Quantum mechanical methods for biomolecular simulations

Kin Yiu Wong, Lingchun Song, Wangshen Xie, Dan T. Major, Yen Lin Lin, Alessandro Cembran, Jiali Gao

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

We discuss quantum mechanical methods for the description of the potential energy surface and for the treatment of nuclear quantum effects in chemical and biological applications. Two novel electronic structure methods are described, including an electronic structure-based explicit polarization (X-Pol) force field and an effective Hamiltonian molecular orbital and valence bond (EH-MOVB) theory. In addition, we present two path integral techniques to treat nuclear quantum effects, which include an analytical pathintegral method based on Kleinert’s variational perturbation theory, and integrated pathintegral free-energy perturbation and umbrella sampling (PI-FEP/UM) simulation. Studies have shown that quantum mechanics can be applied to biocatalytic systems in a variety of ways and scales. We hope that the methods presented in this article can further expand the scope of quantum mechanical applications to biomolecular systems.

Original languageEnglish (US)
Title of host publicationChallenges and Advances in Computational Chemistry and Physics
PublisherSpringer
Pages79-101
Number of pages23
DOIs
StatePublished - 2009

Publication series

NameChallenges and Advances in Computational Chemistry and Physics
Volume7
ISSN (Print)2542-4491
ISSN (Electronic)2542-4483

Bibliographical note

Funding Information:
We than financial supports of this research from the National Institutes of Health (GM46736) and the Office of Naval Research (N 00012-05-01-0538).

Keywords

  • Isotope effects
  • Kleinert’s variational perturbation theory
  • Molecular orbital and valence bond theory
  • Nuclear quantum effects
  • Path integral
  • Polarizable force field

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