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A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes

J. Chem. Phys. 129, 154106 (2008); doi:10.1063/1.2994288

Published 17 October 2008

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Jerry M. Parks, Hao Hu, Aron J. Cohen, and Weitao Yang
Department of Chemistry, Duke University, 124 Science Drive, 5301 French Science Center, Durham, North Carolina 27708-0346, USA
The pseudobond method is used in quantum mechanical/molecular mechanical (QM/MM) simulations in which a covalent bond connects the quantum mechanical and classical subsystems. In this method, the molecular mechanical boundary atom is replaced by a special quantum mechanical atom with one free valence that forms a bond with the rest of the quantum mechanical subsystem. This boundary atom is modified through the use of a parametrized effective core potential and basis set. The pseudobond is designed to reproduce the properties of the covalent bond that it has replaced, while invoking as small a perturbation as possible on the system. Following the work of Zhang [J. Chem. Phys. 122, 024114 (2005)], we have developed new pseudobond parameters for use in the simulation of enzymatic systems. Our parameters yield improved electrostatics and deprotonation energies, while at the same time maintaining accurate geometries. We provide parameters for Cps(sp3)–C(sp3), Cps(sp3)–C(sp2,carbonyl), and Cps(sp3)–N(sp3) pseudobonds, which allow the interface between the quantum mechanical and molecular mechanical subsystems to be constructed at either the Calpha–Cbeta bond of a given amino acid residue or along the peptide backbone. In addition, we demonstrate the efficiency of our parametrization method by generating residue-specific pseudobond parameters for a single amino acid. Such an approach may enable higher accuracy than general purpose parameters for specific QM/MM applications. ©2008 American Institute of Physics
History: Received 27 May 2008; accepted 11 September 2008; published 17 October 2008
Permalink: http://link.aip.org/link/?JCPSA6/129/154106/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.15.Fh
    Bonding of biomolecules; mechanisms of bond breakage
  • 87.15.rs
    Dissociation in biochemical reactions
  • 87.15.ag
    Quantum calculations in molecular biophysics
  • 87.15.ap
    Molecular dynamics simulation in molecular biophysics
  • 87.14.ej
    Enzymes
  • YEAR: 2008

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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