TY - JOUR
T1 - Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Møller-Plesset perturbation (MP2.5) scheme
AU - Yamada, Haruka
AU - Mochizuki, Yuji
AU - Fukuzawa, Kaori
AU - Okiyama, Yoshio
AU - Komeiji, Yuto
N1 - Publisher Copyright:
© 2016 Elsevier B.V.
PY - 2017/2/1
Y1 - 2017/2/1
N2 - A series of fragment molecular orbital (FMO) calculations on DNA models was performed to assess the reliability of the scaled third-order Møller-Plesset perturbation method (MP2.5) (Pitoňák et al., Chem. Phys. Chem., 10 (2009) 282) for the incorporation of higher-order electron correlation. The Watson-Crick H-bonding (horizontal interaction) and the 1,2-stacking (vertical interaction) of four combinations of two base pairs (AT:AT, AT:TA, AT:GC, and CG:GC) were calculated at the levels of MP2, MP3 (nonscaled), MP2.5, and coupled cluster singles and doubles with perturbative triples (CCSD(T)). The comparison showed sufficient agreement between MP2.5 and the reference CCSD(T), and indicated that MP2.5 is an inexpensive but precise alternative to costly CCSD(T). The influence of basis sets including the model core potential (MCP) was also examined for the two base pairs. The Watson-Crick H-bonding interaction energies were fairly uninfluenced by these methods. In contrast, the values of the stacking interactions among bases quantitatively varied depending on the calculation options. As a cost-effective procedure, the FMO-MP2.5/MCP calculations were applied to a couple of realistic DNA models explicitly solvated by water: a 12-base-pair model and a 10-base-pair model cross-linked with cis-platin (Pt(NH3)2). The H-bonding and stacking interactions in them were discussed from a biochemical viewpoint.
AB - A series of fragment molecular orbital (FMO) calculations on DNA models was performed to assess the reliability of the scaled third-order Møller-Plesset perturbation method (MP2.5) (Pitoňák et al., Chem. Phys. Chem., 10 (2009) 282) for the incorporation of higher-order electron correlation. The Watson-Crick H-bonding (horizontal interaction) and the 1,2-stacking (vertical interaction) of four combinations of two base pairs (AT:AT, AT:TA, AT:GC, and CG:GC) were calculated at the levels of MP2, MP3 (nonscaled), MP2.5, and coupled cluster singles and doubles with perturbative triples (CCSD(T)). The comparison showed sufficient agreement between MP2.5 and the reference CCSD(T), and indicated that MP2.5 is an inexpensive but precise alternative to costly CCSD(T). The influence of basis sets including the model core potential (MCP) was also examined for the two base pairs. The Watson-Crick H-bonding interaction energies were fairly uninfluenced by these methods. In contrast, the values of the stacking interactions among bases quantitatively varied depending on the calculation options. As a cost-effective procedure, the FMO-MP2.5/MCP calculations were applied to a couple of realistic DNA models explicitly solvated by water: a 12-base-pair model and a 10-base-pair model cross-linked with cis-platin (Pt(NH3)2). The H-bonding and stacking interactions in them were discussed from a biochemical viewpoint.
KW - Base pair
KW - DNA
KW - FMO
KW - Fragment molecular orbital
KW - Interaction energy
KW - Perturbation calculation
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U2 - 10.1016/j.comptc.2016.12.008
DO - 10.1016/j.comptc.2016.12.008
M3 - Article
AN - SCOPUS:85007318912
SN - 2210-271X
VL - 1101
SP - 46
EP - 54
JO - Computational and Theoretical Chemistry
JF - Computational and Theoretical Chemistry
ER -