Proton transfer in bacteriorhodopsin: Structure, excitation, IR spectra, and potential energy surface analyses by an ab initio QM/MM method

The structures, the optical properties, and the proton-transfer mechanism of bacteriorhodopsin (bR) are investigated by using an ab initio QM/MM calculation. The nature of the hydrogen bond network (HBN) formed in the retinal pocket is examined. The analysis is made for the environmental effect from the molecules involved in this HEN on the geometry and the excitation spectrum of retinal. Tt is found that IR spectra of the O-D stretching of the bound water molecules and the N-D stretching of the Schiff base retinal are very sensitive to the vibration-electron coupling among these molecules in the pocket. The hypothetical proton-transfer reaction path in the bR ground state is investigated, and the environmental effect on it is analyzed. The present calculation reveals that electronic interactions such as charge transfer and polarization, not included in most empirical methods, are very important to describe these properties of bR, the structures of HEN, the IR activities, and the proton-transfer mechanism.