title: Implementation of pi-pi interactions in molecular dynamics simulation.
abstract: No explicit pi-pi 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 pi-pi interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the pi-pi 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 pi-pi interactions in MD simulation.
authors.affiliation: Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan.
authors.forename: Hitomi
authors.initials: H
authors.lastname: Yuki
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Tanaka
authors.forename: Masayuki
authors.initials: M
authors.lastname: Hata
authors.forename: Hidenori
authors.initials: H
authors.lastname: Ishikawa
authors.forename: Saburo
authors.initials: S
authors.lastname: Neya
authors.forename: Tyuji
authors.initials: T
authors.lastname: Hoshino
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D002220:Carbamazepine / Q000737:chemistry / Q000378:metabolism; D003198:Computer Simulation; D051544:Cytochrome P-450 CYP3A; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D010455:Peptides; C508725:Trp-cage peptide; D002220:Carbamazepine; D003577:Cytochrome P-450 Enzyme System; D051544:Cytochrome P-450 CYP3A; C510163:CYP3A4 protein, human