(Left) Photoreaction of retinal in rhodopsin. (Right) Retinal in its binding pocket with closest amino acids, showing movable QM (gray) and MM portions (yellow) of dynamics calculations. The rest of the protein backbone is fixed at crystal structure values.
Distribution of S1 lifetimes and torsion angles at decay point. The height of the bar graphs corresponds to the number of trans (green) and cis (red) photoproducts of individual trajectories.
Dihedral velocities at hop (a) and at 1st to 3rd surface approaches (b)-(d), showing S1/S0 approaches <20 kcal/mol. Trajectories leading to the all-trans photoproduct are marked as green circles, those retaining starting material are in red. Trajectories that do not hop at the corresponding S1/S0 encounter are marked by open blue circles.
(Upper left) S2–S1 and S1–S0 state energy differences in example trajectory leading to the all-trans photoproduct. An oscillation with a ∼190 fs period and 6 kcal/mol amplitude becomes apparent when averaging the energy difference values within a 30 fs window. (Upper right) Trajectories with distinct oscillations in S1-S0 energy difference, aligned at point of surface hop, values averaged within a 50 fs window. (Lower left) Vibrational modes at 120 and 130 cm−1 with geometric planes of moving fragments. (Lower right) Ensemble behavior exclusively considering 70 trajectories leading to the all-trans photoproduct. The average suggests the start of a common oscillation with ∼280 fs period.
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