaling method while maintaining essential advantages such as ease of implementation and high flexibility for postprocessing analysis. In the present work, we propose a simple LBF variant and formulate an efficient protocol for evaluating van der Waals and Coulomb components of an alchemical transformation in tandem, in contrast to the prevalent sequential evaluation mode. To validate our proposal, which results from a careful optimization study, we performed solvation free energy calculations and obtained octanol-water partition coefficients of small organic molecules. Comparisons with results obtained via the sequential mode using either another LBF approach or the soft-core model attest to the effectiveness and correctness of our method. In addition, we show that a reaction field model with an infinite dielectric constant can provide very accurate hydration free energies when used instead of a lattice-sum method to model solute-solvent electrostatics.