Literature DB >> 22815192

Calculating pKa values for substituted phenols and hydration energies for other compounds with the first-order Fuzzy-Border continuum solvation model.

Ity Sharma1, George A Kaminski.   

Abstract

We have computed pK(a) values for 11 substituted phenol compounds using the continuum Fuzzy-Border (FB) solvation model. Hydration energies for 40 other compounds, including alkanes, alkenes, alkynes, ketones, amines, alcohols, ethers, aromatics, amides, heterocycles, thiols, sulfides, and acids have been calculated. The overall average unsigned error in the calculated acidity constant values was equal to 0.41 pH units and the average error in the solvation energies was 0.076 kcal/mol. We have also reproduced pK(a) values of propanoic and butanoic acids within about 0.1 pH units from the experimental values by fitting the solvation parameters for carboxylate ion carbon and oxygen atoms. The FB model combines two distinguishing features. First, it limits the amount of noise which is common in numerical treatment of continuum solvation models by using fixed-position grid points. Second, it uses either second- or first-order approximation for the solvent polarization, depending on a particular implementation. These approximations are similar to those used for solute and explicit solvent fast polarization treatment which we developed previously. This article describes results of using the first-order technique. This approximation places the presented methodology between the Generalized Born and Poisson-Boltzmann continuum solvation models with respect to their accuracy of reproducing the many-body effects in modeling a continuum solvent.
Copyright © 2012 Wiley Periodicals, Inc.

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Year:  2012        PMID: 22815192      PMCID: PMC3472159          DOI: 10.1002/jcc.23074

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  13 in total

1.  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

2.  A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations.

Authors:  George A Kaminski; Richard A Friesner; Ruhong Zhou
Journal:  J Comput Chem       Date:  2003-02       Impact factor: 3.376

3.  A Polarizable Force Field and Continuum Solvation Methodology for Modeling of Protein-Ligand Interactions.

Authors:  Jon R Maple; Yixiang Cao; Wolfgang Damm; Thomas A Halgren; George A Kaminski; Linda Y Zhang; Richard A Friesner
Journal:  J Chem Theory Comput       Date:  2005-07       Impact factor: 6.006

4.  Accurate pKa determination for a heterogeneous group of organic molecules.

Authors:  Marcel Schmidt am Busch; Ernst-Walter Knapp
Journal:  Chemphyschem       Date:  2004-10-18       Impact factor: 3.102

Review 5.  Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

Authors:  William L Jorgensen; Julian Tirado-Rives
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

6.  Absolute pK(a) determinations for substituted phenols.

Authors:  Matthew D Liptak; Kevin C Gross; Paul G Seybold; Steven Feldgus; George C Shields
Journal:  J Am Chem Soc       Date:  2002-06-05       Impact factor: 15.419

7.  Polarizable Simulations with Second order Interaction Model - force field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations.

Authors:  George A Kaminski; Sergei Y Ponomarev; Aibing B Liu
Journal:  J Chem Theory Comput       Date:  2009-10-05       Impact factor: 6.006

8.  Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator.

Authors:  Pedro E M Lopes; Guillaume Lamoureux; Alexander D Mackerell
Journal:  J Comput Chem       Date:  2009-09       Impact factor: 3.376

9.  Generalized born model with a simple smoothing function.

Authors:  Wonpil Im; Michael S Lee; Charles L Brooks
Journal:  J Comput Chem       Date:  2003-11-15       Impact factor: 3.376

10.  Electrostatic polarization is crucial for reproducing pKa shifts of carboxylic residues in Turkey ovomucoid third domain.

Authors:  Christopher M Macdermaid; George A Kaminski
Journal:  J Phys Chem B       Date:  2007-06-28       Impact factor: 2.991

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  3 in total

1.  Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water.

Authors:  Xiongwu Wu; Juyong Lee; Bernard R Brooks
Journal:  J Phys Chem B       Date:  2016-10-18       Impact factor: 2.991

2.  Using polarizable POSSIM force field and fuzzy-border continuum solvent model to calculate pK(a) shifts of protein residues.

Authors:  Ity Sharma; George A Kaminski
Journal:  J Comput Chem       Date:  2016-10-27       Impact factor: 3.376

3.  An Experimental Validated Computational Method for pKa Determination of Substituted 1,2-Dihydroxybenzenes.

Authors:  Romina Romero; Pablo R Salgado; César Soto; David Contreras; Victoria Melin
Journal:  Front Chem       Date:  2018-07-13       Impact factor: 5.221

  3 in total

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