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Aborted double bicycle-pedal isomerization with hydrogen bond breaking is the primary event of bacteriorhodopsin proton pumping

Altoè, Piero, Cembran, Alessandro, Olivucci, Massimo, Garavelli, Marco
Proceedings of the National Academy of Sciences of the United States of America 2010 v.107 no.47 pp. 20172-20177
computer simulation, deformation, energy, evolution, hydrogen bonding, isomerization, quantum mechanics
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 spectra, 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[horizontal line]C11[horizontal line]C12[horizontal line]C13[horizontal line]C14[horizontal line]N moiety of the chromophore dominates the isomerization. On this same stage a N[horizontal line]H/water hydrogen bond is weakened and initiates a breaking process that is completed during stage iii.