Literature DB >> 20354893

Predictions of hydration free energies from continuum solvent with solute polarizable models: the SAMPL2 blind challenge.

Alexandre Meunier1, Jean-François Truchon.   

Abstract

This paper reports the results of our attempt to predict hydration free energies on the SAMPL2 blind challenge dataset. We mostly examine the effects of the solute electrostatic component on the accuracy of the predictions. The usefulness of electronic polarization in predicting hydration free energies is assessed by comparing the Electronic Polarization from Internal Continuum model and the self consistent reaction field IEF-PCM to standard non-polarizable charge models such as RESP and AM1-BCC. We also determine an optimal restraint weight for Dielectric-RESP atomic charges fitting. Statistical analysis of the results could not distinguish the methods from one another. The smallest average unsigned error obtained is 1.9 +/- 0.6 kcal/mol (95% confidence level). A class of outliers led us to investigate the importance of the solute-solvent instantaneous induction energy, a missing term in PB continuum models. We estimated values between -1.5 and -6 kcal/mol for a series of halo-benzenes which can explain why some predicted hydration energies of non-polar molecules significantly disagreed with experiment.

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Year:  2010        PMID: 20354893     DOI: 10.1007/s10822-010-9339-3

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  19 in total

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

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3.  Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model.

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Review 4.  Modeling electrostatic effects in proteins.

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Journal:  Biochim Biophys Acta       Date:  2006-08-25

5.  Continuum treatment of electronic polarization effect.

Authors:  Yu-Hong Tan; Ray Luo
Journal:  J Chem Phys       Date:  2007-03-07       Impact factor: 3.488

Review 6.  Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum.

Authors:  Michael J Schnieders; Nathan A Baker; Pengyu Ren; Jay W Ponder
Journal:  J Chem Phys       Date:  2007-03-28       Impact factor: 3.488

7.  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

8.  A blind challenge for computational solvation free energies: introduction and overview.

Authors:  J Peter Guthrie
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

Review 9.  Classical electrostatics in biology and chemistry.

Authors:  B Honig; A Nicholls
Journal:  Science       Date:  1995-05-26       Impact factor: 47.728

10.  Integrated Continuum Dielectric Approaches to treat Molecular Polarizability and the Condensed Phase: Refractive Index and Implicit Solvation.

Authors:  Jean-François Truchon; Anthony Nicholls; Benoît Roux; Radu I Iftimie; Christopher I Bayly
Journal:  J Chem Theory Comput       Date:  2009-07-14       Impact factor: 6.006

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  3 in total

1.  The SAMPL2 blind prediction challenge: introduction and overview.

Authors:  Matthew T Geballe; A Geoffrey Skillman; Anthony Nicholls; J Peter Guthrie; Peter J Taylor
Journal:  J Comput Aided Mol Des       Date:  2010-05-09       Impact factor: 3.686

2.  Progress in developing Poisson-Boltzmann equation solvers.

Authors:  Chuan Li; Lin Li; Marharyta Petukh; Emil Alexov
Journal:  Mol Based Math Biol       Date:  2013-03-01

3.  Detection of tautomer proportions of dimedone in solution: a new approach based on theoretical and FT-IR viewpoint.

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Journal:  J Comput Aided Mol Des       Date:  2013-08-07       Impact factor: 3.686

  3 in total

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