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.
REFERENCES
1.
M.
Challacombe
and E.
Schwegler
, J. Chem. Phys.
106
, 5526
(1997
).2.
J. J. P.
Stewart
, Int. J. Quantum Chem.
58
, 133
(1996
).3.
4.
E.
Díaz
, J. Chem. Phys.
128
, 175101
(2008
).5.
C. W.
Hsu
, M.
Fyta
, G.
Lakatos
, S.
Melchionna
, and E.
Kaxiras
, J. Chem. Phys.
137
, 105102
(2012
).6.
L. I.
Krishtalik
, Biochim. Biophys. Acta
1807
, 1444
–1456
(2011
).7.
F.
Sato
, T.
Yoshihiro
, M.
Era
, and H.
Kashiwaga
, Chem. Phys. Lett.
341
, 645
(2001
).8.
T.
Yoshihiro
, F.
Sato
, and H.
Kashiwagi
, Chem. Phys. Lett.
346
, 313
(2001
).9.
A.
Warshel
and M.
Levitt
, J. Mol. Biol.
103
, 227
(1976
).10.
U. C.
Singh
and P. A.
Kollman
, J. Comput. Chem.
7
, 718
(1986
).11.
M. J.
Field
, P. A.
Bash
, and M. A.
Karplus
, J. Comput. Chem.
11
, 700
(1990
).12.
H.
Lin
and D. G.
Truhlar
, Theor. Chem. Acc.
117
, 185
(2007
).13.
P. A.
Bash
, M. J.
Field
, and M.
Karplus
, J. Am. Chem. Soc.
109
, 8092
(1987
).14.
J.
Gao
and D. G.
Truhlar
, Annu. Rev. Phys. Chem.
53
, 467
(2002
).15.
R. M.
Abolfath
, P. K.
Biswas
, R.
Rajnarayanam
, T.
Brabec
, R.
Kodym
, and L.
Papiez
, J. Phys. Chem. A
116
, 3940
(2012
).16.
K.
Kitaura
, E.
Ikeo
, T.
Asada
, T.
Nakano
, and M.
Uebayasi
, Chem. Phys. Lett.
313
, 701
(1999
).17.
T.
Nakano
, T.
Kaminuma
, T.
Sato
, Y.
Akiyama
, M.
Uebayasi
, and K.
Kitaura
, Chem. Phys. Lett.
318
, 614
(2000
).18.
K.
Kitaura
, T.
Sawai
, T.
Asada
, T.
Nakano
, and M.
Uebayashi
, Chem. Phys. Lett.
312
, 319
(1999
).19.
K.
Kitaura
, S.
Sugiki
, T.
Nakano
, Y.
Komeiji
, and M.
Uebayashi
, Chem. Phys. Lett.
336
, 163
(2001
).20.
T.
Nakano
, T.
Kaminuma
, T.
Sato
, K.
Fukuzawa
, Y.
Akiyama
, M.
Uebayashi
, and K.
Kitaura
, Chem. Phys. Lett.
351
, 475
(2002
).21.
D. G.
Fedorov
and K.
Kitaura
, J. Phys. Chem. A
111
, 6904
(2007
).22.
D. G.
Fedorov
, T.
Nagata
, and K.
Kitaura
, Phys. Chem. Chem. Phys.
14
, 7562
(2012
).23.
M. S.
Gordon
, D. G.
Fedorov
, S. R.
Pruitt
, and L. V.
Slipchenko
, Chem. Rev.
112
, 632
(2012
).24.
K.
Fukuzawa
, K.
Kitaura
, M.
Uebayashi
, K.
Nakata
, T.
Kaminuma
, and T.
Nakano
, J. Comput. Chem.
26
, 1
(2005
).25.
K.
Fukuzawa
, Y.
Mochizuki
, S.
Tanaka
, K.
Kitaura
, and T.
