Literature DB >> 19961159

Oil/water transfer is partly driven by molecular shape, not just size.

Christopher J Fennell1, Charlie Kehoe, Ken A Dill.   

Abstract

We present a new approach to computer modeling of solvation free energies of oil in water. In Semi-Explicit Assembly, we first precompute structural and thermal properties of TIP3P waters around different Lennard-Jones spheres. This tabulated information is then used to compute the nonpolar solvation properties of arbitrary solutes. By accumulating interactions from whole regions of the solute molecule, Semi-Explicit Assembly more properly accounts for effects of solute shape and solves problems that appear as nonadditivities in traditional gammaA approaches. Semi-Explicit Assembly involves little parameter fitting because the solute and water properties are taken from existing force fields. We tested the predictions on alkanes, alkynes, linear and planar polyaromatic hydrocarbons, and on a diverse set of 504 molecules previously explored by explicit solvent simulations. We found that not all hydrocarbons are the same. Hydrocarbons have "hot spots", places where first-shell waters interact more strongly with the molecule than at other locations. For example, waters are more attracted to hover over hydrocarbon rings than at the edges. By accounting for these collective regional effects, Semi-Explicit Assembly approaches the physical accuracies of explicit solvent models in computing nonpolar solvation free energies, but because of the precomputations and the regional additivities, it is nearly as fast to compute as gammaA methods.

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Year:  2010        PMID: 19961159      PMCID: PMC2810857          DOI: 10.1021/ja906399e

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  27 in total

1.  The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers.

Authors:  J W Pitera; W F van Gunsteren
Journal:  J Am Chem Soc       Date:  2001-04-04       Impact factor: 15.419

2.  The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

Authors:  Emilio Gallicchio; Linda Yu Zhang; Ronald M Levy
Journal:  J Comput Chem       Date:  2002-04-15       Impact factor: 3.376

3.  Development and testing of a general amber force field.

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

4.  Surfaces affect ion pairing.

Authors:  Ilya Chorny; Ken A Dill; Matthew P Jacobson
Journal:  J Phys Chem B       Date:  2005-12-22       Impact factor: 2.991

5.  Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms.

Authors:  Jason A Wagoner; Nathan A Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2006-05-18       Impact factor: 11.205

6.  Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

Authors:  David L Mobley; Elise Dumont; John D Chodera; Ken A Dill
Journal:  J Phys Chem B       Date:  2007-02-10       Impact factor: 2.991

7.  Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.

Authors:  Thomas Steinbrecher; David L Mobley; David A Case
Journal:  J Chem Phys       Date:  2007-12-07       Impact factor: 3.488

8.  Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies.

Authors:  A E Mark; W F van Gunsteren
Journal:  J Mol Biol       Date:  1994-07-08       Impact factor: 5.469

9.  A simple method for displaying the hydropathic character of a protein.

Authors:  J Kyte; R F Doolittle
Journal:  J Mol Biol       Date:  1982-05-05       Impact factor: 5.469

10.  Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects.

Authors:  K A Sharp; A Nicholls; R F Fine; B Honig
Journal:  Science       Date:  1991-04-05       Impact factor: 47.728

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  22 in total

1.  Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction.

Authors:  Traian Sulea; Hervé Hogues; Enrico O Purisima
Journal:  J Comput Aided Mol Des       Date:  2011-12-25       Impact factor: 3.686

2.  Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models.

Authors:  Traian Sulea; Enrico O Purisima
Journal:  J Comput Aided Mol Des       Date:  2011-12-22       Impact factor: 3.686

3.  Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test.

Authors:  Charles W Kehoe; Christopher J Fennell; Ken A Dill
Journal:  J Comput Aided Mol Des       Date:  2011-12-29       Impact factor: 3.686

4.  Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules.

Authors:  Emiliano Brini; S Shanaka Paranahewage; Christopher J Fennell; Ken A Dill
Journal:  J Comput Aided Mol Des       Date:  2016-09-08       Impact factor: 3.686

5.  Modeling aqueous solvation with semi-explicit assembly.

Authors:  Christopher J Fennell; Charles W Kehoe; Ken A Dill
Journal:  Proc Natl Acad Sci U S A       Date:  2011-02-07       Impact factor: 11.205

6.  Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion.

Authors:  Libo Li; Christopher J Fennell; Ken A Dill
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

7.  Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles.

Authors:  Shu-Ching Ou; B Montgomery Pettitt
Journal:  J Chem Theory Comput       Date:  2019-03-06       Impact factor: 6.006

8.  Surveying implicit solvent models for estimating small molecule absolute hydration free energies.

Authors:  Jennifer L Knight; Charles L Brooks
Journal:  J Comput Chem       Date:  2011-07-06       Impact factor: 3.376

9.  Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge.

Authors:  Libo Li; Ken A Dill; Christopher J Fennell
Journal:  J Comput Aided Mol Des       Date:  2014-01-29       Impact factor: 3.686

10.  Physical Modeling of Aqueous Solvation.

Authors:  Christopher J Fennell; Ken A Dill
Journal:  J Stat Phys       Date:  2011-10-01       Impact factor: 1.548

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