Excited state dynamics in the early stages of the bR and Rh photocycle

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The very first step in the complex function of all the retinal proteins considered in this proposal is the absorption of light which is followed by an isomerization of the chromophore within the protein. The high speed, efficiency and selectivity of the process are directly related to the optimized molecular arrangement of the binding pocket. Different factors have so far limited the theoretical description of these systems. First, the reaction occurs in an excited electronic state for which quantum chemical calculations provide accurate solutions only at high computational cost. Second, the dynamics in the retinal proteins are believed to happen on strongly coupled potential energy surfaces. This makes the use of advanced nonadiabatic molecular dynamics schemes mandatory in order to obtain realistic values for reaction time scales and quantum yields. Finally, the complexity of the protein interaction with the chromophore requires the inclusion of a large part of the binding pocket in structural models for the active site, which involves a high computational effort. In this project we will therefore use a recently developed approximate but yet predictive method to analyze the early stages of the bR and Rh photocycles. After preliminary calculations on small retinal models used to validate the method, we will perform nonadiabatic molecular dynamic simulations on structural models of the protein with increasing complexity. That is, we stepwise refine the model by inclusion of more and more neighbouring functional groups and amino acids in the chromophore surrounding. In this way we hope to identify the important interactions which allow the bR and Rh proteins to achieve their near optimal efficiency. Finally, simulations of the whole protein are envisaged using a TDQM-MM approach. These calculations will provide structural information on intermediates in the photocycle and lead to a detailed picture of the complex retinal photoreaction.