Computation of the reduction free energy of coenzyme in water: A novel approach within the framework of the QM/MM-ER method

Hideaki Takahashi, Hajime Ohno, Ryohei Kishi, Shin Ichi Furukawa, Masayoshi Nakano

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We have computed free energy for one-electron reduction of the active site of the coenzyme (flavin adenine dinucleotide (FAD)) in aqueous solution by means of the QM/MM method combined with the theory of energy representation (QM/MM-ER). In the present work, we have proposed a novel approach that the excess electron to be attached on the FAD has been regarded as a solute, while the remaining molecules including the active site of FAD have been considered as solvent in the implementation of the method of energy representation. The efficiency and the accuracy of the method have been examined by performing the conventional simulations where the oxidized and the reduced active sites of FAD are regarded as solutes and the surrounding water molecules are treated as solvent. The present approach is computationally more advantageous and is amenable to the extension to the reaction in the protein systems as compared with the conventional one. It has been found that the reduction free energy obtained by the present method is in excellent agreement with that computed by the conventional approach, which guarantees the robustness of the method.

Original languageEnglish
Title of host publicationSelected Papers from ICNAAM 2007 and ICCMSE 2007 - Special Presentations Int. Conf. Numerical Analysis and Applied Mathematics 2007 and Int. Conf. Computational Methods in Science and Engineering 2007
Pages56-59
Number of pages4
DOIs
Publication statusPublished - 2008 Oct 22
Externally publishedYes
EventInternational Conference on Numerical Analysis and Applied Mathematics, ICNAAM 2007 and International Conference on Computational Methods in Science and Engineering, ICCMSE 2007 - Corfu, Greece
Duration: 2007 Sep 252007 Sep 30

Publication series

NameAIP Conference Proceedings
Volume1046
ISSN (Print)0094-243X
ISSN (Electronic)1551-7616

Other

OtherInternational Conference on Numerical Analysis and Applied Mathematics, ICNAAM 2007 and International Conference on Computational Methods in Science and Engineering, ICCMSE 2007
CountryGreece
CityCorfu
Period07/9/2507/9/30

Keywords

  • DFT
  • Free energy
  • QM/MM
  • QM/MM-ER
  • Real-space grids
  • Theory of energy representation

ASJC Scopus subject areas

  • Physics and Astronomy(all)

Fingerprint Dive into the research topics of 'Computation of the reduction free energy of coenzyme in water: A novel approach within the framework of the QM/MM-ER method'. Together they form a unique fingerprint.

  • Cite this

    Takahashi, H., Ohno, H., Kishi, R., Furukawa, S. I., & Nakano, M. (2008). Computation of the reduction free energy of coenzyme in water: A novel approach within the framework of the QM/MM-ER method. In Selected Papers from ICNAAM 2007 and ICCMSE 2007 - Special Presentations Int. Conf. Numerical Analysis and Applied Mathematics 2007 and Int. Conf. Computational Methods in Science and Engineering 2007 (pp. 56-59). (AIP Conference Proceedings; Vol. 1046). https://doi.org/10.1063/1.2997315