Coupled semiempirical quantum mechanics and molecular mechanics (QM/MM) calculations on the aqueous solvation free energies of ionized molecules

1999 ◽  
Vol 20 (10) ◽  
pp. 1028-1038 ◽  
Author(s):  
Peter L. Cummins ◽  
Jill E. Gready
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Free Energies ◽  
Aqueous 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.

An efficient method for the calculation of quantum mechanics/molecular mechanics free energies

2008 ◽  
Vol 128 (1) ◽  
pp. 014109 ◽  
Author(s):  
Christopher J. Woods ◽  
Frederick R. Manby ◽  
Adrian J. Mulholland
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Efficient Method ◽  
Free Energies

Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD, and SMD solvation models

2010 ◽  
Vol 24 (4) ◽  
pp. 317-333 ◽  
Author(s):  
Raphael F. Ribeiro ◽  
Aleksandr V. Marenich ◽  
Christopher J. Cramer ◽  
Donald G. Truhlar
Keyword(s):  
Free Energies ◽  
Aqueous Solvation ◽  
Solvation Models ◽  
Solvation Free Energies
Sign in / Sign up

Export Citation Format

Share Document