Extended Data Fig. 1: PYP chromophore in trans configuration and structure dynamical modes obtained by our approach.
From: Few-fs resolution of a photoactive protein traversing a conical intersection
a, The PYP chromophore in the trans configuration. The oval contains the primary structure-dynamically active region, with the numbered atoms and aromatic structures identified. C: carbon, N: nitrogen, O: oxygen, S: sulfur. b, c, The structure dynamical modes obtained by our approach can be combined to yield the more intuitive torsional angle, which is commonly chosen as the primary reaction coordinate for isomerization in PYP. Changes in the torsional angle and the bend of the chromophore axis relative to equilibrium values necessarily increase the energy of the ground state structure. Near the CI the structure on the ground state PES and that on the excited state PES are essentially identical with very similar energies. The structure on the excited state PES determined at 615 fs is therefore an excellent model for the electronic ground state structure near the PYP conical intersection.
