title: Trimer effects in fragment molecular orbital-linear combination of molecular orbitals calculation of one-electron orbitals for biomolecules.
abstract: 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.
authors.affiliation: RIKEN Quantitative Biology Center (QBiC), 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Tomoki
authors.initials: T
authors.lastname: Kobori
authors.forename: Keitaro
authors.initials: K
authors.lastname: Sodeyama
authors.forename: Takao
authors.initials: T
authors.lastname: Otsuka
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Tateyama
authors.forename: Shinji
authors.initials: S
authors.lastname: Tsuneyuki
mesh_terms: D000409:Alanine / Q000737:chemistry*; D004583:Electrons; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory
chemical_list: D009842:Oligopeptides; C506175:chignolin; D000409:Alanine