Implementation of pi-pi interactions in molecular dynamics simulation.
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.
Yuki
Hitomi
H
Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan.
Tanaka
Yoshikazu
Y
Hata
Masayuki
M
Ishikawa
Hidenori
H
Neya
Saburo
S
Hoshino
Tyuji
T
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
D010455:Peptides; C508725:Trp-cage peptide; D002220:Carbamazepine; D003577:Cytochrome P-450 Enzyme System; D051544:Cytochrome P-450 CYP3A; C510163:CYP3A4 protein, human