engleski

Nonadiabatic QM/MM dynamics: Technical details

Internal conversion, isomerization and electron transfer are examples of ultrafast processes of polyatomic molecules where the nonadiabatic coupling of electronic and nuclear degrees of freedom cannot be neglected. Dynamics of the nuclei is treated within classical molecular dynamics, while forces acting on them are calculated 'on the fly' by ab initio methods. Implementation of nonadiabatic dynamics within the hybrid ONIOM scheme has enabled us to explore the photochemistry of biologically interesting molecules. The all-trans protonated Schiff base of retinal (at-PSBR) is the chromophore of bacteriorhodopsin. The light triggered isomerization of the chromophore in solution is significantly slower, less effective and less specific than in the protein pocket. We have used nonadiabatic dynamics simulations based on TDDFT to investigate the reaction in various solvents. The analysis of nonadiabatic dynamics trajectories point to the mechanism responsible for the loss of efficiency.

QM/MM; neadijabatska dinamika; retinal

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