TY - JOUR
T1 - Modeling of peptide-silica interaction based on four-body corrected fragment molecular orbital (FMO4) calculations
AU - Okiyama, Yoshio
AU - Tsukamoto, Takayuki
AU - Watanabe, Chiduru
AU - Fukuzawa, Kaori
AU - Tanaka, Shigenori
AU - Mochizuki, Yuji
N1 - Funding Information:
This work was supported by the ‘Research and Development of Innovative Simulation Software’ (RISS) project (whose Leader is Prof. Chisachi Kato) at the Institute of Industrial Science (IIS) of the University of Tokyo. The authors are grateful to technical supports by Dr. Jun-ichi Yamamoto and Dr. Kouta Sakakura of NEC Corp. Ltd. Y.M. and K.F. acknowledge the SFR-aid by Rikkyo University. Large-scale parallel jobs were performed with the Xeon/L5640-based supercomputer (System A) at the Foundation for Computational Science (FOCUS), Kobe. Y.M. thanks Dr. Yuto Komeiji for fruitful discussion and critical comments on the manuscript. Finally, the authors are grateful for the reviewer comments to attempt the FF-based IF-E analysis of the silica – RKLPDA interaction.
PY - 2013/4/12
Y1 - 2013/4/12
N2 - We have applied the four-body corrected fragment molecular orbital (FMO4) method to the investigation of the interaction between an artificially designed peptide, with sequence of Arg1-Lys2-Leu3-Pro4-Asp5-Ala6 [Sano et al., Langmuir, 21 (2005) 3090], and the silica surface modeled by a large cluster model including 257 silicon atoms. The second-order Møller-Plesset perturbation calculation was accelerated by the Cholesky decomposition with adaptive metric technique (CDAM-MP2). Systematic analyses were made for inter-fragment interaction energies (IFIEs) with and without a statistical correction for screening. As the result, the importance of three charged residues (Arg1, Lys2 and Asp5) in the peptide-silica interaction was illuminated.
AB - We have applied the four-body corrected fragment molecular orbital (FMO4) method to the investigation of the interaction between an artificially designed peptide, with sequence of Arg1-Lys2-Leu3-Pro4-Asp5-Ala6 [Sano et al., Langmuir, 21 (2005) 3090], and the silica surface modeled by a large cluster model including 257 silicon atoms. The second-order Møller-Plesset perturbation calculation was accelerated by the Cholesky decomposition with adaptive metric technique (CDAM-MP2). Systematic analyses were made for inter-fragment interaction energies (IFIEs) with and without a statistical correction for screening. As the result, the importance of three charged residues (Arg1, Lys2 and Asp5) in the peptide-silica interaction was illuminated.
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U2 - 10.1016/j.cplett.2013.02.020
DO - 10.1016/j.cplett.2013.02.020
M3 - Article
AN - SCOPUS:84875716678
SN - 0009-2614
VL - 566
SP - 25
EP - 31
JO - Chemical Physics Letters
JF - Chemical Physics Letters
ER -