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Application of Fragment Molecular Orbital (FMO) Method to Nano-Bio Field

Tatsuya NAKANOa,b*, Yuji MOCHIZUKIb,c, Shinji AMARId, Masato KOBAYASHIe, Kaori FUKUZAWAb,f and Shigenori TANAKAb,g

aDivision of Medicinal Safety Science, National Institute of Health Sciences
1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
bCREST Project, Japan Science and Technology Agency
4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
cDepartment of Chemistry, Faculty of Science, Rikkyo University
3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
dInstitute of Industrial Science, The University of Tokyo
4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
eAdvanceSoft, Center for Collaborative Research, The University of Tokyo
4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
fMizuho Information and Research Institute, Inc.
2-3 Kanda Nishiki-cho, Chiyoda-ku, Tokyo 101-8443, Japan
gGraduate School of Science and Technology, Kobe University
1-1 Rokkodai, Nada-ku, Kobe City, Hyogo 657-8501, Japan

(Received: March 29, 2007; Accepted for publication: June 28, 2007; Published on Web: August 20, 2007)

Kitaura et al. (Chem. Phys. Lett. 312, 319-324 (1999)) have proposed an ab initio fragment molecular orbital (FMO) method by which large molecules such as proteins can be easily treated with chemical accuracy. In the ab initio FMO method, a molecule or a molecular cluster is divided into fragments, and the MO calculations on the fragments (monomers) and the fragment pairs (dimers) are performed to obtain the total energy that is expressed as a summation of the fragment energies and inter-fragment interaction energies (IFIEs). In this paper, we provide a brief description of the ab initio FMO method and demonstrate recent applications in the nano-bio field.

Keywords: Fragment molecular orbital method, MP2, CIS(D), CAFI, VISCANA, ABINIT-MP


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