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Journal Article

Importance of MM Polarization in QM/MM Studies of Enzymatic Reactions: Assessment of the QM/MM Drude Oscillator Model

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Ganguly,  Abir
Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society;

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Boulanger,  Eliot
Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society;

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Thiel,  Walter
Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society;

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ct7b00016_si_001.pdf
(Supplementary material), 663KB

Citation

Ganguly, A., Boulanger, E., & Thiel, W. (2017). Importance of MM Polarization in QM/MM Studies of Enzymatic Reactions: Assessment of the QM/MM Drude Oscillator Model. Journal of Chemical Theory and Computation, 13(6), 2954-2961. doi:10.1021/acs.jctc.7b00016.


Cite as: https://hdl.handle.net/11858/00-001M-0000-002D-82F8-D
Abstract
For accurate quantum mechanics/molecular mechanics (QM/MM) studies of enzymatic reactions, it is desirable to include MM polarization, for example by using the Drude oscillator (DO) model. For a long time, such studies were hampered by the lack of well-tested polarizable force fields for proteins. Following up on a recent preliminary QM/MM-DO assessment (J. Chem. Theory. Comput. 2014, 10, 1795–1809), we now report a comprehensive investigation of the effects of MM polarization on two enzymatic reactions, namely the Claisen rearrangement in chorismate mutase and the hydroxylation reaction in p-hydroxybenzoate hydroxylase, using the QM/CHARMM-DO model and two QM methods (B3LYP, OM2). We compare the results from extensive geometry optimizations and free energy simulations at the QM/MM-DO level to those obtained from analogous calculations at the conventional QM/MM level.