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Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database

Guilherme Duarte Ramos Matos, Daisy Y. Kyu, Hannes H. Loeffler, John D. Chodera, Michael R. Shirts, David L. Mobley
doi: https://doi.org/10.1101/104281
Guilherme Duarte Ramos Matos
1Department of Chemistry, University of California, Irvine
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Daisy Y. Kyu
2Department of Pharmaceutical Sciences, University of California, Irvine
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Hannes H. Loeffler
3Scientific Computing Department, STFC, UK
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John D. Chodera
4Computational and Systems Biology Program, Sloan Kettering Institute
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Michael R. Shirts
5Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder
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David L. Mobley
6Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
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Abstract

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 by applying them to calculate aqueous solvation free energies (hydration free energies). These approaches use a non-physical 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 copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 30, 2017.
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Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database
Guilherme Duarte Ramos Matos, Daisy Y. Kyu, Hannes H. Loeffler, John D. Chodera, Michael R. Shirts, David L. Mobley
bioRxiv 104281; doi: https://doi.org/10.1101/104281
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Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database
Guilherme Duarte Ramos Matos, Daisy Y. Kyu, Hannes H. Loeffler, John D. Chodera, Michael R. Shirts, David L. Mobley
bioRxiv 104281; doi: https://doi.org/10.1101/104281

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