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Alchemical free energy calculations via molecular dynamics have been widelyused to obtain thermodynamic properties related to protein-ligand binding andsolute-solvent interactions. Although soft-core modeling is the most commonapproach, 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 asuitable alternative. It overcomes the end-point singularity of the scalingmethod while maintaining essential advantages such as ease of implementationand high flexibility for postprocessing analysis. In the present work, wepropose a simple LBF variant and formulate an efficient protocol for evaluatingvan der Waals and Coulomb components of an alchemical transformation in tandem,in contrast to the prevalent sequential evaluation mode. To validate ourproposal, which results from a careful optimization study, we performedsolvation free energy calculations and obtained octanol-water partitioncoefficients of small organic molecules. Comparisons with results obtained viathe sequential mode using either another LBF approach or the soft-core modelattest to the effectiveness and correctness of our method. In addition, we showthat a reaction field model with an infinite dielectric constant can providevery accurate hydration free energies when used instead of a lattice-sum methodto model solute-solvent electrostatics.

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