Literature DB >> 29392951

Correction to Multiscale Reactive Molecular Dynamics for Absolute pKa Predictions and Amino Acid Deprotonation.

J Gard Nelson, Yuxing Peng, Daniel W Silverstein, Jessica M J Swanson.   

Abstract

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Year:  2018        PMID: 29392951      PMCID: PMC8154317          DOI: 10.1021/acs.jctc.8b00044

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


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With this erratum, we present a correction to the equation for the calculation of a pKa from a PMF (eq 9 in the original publication)[1]where w(r) is the free energy from the PMF, and β is the product of the simulation temperature and the Boltzmann constant. The integral is calculated from zero to the transition state, as denoted by †. C0 is the standard state concentration whose value is 1 molecule/1660 Å3 and results from the entropic freedom that is gained by the proton when it dissociates from the acid.[2,3] The pKa was calculated correctly in the original publication; this correction does not influence the results presented therein.[1]
  3 in total

1.  The statistical-thermodynamic basis for computation of binding affinities: a critical review.

Authors:  M K Gilson; J A Given; B L Bush; J A McCammon
Journal:  Biophys J       Date:  1997-03       Impact factor: 4.033

2.  Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy.

Authors:  Jianhan Chen; Charles L Brooks; Harold A Scheraga
Journal:  J Phys Chem B       Date:  2007-09-19       Impact factor: 2.991

3.  Multiscale Reactive Molecular Dynamics for Absolute pKa Predictions and Amino Acid Deprotonation.

Authors:  J Gard Nelson; Yuxing Peng; Daniel W Silverstein; Jessica M J Swanson
Journal:  J Chem Theory Comput       Date:  2014-05-06       Impact factor: 6.006

  3 in total

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