A multicore QM/MM approach for the geometry optimization of chromophore aggregate in protein

✍ Scribed by Yasuomi Kiyota; Jun-Ya Hasegawa; Kazuhiro Fujimoto; Ben Swerts; Hiroshi Nakatsuji

• Publisher: John Wiley and Sons
• Year: 2009
• Tongue: English
• Weight: 821 KB
• Volume: 30
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.21156

✦ Synopsis

Abstract

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 Å, 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. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009