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  Toward QM/MM Simulation of Enzymatic Reactions with the Drude Oscillator Polarizable Force Field

Boulanger, E., & Thiel, W. (2014). Toward QM/MM Simulation of Enzymatic Reactions with the Drude Oscillator Polarizable Force Field. Journal of Chemical Theory and Computation, 10(4), 1795-1809. doi:10.1021/ct401095k.

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 Urheber:
Boulanger, Eliot1, Autor           
Thiel, Walter1, Autor           
Affiliations:
1Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society, ou_1445590              

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 Zusammenfassung: The polarization of the environment can influence the results from hybrid quantum mechanical/molecular mechanical (QM/MM) simulations of enzymatic reactions. In this article, we address several technical aspects in the development of polarizable QM/MM embedding using the Drude Oscillator (DO) force field. We propose a stable and converging update of the DO polarization state for geometry optimizations and a suitable treatment of the QM/MM-DO boundary when the QM and MM regions are separated by cutting through a covalent bond. We assess the performance of our approach by computing binding energies and geometries of three selected complexes relevant to biomolecular modeling, namely the water trimer, the N-methylacetamide dimer, and the cationic bis(benzene)sodium sandwich complex. Using a recently published MM-DO force field for proteins, we evaluate the effect of MM polarization on the QM/MM energy profiles of the enzymatic reactions catalyzed by chorismate mutase and by phydroxybenzoate hydroxylase. We find that inclusion of MM polarization affects the computed barriers by about 10%.

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Sprache(n): eng - English
 Datum: 2013-12-192014-03-132014-04-08
 Publikationsstatus: Erschienen
 Seiten: 15
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: -
 Art der Begutachtung: Expertenbegutachtung
 Identifikatoren: DOI: 10.1021/ct401095k
 Art des Abschluß: -

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Titel: Journal of Chemical Theory and Computation
  Andere : J. Chem. Theory Comput.
Genre der Quelle: Zeitschrift
 Urheber:
Affiliations:
Ort, Verlag, Ausgabe: Washington, D.C. : American Chemical Society
Seiten: - Band / Heft: 10 (4) Artikelnummer: - Start- / Endseite: 1795 - 1809 Identifikator: Anderer: 1549-9618
CoNE: https://pure.mpg.de/cone/journals/resource/111088195283832