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Implementation of π‐π interactions in molecular dynamics simulation
Author(s) -
Yuki Hitomi,
Tanaka Yoshikazu,
Hata Masayuki,
Ishikawa Hidenori,
Neya Saburo,
Hoshino Tyuji
Publication year - 2007
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20557
Subject(s) - molecular dynamics , pi , folding (dsp implementation) , computer science , cluster analysis , function (biology) , energy (signal processing) , computational science , computational chemistry , statistical physics , physics , chemistry , quantum mechanics , engineering , biology , artificial intelligence , biochemistry , evolutionary biology , electrical engineering
No explicit π‐π interaction term has been incorporated in the conventional molecular dynamics (MD) simulation programs in spite of its significant role in the folding of biomolecules and the clustering of organic chemicals. In this article, we propose a technique to emphasize the effect of π‐π interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the π‐π incorporated program gives improved results consistent with experimental data on atom geometry and has no unfavorable interference with the conventional computational framework. This indicates an importance of the explicit consideration of π‐π interactions in MD simulation. © 2007 Wiley Periodicals, Inc.J Comput Chem 2007