The fragment molecular orbital (FMO)-linear combination of molecular orbitals (LCMO) method incorporates as an efficient post-process calculation of one-electron orbitals of the whole system after the FMO total energy calculation. A straightforward way to increase the accuracy is inclusion of the trimer effect. Here, we derive a comprehensive formulation called the FMO3-LCMO method. To keep the computational costs of the trimer term low enough, we use a matrix-size reduction technique. We evaluated the accuracy and efficiency of the FMO3-LCMO scheme in model biological systems (alanine oligomer and chignolin). The results show that delocalized electronic orbitals with covalent and hydrogen bonds are better described at the trimer level, and the FMO3-LCMO method is applicable to quantitative evaluations of a wide range of frontier orbitals in large biosystems.
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7 September 2013
Research Article|
September 04 2013
Trimer effects in fragment molecular orbital-linear combination of molecular orbitals calculation of one-electron orbitals for biomolecules
Tomoki Kobori;
Tomoki Kobori
1
RIKEN Quantitative Biology Center (QBiC)
, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
2International Center for Materials Nanoarchitectonics (WPI-MANA),
National Institute for Materials Science (NIMS)
, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
3Department of Physics,
The University of Tokyo
, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Keitaro Sodeyama;
Keitaro Sodeyama
2International Center for Materials Nanoarchitectonics (WPI-MANA),
National Institute for Materials Science (NIMS)
, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
3Department of Physics,
The University of Tokyo
, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Takao Otsuka;
Takao Otsuka
1
RIKEN Quantitative Biology Center (QBiC)
, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Yoshitaka Tateyama;
Yoshitaka Tateyama
2International Center for Materials Nanoarchitectonics (WPI-MANA),
National Institute for Materials Science (NIMS)
, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
4PRESTO and CREST,
Japan Science and Technology Agency (JST)
, 4-1-8 Honcho, Kawaguchi, Saitama 333-0012, Japan
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Shinji Tsuneyuki
Shinji Tsuneyuki
a)
3Department of Physics,
The University of Tokyo
, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Tomoki Kobori
1,2,3
Keitaro Sodeyama
2,3
Takao Otsuka
1
Yoshitaka Tateyama
2,4
Shinji Tsuneyuki
3,a)
1
RIKEN Quantitative Biology Center (QBiC)
, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
2International Center for Materials Nanoarchitectonics (WPI-MANA),
National Institute for Materials Science (NIMS)
, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
3Department of Physics,
The University of Tokyo
, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
4PRESTO and CREST,
Japan Science and Technology Agency (JST)
, 4-1-8 Honcho, Kawaguchi, Saitama 333-0012, Japan
a)
Electronic mail: [email protected]
J. Chem. Phys. 139, 094113 (2013)
Article history
Received:
January 17 2013
Accepted:
July 24 2013
Citation
Tomoki Kobori, Keitaro Sodeyama, Takao Otsuka, Yoshitaka Tateyama, Shinji Tsuneyuki; Trimer effects in fragment molecular orbital-linear combination of molecular orbitals calculation of one-electron orbitals for biomolecules. J. Chem. Phys. 7 September 2013; 139 (9): 094113. https://doi.org/10.1063/1.4818599
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