Nature of the Surface Crossing Process in Bacteriorhodopsin: Computer Simulations of the Quantum Dynamics of the Primary Photochemical Event

Abstract

The quantum dynamics of the primary photoisomerization event in bacteriorhodopsin is studied by a semiclassical trajectory approach. The relevant surface crossing probability is evaluated from the wave functions and potential surfaces of a hybrid quantum mechanical/molecular mechanics (QM/MM) Hamiltonian of the complete chromophore−protein−solvent system. The QM/MM model combines consistently the quantum mechanical Hamiltonian of the chromophore with the microscopic electric field of the ionized groups and induced dipoles of the protein−solvent system. The QCFF/PI Hamiltonian of the chromophore is adjusted to reproduce relevant ab initio results. The nonadiabatic coupling term is calculated numerically from the corresponding wave functions. The simulations are performed by combining the ENZYMIX and QCFF/PI molecular modeling programs. The effect of the protein on the absorption spectrum of the chromophore is examined. It is found that this spectrum reflects the effect of the protein permanent ...