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

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.

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Ganguly, Abir1, Author              
Boulanger, Eliot1, Author              
Thiel, Walter1, Author              
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1Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society, ou_1445590              

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 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.

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Language(s): eng - English
 Dates: 2017-01-072017-04-242017-06-13
 Publication Status: Published in print
 Pages: 8
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1021/acs.jctc.7b00016
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Title: Journal of Chemical Theory and Computation
  Abbreviation : J. Chem. Theory Comput.
Source Genre: Journal
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Publ. Info: Washington, D.C. : American Chemical Society
Pages: - Volume / Issue: 13 (6) Sequence Number: - Start / End Page: 2954 - 2961 Identifier: ISSN: 1549-9618
CoNE: https://pure.mpg.de/cone/journals/resource/111088195283832