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Journal of Computer-Aided Molecular Design

, Volume 28, Issue 7, pp 711–720 | Cite as

FreeSolv: a database of experimental and calculated hydration free energies, with input files

  • David L. MobleyEmail author
  • J. Peter Guthrie
Article

Abstract

This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz.

Keywords

Hydration free energy Transfer free energy Alchemical Molecular dynamics Free energy calculations 

Notes

Acknowledgments

We thank Robert C. Rizzo (Stony Brook University) for help tracking down an issue with hexafluoropropene, and many others who have been involved in work on the experimental and calculated values represented in this database, including Élise Dumont, John D. Chodera, Ken A. Dill, Alan E. Barber, II, Anthony Nicholls, Christopher I. Bayly, Matthew D. Cooper, Vijay S. Pande, Michael R. Shirts, Pavel V. Klimovich, Shuai Liu, David S. Cerutti, William C. Swope, Julia E. Rice, Christopher J. Fennell, Nathan M. Lim, and Karisa L. Wymer. We also appreciate work done by Karisa Wymer and Jessica Fuselier towards initial curation of the set. DLM appreciates financial support from the National Institutes of Health (1R15GM096257-01A1), and computing support from the UCI GreenPlanet cluster, supported in part by NSF Grant CHE-0840513.

Supplementary material

10822_2014_9747_MOESM1_ESM.pdf (102 kb)
Supplementary material 1 (pdf 102 KB)

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  1. 1.Department of Pharmaceutical Sciences and Department of ChemistryUniversity of CaliforniaIrvineUSA
  2. 2.Department of ChemistryUniversity of New OrleansNew OrleansUSA
  3. 3.Department of ChemistryUniversity of Western OntarioLondonCanada

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