Open Access
Article
A quantum chemical approach to biological reaction with a theory of solutions
Hideaki Takahashi1
1
Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan. takahasi@cheng.es.osaka-u.ac.jp
DOI: 10.2741/3337 Volume 14 Issue 5, pp.1745-1760
Published: 01 January 2009
(This article belongs to the Special Issue Theoretical studies on water roles in biological systems)
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.

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Hideaki Takahashi. A quantum chemical approach to biological reaction with a theory of solutions. Frontiers in Bioscience-Landmark. 2009. 14(5); 1745-1760.