Literature DB >> 27367817

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

J Johnson1, D A Case, T Yamazaki, S Gusarov, A Kovalenko, T Luchko.   

Abstract

Implicit solvent models offer an attractive way to estimate the effects of a solvent environment on the properties of small or large solutes without the complications of explicit simulations. One common test of accuracy is to compute the free energy of transfer from gas to liquid for a variety of small molecules, since many of these values have been measured. Studies of the temperature dependence of these values (i.e. solvation enthalpies and entropies) can provide additional insights into the performance of implicit solvent models. Here, we show how to compute temperature derivatives of hydration free energies for the 3D-RISM integral equation approach. We have computed hydration free energies of 1123 small drug-like molecules (both neutral and charged). Temperature derivatives were also used to calculate hydration energies and entropies of 74 of these molecules (both neutral and charged) for which experimental data is available. While direct results have rather poor agreement with experiment, we have found that several previously proposed linear hydration free energy correction schemes give good agreement with experiment. These corrections also provide good agreement for hydration energies and entropies though simple extensions are required in some cases.

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Year:  2016        PMID: 27367817      PMCID: PMC5118872          DOI: 10.1088/0953-8984/28/34/344002

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


  29 in total

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Authors:  Junmei Wang; Romain M Wolf; James W Caldwell; Peter A Kollman; David A Case
Journal:  J Comput Chem       Date:  2004-07-15       Impact factor: 3.376

2.  Estimating entropies from molecular dynamics simulations.

Authors:  Christine Peter; Chris Oostenbrink; Arthur van Dorp; Wilfred F van Gunsteren
Journal:  J Chem Phys       Date:  2004-02-08       Impact factor: 3.488

3.  An MM/3D-RISM approach for ligand binding affinities.

Authors:  Samuel Genheden; Tyler Luchko; Sergey Gusarov; Andriy Kovalenko; Ulf Ryde
Journal:  J Phys Chem B       Date:  2010-07-01       Impact factor: 2.991

4.  Treating entropy and conformational changes in implicit solvent simulations of small molecules.

Authors:  David L Mobley; Ken A Dill; John D Chodera
Journal:  J Phys Chem B       Date:  2008-01-03       Impact factor: 2.991

5.  Closed-form expressions of the chemical potential for integral equation closures with certain bridge functions.

Authors:  Stefan M Kast; Thomas Kloss
Journal:  J Chem Phys       Date:  2008-12-21       Impact factor: 3.488

6.  Hydration effects on the HET-s prion and amyloid-beta fibrillous aggregates, studied with three-dimensional molecular theory of solvation.

Authors:  Takeshi Yamazaki; Nikolay Blinov; David Wishart; Andriy Kovalenko
Journal:  Biophys J       Date:  2008-08-08       Impact factor: 4.033

7.  Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects.

Authors:  Gabriel J Rocklin; David L Mobley; Ken A Dill; Philippe H Hünenberger
Journal:  J Chem Phys       Date:  2013-11-14       Impact factor: 3.488

8.  Solvation thermodynamics of organic molecules by the molecular integral equation theory: approaching chemical accuracy.

Authors:  Ekaterina L Ratkova; David S Palmer; Maxim V Fedorov
Journal:  Chem Rev       Date:  2015-06-15       Impact factor: 60.622

9.  Solvation free-energy pressure corrections in the three dimensional reference interaction site model.

Authors:  Volodymyr Sergiievskyi; Guillaume Jeanmairet; Maximilien Levesque; Daniel Borgis
Journal:  J Chem Phys       Date:  2015-11-14       Impact factor: 3.488

10.  Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.

Authors:  In Suk Joung; Thomas E Cheatham
Journal:  J Phys Chem B       Date:  2008-07-02       Impact factor: 2.991

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  6 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.  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

5.  How Water's Properties Are Encoded in Its Molecular Structure and Energies.

Authors:  Emiliano Brini; Christopher J Fennell; Marivi Fernandez-Serra; Barbara Hribar-Lee; Miha Lukšič; Ken A Dill
Journal:  Chem Rev       Date:  2017-09-26       Impact factor: 60.622

6.  An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets.

Authors:  Brian Olson; Anthony Cruz; Lieyang Chen; Mossa Ghattas; Yeonji Ji; Kunhui Huang; Steven Ayoub; Tyler Luchko; Daniel J McKay; Tom Kurtzman
Journal:  J Comput Aided Mol Des       Date:  2020-09-12       Impact factor: 4.179

  6 in total

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