力场(虚构)
化学物理
密度泛函理论
光合作用
紫色细菌
势能
分子物理学
从头算量子化学方法
作者
Matteo Ceccarelli,Piero Procacci,Massimo Marchi
摘要
This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for photosynthetic cofactors based on a reliable set of ab initio density functional reference data for methyl bacteriochlorophyll a, methyl bacteriopheophytin a, and of a derivative of ubiquinone. Indeed, the new molecular mechanics force field is able to reproduce very well not only the experimental and ab initio structural properties and the vibrational spectra of the molecules, but also the eigenvectors of the molecular normal modes. For this reason it might also be helpful to understand vibrational spectroscopy results obtained on reaction center proteins. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 129–142, 2003
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