Literature DB >> 16851640

Accurate prediction of absolute acidity constants in water with a polarizable force field: substituted phenols, methanol, and imidazole.

George A Kaminski1.   

Abstract

Validity of a force field with explicit treatment of electrostatic polarization in a form of inducible point dipoles for computing acidity constants was tested by calculating absolute pK(a) values of substituted phenols, methanol, and imidazole in water with the molecular dynamics technique. The last two systems were selected as tyrosine and histidine side-chain analogues, respectively. The solvent was represented by an explicit polarizable water model. Similar calculations were also performed with a modified OPLS-AA nonpolarizable force field. The resulting pK(a) values were compared with available experimental data. While the nonpolarizable force field yields errors of about 5 units in the absolute pK(a) values for the phenols and methanol, the polarizable force field produces the acidity constant values within a ca. 0.8 units accuracy. For the case of imidazole, the fixed-charges force field was capable of reproducing the experimental value of pK(a) (6.4 versus the experimental 7.0 units), but only at a cost of dramatically underestimating dimerization energy for the imidazolium-water complex. At the same time, the polarizable force field yields an even more accurate result of pK(a) = 6.96 without any sacrifice of the accuracy in the dimerization energy. It has also been demonstrated that application of Ewald summation for the long-range electrostatics is important, and substitution of a simple cutoff procedure with Born correction for ions can lead to underestimation of absolute pK(a) values by more than 5 units. The accuracy of the absolute acidity constants computed with the polarizable force field is very encouraging and opens road for further tests on more diverse organic molecules sets, as well as on proteins.

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Year:  2005        PMID: 16851640     DOI: 10.1021/jp050156r

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  15 in total

Review 1.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

2.  Importance of electrostatic polarizability in calculating cysteine acidity constants and copper(I) binding energy of Bacillus subtilis CopZ.

Authors:  Timothy H Click; Sergei Y Ponomarev; George A Kaminski
Journal:  J Comput Chem       Date:  2012-02-27       Impact factor: 3.376

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

Authors:  Ity Sharma; George A Kaminski
Journal:  J Comput Chem       Date:  2012-07-19       Impact factor: 3.376

4.  Single-ion solvation free energies and the normal hydrogen electrode potential in methanol, acetonitrile, and dimethyl sulfoxide.

Authors:  Casey P Kelly; Christopher J Cramer; Donald G Truhlar
Journal:  J Phys Chem B       Date:  2007-01-18       Impact factor: 2.991

5.  Developing multisite empirical force field models for Pt(II) and cisplatin.

Authors:  John P Cvitkovic; George A Kaminski
Journal:  J Comput Chem       Date:  2016-11-11       Impact factor: 3.376

6.  Electrostatic polarization is crucial in reproducing Cu(I) interaction energies and hydration.

Authors:  Sergei Y Ponomarev; Timothy H Click; George A Kaminski
Journal:  J Phys Chem B       Date:  2011-07-28       Impact factor: 2.991

7.  pKa Calculations with the Polarizable Drude Force Field and Poisson-Boltzmann Solvation Model.

Authors:  Alexey Aleksandrov; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2020-06-12       Impact factor: 6.006

8.  Polarizable simulations with second order interaction model (POSSIM) force field: developing parameters for protein side-chain analogues.

Authors:  Xinbi Li; Sergei Y Ponomarev; Qina Sa; Daniel L Sigalovsky; George A Kaminski
Journal:  J Comput Chem       Date:  2013-02-19       Impact factor: 3.376

9.  Comparison of nine programs predicting pK(a) values of pharmaceutical substances.

Authors:  Chenzhong Liao; Marc C Nicklaus
Journal:  J Chem Inf Model       Date:  2009-12       Impact factor: 4.956

10.  Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants.

Authors:  Casey P Kelly; Christopher J Cramer; Donald G Truhlar
Journal:  J Phys Chem A       Date:  2006-02-23       Impact factor: 2.781

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