Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids

2006 ◽  
Vol 124 (12) ◽  
pp. 124106 ◽  
Author(s):  
M. A. Kastenholz ◽  
Philippe H. Hünenberger
Keyword(s):  
Electrostatic Potential ◽  
Molecular Simulations ◽  
Free Energies ◽  
Molecular Liquids ◽  
Ionic Solvation ◽  
Solvation Free Energies

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

2017 ◽  
Author(s):  
Guilherme Duarte Ramos Matos ◽  
Daisy Y. Kyu ◽  
Hannes H. Loeffler ◽  
John D. Chodera ◽  
Michael R. Shirts ◽  
...  
Keyword(s):  
Free Energy ◽  
Organic Molecules ◽  
Molecular Simulations ◽  
General Purpose ◽  
Free Energies ◽  
Energy Functions ◽  
Neutral Compounds ◽  
Aqueous Solvation ◽  
Solvation Free Energies

AbstractSolvation 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.

Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies

2017 ◽  
Vol 121 (7) ◽  
pp. 1525-1530 ◽  
Author(s):  
Thomas Simonson ◽  
Gerhard Hummer ◽  
Benoît Roux
Keyword(s):  
Free Energies ◽  
Ionic Solvation ◽  
Solvation Free Energies

scholarly journals Ion sizes and finite-size corrections for ionic-solvation free energies

1997 ◽  
Vol 107 (21) ◽  
pp. 9275-9277 ◽  
Author(s):  
Gerhard Hummer ◽  
Lawrence R. Pratt ◽  
Angel E. García
Keyword(s):  
Finite Size ◽  
Free Energies ◽  
Ionic Solvation ◽  
Solvation Free Energies ◽  
Finite Size Corrections

scholarly journals Resolving solvophobic interactions inferred from experimental solvation free energies and evaluated from molecular simulations

2017 ◽  
Vol 667 ◽  
pp. 62-67 ◽  
Author(s):  
J. Wesley Barnett ◽  
Amna Bhutta ◽  
Sarah C. Bierbrier ◽  
Natalia da Silva Moura ◽  
Henry S. Ashbaugh
Keyword(s):  
Molecular Simulations ◽  
Free Energies ◽  
Solvophobic Interactions ◽  
Solvation Free Energies

scholarly journals 1-Octanol/Water Partition Coefficients of n-Alkanes from Molecular Simulations of Absolute Solvation Free Energies

2009 ◽  
Vol 5 (9) ◽  
pp. 2436-2446 ◽  
Author(s):  
Nuno M. Garrido ◽  
António J. Queimada ◽  
Miguel Jorge ◽  
Eugénia A. Macedo ◽  
Ioannis G. Economou
Keyword(s):  
Partition Coefficients ◽  
Molecular Simulations ◽  
Free Energies ◽  
Solvation Free Energies
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