Nakano
, J. Phys. Chem. B
110
, 16102
(2006
);
[PubMed]
K.
Fukuzawa
, Y.
Mochizuki
, S.
Tanaka
, K.
Kitaura
, and T.
Nakano
, J. Phys. Chem. B
110
, 24276
(2006
).26.
K.
Fukuzawa
, Y.
Komeiji
, Y.
Mochizuki
, A.
Kato
, T.
Nakano
, and S.
Tanaka
, J. Comput. Chem.
27
, 948
(2006
);
[PubMed]
K.
Fukuzawa
, Y.
Komeiji
, Y.
Mochizuki
, A.
Kato
, T.
Nakano
, and S.
Tanaka
, J. Comput. Chem.
28
, 2237
(2007
).27.
28.
I.
Nakanishi
, D. G.
Fedorov
, and K.
Kitaura
, Proteins: Struct., Funct., Bioinf.
68
, 145
(2007
).29.
M. P.
Mazanetz
, O.
Ichihara
, R. J.
Law
, and M.
Whittaker
, J. Cheminformatics
3
, 2
(2011
).30.
Y.
Inadomi
, T.
Nakano
, K.
Kitaura
, and U.
Nagashima
, Chem. Phys. Lett.
364
, 139
(2002
).31.
T.
Watanabe
, Y.
Inadomi
, H.
Umeda
, K.
Fukuzawa
, S.
Tanaka
, T.
Nakano
, and U.
Nagashima
, J. Comput. Theor. Nanosci.
6
, 1328
(2009
).32.
T.
Sakurai
and H.
Sugiura
, J. Comput. Appl. Math.
159
, 119
(2003
).33.
S.
Tsuneyuki
, T.
Kobori
, K.
Akagi
, K.
Sodeyama
, K.
Terakura
, and H.
Fukuyama
, Chem. Phys. Lett.
476
, 104
(2009
).34.
T.
Kobori
, K.
Sodeyama
, T.
Otsuka
, Y.
Tateyama
, and S.
Tsuneyuki
, FMO-LCMO program version 2.0 (2012
).35.
H.
Nishioka
and K.
Ando
, J. Chem. Phys.
134
, 204109
(2011
).36.
H.
Kitoh-Nishioka
and K.
Ando
, J. Phys. Chem. B
116
, 12933
(2012
).37.
D. G.
Fedorov
and K.
Kitaura
, J. Chem. Phys.
131
, 171106
(2009
).38.
S.
Honda
, K.
Yamasaki
, Y.
Sawada
, and H.
Morii
, Structure (London)
12
, 1507
–1518
(2004
).39.
A. D.
Becke
, Phys. Rev. A
38
, 3098
(1988
).40.
A. D.
Becke
, J. Chem. Phys.
98
, 5648
(1993
).41.
P. C.
Haharan
and J. A.
Pople
, Theor. Chim. Acta
28
, 213
(1973
).42.
M.
Suenaga
, J. Comput. Chem. Jpn.
4
(1
), 25
–32
(2005
).43.
M. W.
Schmidt
, K. K.
Baldridge
, J. A.
Boatz
, S. T.
Elbert
, M. S.
Gordon
, J. H.
Jensen
, S.
Koseki
, N.
Matsunaga
, K. A.
Nguyen
, S.
Su
, T. L.
Windus
, M.
Dupuis
, and J. A.
Montgomery
, J. Comput. Chem.
14
, 1347
(1993
).44.
D. G.
Fedorov
and K.
Kitaura
, J. Chem. Phys.
120
, 6832
(2004
).45.
D. G.
Fedorov
and K.
Kitaura
, Chem. Phys. Lett.
389
, 129
(2004
).46.
D. G.
Fedorov
and K.
Kitaura
, Chem. Phys. Lett.
433
, 182
(2006
).47.
See supplementary material at http://dx.doi.org/10.1063/1.4818599 for detailed analysis of the orbital energy and the error.
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