A multicore QM/MM approach for the geometry optimization of chromophore aggregate in protein.
In this article, we present the multicore (mc) QM/MM method, a QM/MM method that can optimize the structure of chromophore aggregate in protein. A QM region is composed of the sum of the QM subregions that are small enough to apply practical electronic structure calculations. QM/MM energy gradient calculations are performed for each QM subregion. Several benchmark examinations were carried out to figure out availabilities and limitations. In the interregion distances of more than 3.5-4.0 A, the mcQM/MM energy gradient is very close to that obtained by the ordinary QM/MM method in which all the QM subregions were treated together as a single QM region. In van der Waals complex, the error exponentially drops with the distance, while the error decreases slowly in a hydrogen bonding complex. On the other hand, the optimized structures were reproduced with reasonable accuracy in both cases. The computational efficiency is the best advantage in the mcQM/MM approach, especially when the QM region is significantly large and the QM method used is computationally demanding. With this approach, we could optimize the structures of a bacterial photosynthetic reaction center protein in the ground and excited states, which consists of more than 14,000 atoms.
Kiyota
Yasuomi
Y
Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
Hasegawa
Jun-ya
JY
Fujimoto
Kazuhiro
K
Swerts
Ben
B
Nakatsuji
Hiroshi
H
D003198:Computer Simulation; D018360:Crystallography, X-Ray; D019281:Dimerization; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory
D011506:Proteins