A quantum chemical approach to biological reaction with a theory of solutions

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2 Citations (Scopus)

Abstract

We recently developed a novel computational methodology, referred to as QM/MM-ER, to compute free energy change associated with a chemical reaction in a condensed phase by combining the quantum mechanical / molecular mechanical (QM/MM) method with a theory of solutions. In the present review article we illustrate an outline of the QM/MM-ER method. We also present an extension of the QM/MM-ER method to compute reduction free energy of cofactor FAD (Flavin Adenine Dinucleotide) in water as well as in apoprotein by introducing a novel approach. The key of the approach is that only the excess charge involved in the reduction process is identified as a solute. The adequacy of the method is examined for the reaction in aqueous solution by comparing the result with that obtained by a conventional approach. The reduction free energy of cofactor FAD embedded in a cholesterol oxidase (PDB id = 1B4V) is computed as -163.1 kcal/mol by the QM/MM-ER approach, while it is obtained as -80.1 kcal/mol for the cofactor in water solution.

Original languageEnglish
Pages (from-to)1745-1760
Number of pages16
JournalFrontiers in Bioscience
Volume14
Issue number5
DOIs
Publication statusPublished - 2009 Jan 1
Externally publishedYes

Keywords

  • Free energy
  • Kohn-sham DFT
  • QM/MM
  • Quantum chemistry
  • Theory of energy representation
  • Theory of solutions

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

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