Modeling the Bacterial Photosynthetic Reaction Center. 2. A Combined Quantum Mechanical/Molecular Mechanical Study of the Structure of the Cofactors in the Reaction Centers of Purple Bacteria

Abstract

Ab initio and other computational studies of bacterial reaction center cofactors are usually performed using the observed (low-resolution) X-ray structures. Unfortunately, these geometries are necessarily approximate and this can have dramatic influences on calculated properties. For example, the calculated energies of the four bacteriochlorophylls in Rhodobacter sphaeroides vary by over 160 kcal mol-1. To overcome this problem, a combined quantum mechanical/molecular mechanical (QM/MM) method is employed to optimize the structure of the special pair and other cofactors in the photosynthetic reaction centers of Rhodopseudomonas viridis and Rhodobacter sphaeroides, while a purely MM model is used to refine the structure of the remaining protein environment. Specifically, the QM/MM optimizations are performed using a semiempirical AM1-based formalism. After relaxation, the energies of the bacteriochlorophylls differ by only typical conformer relative energies, ca. 5 kcal mol-1. Another example of improved c...