pK(sub a) calculations with QM/MM free energy perturbations

Article Abstract:

A new approach for computing pK(sub a) for a specific residue in complex environments based on a combination of hybrid Quantum mechanical/molecular mechanical (QM/MM) potential and the free energy perturbation (FEP) technique is presented. The current approach is made possible by the recent development of a dual-topology-single-coordinate (DTSC) scheme for performing free energy perturbation calculations with hybrid QM/MM potentials.

Molecular dynamics, Gibbs' free energy

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Free energy perturbation calculations with combined QM/MM potentials complications, simplifications, and applications to redox potential calculations

Article Abstract:

A formal discussion on complications associated with using combined quantum mechanical and molecular mechanical (QM/MM) potentials in free energy perturbations simulations is presented. The method is illustrated with an application to the redox potential of FAD with small reorganization energy; the bulk solvent makes an essential contribution to compensate for the reorganization of the protein.

Analysis, Simulation methods, Simulation, Chemistry, Physical and theoretical, Physical chemistry, Perturbation (Mathematics)

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pK(sub a) calculations in solution and proteins with QM/MM free energy perturbation simulations: A quantitative test of QM/MM protocols

Article Abstract:

The overall goal of the study is to rigorously test typical quantum mechanical and molecular mechanics (QM/MM) protocols in order to provide a clear picture of the accuracy and relative importance of various factors in determining the accuracy. The results will provide useful guidance to the quantitative application of QM/MM simulations in general.

Chemical synthesis

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