Photochemistry of visual pigment chromophore models by ab initio molecular dynamics

Article Abstract:

Ab initio excited-state molecular dynamics calculations are used to study the effect of methyl substitution and chromophore distortion on the photoreaction of different four-double-bond retinal model chromophores. The results have indicated that apart from the geometric distortions caused by the protein pocket it is not required for postulating other specific interactions between the protein and the chromophore to effect the selective and ultrafast photoreaction in rhodopsin.

Analysis, Optical properties, Mechanical properties, Structure, Potential energy

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How the counterion affects ground- and excited-state properties of the rhodopsin chromophore

Article Abstract:

High-level density functional theory (DFT) and ab-initio CASSCF/CASPT2 methodologies are applied to study the ground and excited states of the retinal chromophore as a function of counterions of different complexities. On the basis 2.8 angstrom X-ray structure of rhodopsin, the complete retinal chromophore was optimized in the presence of anionic Glu113, Thr94, and a water molecule (Wat2b), which together form a complex counterion of the protonated Schiff base.

Excited state chemistry, Atomic properties

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The nature of complex counterion of the chromosphore in rhodopsin

Article Abstract:

The interaction of the rhodopsin chromosphore with different complex counterions is investigated using density functional theory methodology for both energy minimization and molecular dynamics calculations. The initial geometry of the retinal chromophore attached to Lys296 and of other amino acid residues close to the retinal binding site was taken from the rhodopsin X-ray structure.

Usage, Density functionals, Density functional theory

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