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Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database

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    Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database
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    † Department of Chemistry, University of California, Irvine, California 92697, United States
    ‡ Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
    § Scientific Computing Department, STFC, Daresbury WA4 4AD, U.K.
    ∥ Computational and Systems Biology Program, Sloan Kettering Institute, New York, New York 10065, United States
    ⊥ Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
    *E-mail: [email protected]. Phone: 949-824-6383.
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    Cite this: J. Chem. Eng. Data 2017, 62, 5, 1559–1569
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    https://doi.org/10.1021/acs.jced.7b00104
    Published April 24, 2017
    Copyright © 2017 American Chemical Society
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    Abstract

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    Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here we briefly review “alchemical” approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations and illustrate these approaches by applying them to calculate aqueous solvation free energies (hydration free energies). These approaches use a nonphysical pathway to compute free energy differences from a simulation or set of simulations and appear to be a particularly robust and general-purpose approach for this task. We also present an update (version 0.5) to our FreeSolv database of experimental and calculated hydration free energies of neutral compounds and provide input files in formats for several simulation packages. This revision to FreeSolv provides calculated values generated with a single protocol and software version rather than the heterogeneous protocols used in the prior version of the database. We also further update the database to provide calculated enthalpies and entropies of hydration and some experimental enthalpies and entropies as well as electrostatic and nonpolar components of solvation free energies.

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jced.7b00104.

    • Additional discussion; correlation plots between calculated free energies, enthalpies, and entropies; and simulation details (PDF)

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    Cite this: J. Chem. Eng. Data 2017, 62, 5, 1559–1569
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