Literature DB >> 21406779

Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction.

David S Palmer1, Andrey I Frolov, Ekaterina L Ratkova, Maxim V Fedorov.   

Abstract

We report a simple universal method to systematically improve the accuracy of hydration free energies calculated using an integral equation theory of molecular liquids, the 3D reference interaction site model. A strong linear correlation is observed between the difference of the experimental and (uncorrected) calculated hydration free energies and the calculated partial molar volume for a data set of 185 neutral organic molecules from different chemical classes. By using the partial molar volume as a linear empirical correction to the calculated hydration free energy, we obtain predictions of hydration free energies in excellent agreement with experiment (R = 0.94, σ = 0.99 kcal mol (- 1) for a test set of 120 organic molecules).

Year:  2010        PMID: 21406779     DOI: 10.1088/0953-8984/22/49/492101

Source DB:  PubMed          Journal:  J Phys Condens Matter        ISSN: 0953-8984            Impact factor:   2.333


  16 in total

1.  Predicting skin permeability using the 3D-RISM-KH theory based solvation energy descriptors for a diverse class of compounds.

Authors:  Vijaya Kumar Hinge; Dipankar Roy; Andriy Kovalenko
Journal:  J Comput Aided Mol Des       Date:  2019-05-13       Impact factor: 3.686

2.  SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling.

Authors:  Tyler Luchko; Nikolay Blinov; Garrett C Limon; Kevin P Joyce; Andriy Kovalenko
Journal:  J Comput Aided Mol Des       Date:  2016-09-01       Impact factor: 3.686

3.  Application of the 3D-RISM-KH molecular solvation theory for DMSO as solvent.

Authors:  Dipankar Roy; Andriy Kovalenko
Journal:  J Comput Aided Mol Des       Date:  2019-10-21       Impact factor: 3.686

4.  New theoretical method for rapid prediction of solvation free energy in water.

Authors:  Shuangliang Zhao; Zhehui Jin; Jianzhong Wu
Journal:  J Phys Chem B       Date:  2011-05-10       Impact factor: 2.991

5.  Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.

Authors:  Lauren Wickstrom; Emilio Gallicchio; Lieyang Chen; Tom Kurtzman; Nanjie Deng
Journal:  Phys Chem Chem Phys       Date:  2022-03-09       Impact factor: 3.945

6.  Uniting cheminformatics and chemical theory to predict the intrinsic aqueous solubility of crystalline druglike molecules.

Authors:  James L McDonagh; Neetika Nath; Luna De Ferrari; Tanja van Mourik; John B O Mitchell
Journal:  J Chem Inf Model       Date:  2014-03-11       Impact factor: 4.956

7.  Simple electrolyte solutions: comparison of DRISM and molecular dynamics results for alkali halide solutions.

Authors:  In Suk Joung; Tyler Luchko; David A Case
Journal:  J Chem Phys       Date:  2013-01-28       Impact factor: 3.488

8.  Small molecule hydration energy and entropy from 3D-RISM.

Authors:  J Johnson; D A Case; T Yamazaki; S Gusarov; A Kovalenko; T Luchko
Journal:  J Phys Condens Matter       Date:  2016-07-01       Impact factor: 2.333

9.  Predicting PAMPA permeability using the 3D-RISM-KH theory: are we there yet?

Authors:  Dipankar Roy; Devjyoti Dutta; David S Wishart; Andriy Kovalenko
Journal:  J Comput Aided Mol Des       Date:  2021-01-04       Impact factor: 3.686

10.  Introducing Charge Hydration Asymmetry into the Generalized Born Model.

Authors:  Abhishek Mukhopadhyay; Boris H Aguilar; Igor S Tolokh; Alexey V Onufriev
Journal:  J Chem Theory Comput       Date:  2014-02-18       Impact factor: 6.006

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