scholarly journals Graphical Gaussian Process Regression Model for Aqueous Solvation Free Energy Prediction of Organic Molecules in Redox Flow Battery

2021 ◽  
Author(s):  
Peiyuan Gao ◽  
Xiu Yang ◽  
Yuhang Tang ◽  
Muqing Zheng ◽  
Amity Andersen ◽  
...  
Keyword(s):  
Free Energy ◽  
Organic Molecules ◽  
Equilibrium Constants ◽  
Gaussian Process Regression ◽  
Solvation Free Energy ◽  
Emergent Properties ◽  
Redox Potentials ◽  
Energy Prediction ◽  
Aqueous Solvation ◽  
Graphical Gaussian

The solvation free energy of organic molecules is a critical parameter in determining emergent properties such as solubility, liquid-phase equilibrium constants, and pKa and redox potentials in an organic redox...

scholarly journals Solvation Free Energy Prediction from Pairwise Atomistic Interactions by Machine Learning

2021 ◽  
Author(s):  
Hyuntae Lim ◽  
YounJoon Jung
Keyword(s):  
Machine Learning ◽  
Free Energy ◽  
Chemical Properties ◽  
Solvation Energy ◽  
Solvation Free Energy ◽  
Learning Technologies ◽  
Training Data ◽  
Inner Product ◽  
Structure Property ◽  
Energy Prediction

Abstract Recent advances in machine learning technologies and their applications have led to the development of diverse structure-property relationship models for crucial chemical properties. The solvation free energy is one of them. Here, we introduce a novel ML-based solvation model, which calculates the solvation energy from pairwise atomistic interactions. The novelty of the proposed model consists of a simple architecture: two encoding functions extract atomic feature vectors from the given chemical structure, while the inner product between the two atomistic features calculates their interactions. The results of 6,493 experimental measurements achieve outstanding performance and transferability for enlarging training data owing to its solvent-non-specific nature. An analysis of the interaction map shows that our model has significant potential for producing group contributions on the solvation energy, which indicates that the model provides provides not only predictions of target properties but also more detailed physicochemical insights.

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.

Calculation of the aqueous solvation free energy of the proton

1998 ◽  
Vol 109 (12) ◽  
pp. 4852-4863 ◽  
Author(s):  
G. J. Tawa ◽  
I. A. Topol ◽  
S. K. Burt ◽  
R. A. Caldwell ◽  
A. A. Rashin
Keyword(s):  
Free Energy ◽  
Solvation Free Energy ◽  
Aqueous Solvation

scholarly journals MLSolvA: solvation free energy prediction from pairwise atomistic interactions by machine learning

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Hyuntae Lim ◽  
YounJoon Jung
Keyword(s):  
Machine Learning ◽  
Free Energy ◽  
Solvation Energy ◽  
Solvation Free Energy ◽  
Learning Technologies ◽  
Training Data ◽  
Inner Product ◽  
Structure Property ◽  
Energy Prediction ◽  
Feature Vectors

AbstractRecent advances in machine learning technologies and their applications have led to the development of diverse structure–property relationship models for crucial chemical properties. The solvation free energy is one of them. Here, we introduce a novel ML-based solvation model, which calculates the solvation energy from pairwise atomistic interactions. The novelty of the proposed model consists of a simple architecture: two encoding functions extract atomic feature vectors from the given chemical structure, while the inner product between the two atomistic feature vectors calculates their interactions. The results of 6239 experimental measurements achieve outstanding performance and transferability for enlarging training data owing to its solvent-non-specific nature. An analysis of the interaction map shows that our model has significant potential for producing group contributions on the solvation energy, which indicates that the model provides not only predictions of target properties but also more detailed physicochemical insights.

“Bimolecular” QSPR: Estimation of the solvation free energy of organic molecules in different solvents

2007 ◽  
Vol 414 (1) ◽  
pp. 128-131 ◽  
Author(s):  
A. A. Kravtsov ◽  
P. V. Karpov ◽  
I. I. Baskin ◽  
V. A. Palyulin ◽  
N. S. Zefirov
Keyword(s):  
Free Energy ◽  
Organic Molecules ◽  
Solvation Free Energy

scholarly journals Breaking the polar-nonpolar division in solvation free energy prediction

2017 ◽  
Vol 39 (4) ◽  
pp. 217-233 ◽  
Author(s):  
Bao Wang ◽  
Chengzhang Wang ◽  
Kedi Wu ◽  
Guo-Wei Wei
Keyword(s):  
Free Energy ◽  
Solvation Free Energy ◽  
Energy Prediction
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