Extended Data Table 2 Vertical excitation energies computed by quantum mechanics/molecular mechanics (QM/MM) calculation

From: Ultrafast structural changes direct the first molecular events of vision

  1. Vertical excitation energies (ΔEcalc) and oscillator strengths for dark, 1 ps, and 100 ps photoactivated rhodopsin. The excitation energies were calculated on both QM/MM optimized and non-optimized geometries. In case of QM/MM optimized geometries, two QM regions were considered: a) retinal protonated Schiff base (RPSB), and b) retinal PSB including key nearby polar residues and a water molecule (RPSB, E113, E181, S186, Y191, Y268, W01). The values were computed with the RI‐ADC(2) method using the cc-pVTZ basis set. The experimental values for the absorption maxima of each state (exp. λmax) are provided for comparison. In case of the 1 ps intermediate, we observe a difference of 22 nm in the calculated red-shifts between the QM/MM optimized and no-optimized structures, which can be attributed to the small structural rearrangement triggered due to geometry optimization near retinal PSB region. For 100 ps, the red-shifts of the optimized and non-optimized structures are comparable, but considerably smaller than the 1 ps rhodopsin red-shift.
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