Multiscale Reactive Molecular Dynamics for Absolute pKa Predictions and Amino Acid Deprotonation.
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ABSTRACT:
SUBMITTER: Nelson JG
PROVIDER: S-EPMC4095931 | biostudies-literature | 2014 Jul
REPOSITORIES: biostudies-literature
Publications
Multiscale Reactive Molecular Dynamics for Absolute p<i>K</i><sub>a</sub> Predictions and Amino Acid Deprotonation.
Nelson J Gard JG Peng Yuxing Y Silverstein Daniel W DW Swanson Jessica M J JM
Journal of chemical theory and computation 20140506 7
Accurately calculating a weak acid's p<i>K</i><sub>a</sub> from simulations remains a challenging task. We report a multiscale theoretical approach to calculate the free energy profile for acid ionization, resulting in accurate absolute p<i>K</i><sub>a</sub> values in addition to insights into the underlying mechanism. Importantly, our approach minimizes empiricism by mapping electronic structure data (QM/MM forces) into a reactive molecular dynamics model capable of extensive sampling. Conseque ...[more]
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