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

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.

scholarly journals Solvation free energies for periodic surfaces: comparison of implicit and explicit solvation models

2016 ◽  
Vol 18 (46) ◽  
pp. 31850-31861 ◽  
Author(s):  
Stephan N. Steinmann ◽  
Philippe Sautet ◽  
Carine Michel
Keyword(s):  
Free Energy ◽  
Liquid Interfaces ◽  
Free Energies ◽  
Periodic Surfaces ◽  
Solvation Energies ◽  
Solvation Models ◽  
Implicit And Explicit ◽  
Solvation Free Energies ◽  
Solid Liquid ◽  
Explicit Solvation

A strategy based on molecular mechanics free energy of perturbation, seeded by quantum mechanics, is presented to take solvation energies into account in the context of periodic, solid–liquid interfaces.

scholarly journals Improved prediction of solvation free energies by machine-learning polarizable continuum solvation model

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Amin Alibakhshi ◽  
Bernd Hartke
Keyword(s):  
Machine Learning ◽  
Free Energy ◽  
Solvation Free Energy ◽  
Continuum Solvation ◽  
Free Energies ◽  
Solvation Model ◽  
Continuum Solvation Model ◽  
Solvation Models ◽  
Solvation Free Energies ◽  
Polarizable Continuum

AbstractTheoretical estimation of solvation free energy by continuum solvation models, as a standard approach in computational chemistry, is extensively applied by a broad range of scientific disciplines. Nevertheless, the current widely accepted solvation models are either inaccurate in reproducing experimentally determined solvation free energies or require a number of macroscopic observables which are not always readily available. In the present study, we develop and introduce the Machine-Learning Polarizable Continuum solvation Model (ML-PCM) for a substantial improvement of the predictability of solvation free energy. The performance and reliability of the developed models are validated through a rigorous and demanding validation procedure. The ML-PCM models developed in the present study improve the accuracy of widely accepted continuum solvation models by almost one order of magnitude with almost no additional computational costs. A freely available software is developed and provided for a straightforward implementation of the new approach.

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