An aborted double bicycle-pedal isomerization with hydrogen bond-breaking is the primary event in the Bacteriorhodopsin proton-pumping

Quantum mechanics/molecular mechanics calculations based on ab initio multiconfigurational second order perturbation theory are employed to construct a computer model of Bacteriorhodopsin that reproduces the observed static and transient electronic spec-tra, the dipole moment changes, and the energy stored in the photocycle intermediate K. The computed reaction coordinate indicates that the isomerization of the retinal chromophore occurs via a complex motion accounting for three distinct regimes: (i) production of the excited state intermediate I, (ii) evolution of I toward a conical intersection between the excited state and the ground state, and (iii) formation of K. We show that, during stage ii, a space-saving mechanism dominated by an asynchronous double bicycle-pedal deformation of the C10 ═ C11 ─ C12 ═ C13 ─ C14 ═ N moiety of the chromophore dominates the isomerization. On this same stage a N ─ H∕water hydrogen bond is weakened and initiates a breaking process that is completed during stage iii.