title: Effect of polarization on the opsin shift in rhodopsins. 1. A combined QM/QM/MM model for bacteriorhodopsin and pharaonis sensory rhodopsin II.
abstract: The optical and IR-spectroscopic properties of the protonated Schiff base of retinal are highly sensitive to the electrostatic environment. This feature makes retinal a useful probe to study structural differences and changes in rhodopsins. It also raises an interest to theoretically predict the spectroscopic response to mutation and structural evolution. Computational models appropriate for this purpose usually combine sophisticated quantum mechanical (QM) methods with molecular mechanics (MM) force fields. In an effort to test and improve the accuracy of these QM/MM models, we consider in this article the effects of polarization and inter-residual charge transfer within the binding pocket of bacteriorhodopsin (bR) and pharaonis sensory rhodopsin II (psRII, also called pharaonis phoborhodopsin, ppR) on the excitation energy using an ab initio QM/QM/MM approach. The results will serve as reference for assessing empirical polarization models in a consecutive article.
authors.affiliation: BCCMS, Universitat Bremen, Bremen, Germany.
authors.forename: Marius
authors.initials: M
authors.lastname: Wanko
authors.forename: Michael
authors.initials: M
authors.lastname: Hoffmann
authors.forename: Thomas
authors.initials: T
authors.lastname: Frauenheim
authors.forename: Marcus
authors.initials: M
authors.lastname: Elstner
mesh_terms: D001436:Bacteriorhodopsins / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D055095:Optics and Photonics; D011522:Protons; D011789:Quantum Theory; D025603:Sensory Rhodopsins / Q000737:chemistry*; D013055:Spectrophotometry, Infrared
chemical_list: D011522:Protons; D025603:Sensory Rhodopsins; D001436:Bacteriorhodopsins