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

MPG-Autoren
http://pubman.mpdl.mpg.de/cone/persons/resource/persons58452

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

http://pubman.mpdl.mpg.de/cone/persons/resource/persons59045

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

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Zitation

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.


Zitierlink: http://hdl.handle.net/11858/00-001M-0000-0023-CC5C-3
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%.