title: Effect of polarization on the opsin shift in rhodopsins. 2. Empirical polarization models for proteins.
abstract: The explicit treatment of polarization as a many-body interaction in condensed-phase systems represents a current problem in empirical force-field development. Although a variety of efficient models for molecular polarization have been suggested, polarizable force fields are still far from common use nowadays. In this work, we consider interactive polarization models employing Thole's short-range damping scheme and assess them for application on polypeptides. Despite the simplicity of the model, we find mean polarizabilities and anisotropies of amino acid side chains in excellent agreement with MP2/cc-pVQZ benchmark calculations. Combined with restrained electrostatic potential (RESP) derived atomic charges, the models are applied in a quantum-mechanical/molecular-mechanical (QM/MM) approach. An iterative scheme is used to establish a self-consistent mutual polarization between the QM and MM moieties. This ansatz is employed to study the influence of the protein polarizability on calculated optical properties of the protonated Schiff base of retinal in rhodopsin (Rh), bacterio-rhodopsin (bR), and pharaonis sensory rhodopsin II (psRII). The shifts of the excitation energy due to the instantaneous polarization response of the protein to the charge transfer on the retinal chromophore are quantified using the high level ab initio multireference spectroscopy-oriented configuration interaction (SORCI) method. The results are compared with those of previously published QM1/QM2/MM models for bR and psRII.
authors: BCCMS, Universitat Bremen, Bremen, Germany.
authors: Marius
authors: M
authors: Wanko
authors: Michael
authors: M
authors: Hoffmann
authors: Jan
authors: J
authors: Frähmcke
authors: Thomas
authors: T
authors: Frauenheim
authors: Marcus
authors: M
authors: Elstner
mesh_terms: D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D055095:Optics and Photonics; D011506:Proteins / Q000737:chemistry*; D011522:Protons; D011789:Quantum Theory; D012243:Rhodopsin / Q000737:chemistry*; D012545:Schiff Bases; D012997:Solvents / Q000737:chemistry; D013057:Spectrum Analysis; D055672:Static Electricity; D013816:Thermodynamics; D014364:Tryptophan / Q000737:chemistry; D014443:Tyrosine / Q000737:chemistry
chemical_list: D011506:Proteins; D011522:Protons; D012545:Schiff Bases; D012997:Solvents; D014443:Tyrosine; D014364:Tryptophan; D012243:Rhodopsin