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Computational photochemistry of retinal proteins

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Abstract

High spectral tunability and quantum yield are the striking features of rhodopsin photochemistry. They rely on a strong and complex interaction of their chromophore, the protonated Schiff base of retinal, with its protein environment. In this article, we review the progress in the computational modeling of these systems, focusing on the optical properties and the excited state dynamics. While the earlier success of atomistic theoretical models was based on the breakthrough in X-ray crystallography and combined quantum mechanical molecular mechanical (QM/MM) methodology, recent advances point out the importance of high-level QM methods and the incorporation of effects that are neglected in conventional QM/MM or ONIOM schemes, like polarization and charge transfer.

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Notes

  1. Which partially have been included in earlier cluster models.

  2. The basis set limit of the MP2 PAs for the PSB6 model is extrapolated from the results of cc-pVTZ, cc-pVQZ, and cc-pV5Z calculations using the Schwartz formula [29].

  3. Note, that HF besides a systematic overestimation due to the lack of dynamic correlation shows the same length-dependency as the post-HF methods.

Abbreviations

B3LYP:

Becke-3-parameter hybrid exchange and Lee–Yang–Parr correlation functional

BLA:

Bond length alternation

bR:

Bacteriorhodopsin

CASSCF:

Complete active space self consistent field method

CASPT2:

Complete active space method with second order perturbation correction

CCSD:

Coupled cluster singles doubles

CHARMM:

Chemistry at HArvard molecular mechanics

(TD)DFT:

(Time-dependent) density functional theory

GGA:

Generalized gradient approximation

HBN:

Hydrogen bonded network

HF:

Hartree–Fock method

LDA:

Local density approximation

MP2:

Second order Møller–Plesset perturbation theory

MRCI:

Multi-reference configuration interaction

OM2:

Orthogonalization method 2

PA:

Proton affinity

ppR:

Pharaonis phoborhodopsin (also called sensory rhodopsin II)

PSB:

Protonated Schiff base

QM/MM:

Combined quantum mechanical molecular mechanical method

SCC-DFTB:

Self-consistent charge density functional based tight binding method

SORCI:

Spectroscopy oriented configuration interaction

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Authors and Affiliations

  1. BCCMS, Universität Bremen, Bremen, 28334, Germany

    Marius Wanko, Michael Hoffmann & Thomas Frauenheim

  2. Theoretische Chemie, TU Braunschweig, Braunschweig, 38106, Germany

    Marcus Elstner

  3. Department of Molecular Biophysics, German Cancer Research Center, Heidelberg, 60120, Germany

    Marcus Elstner

Authors
  1. Marius Wanko
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  2. Michael Hoffmann
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  3. Thomas Frauenheim
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  4. Marcus Elstner
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Correspondence to Marcus Elstner.

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Wanko, M., Hoffmann, M., Frauenheim, T. et al. Computational photochemistry of retinal proteins. J Comput Aided Mol Des 20, 511–518 (2006). https://doi.org/10.1007/s10822-006-9069-8

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