Photoisomerization Control Mechanisms in Protonated Schiff Bases

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We have performed ab initio excited-state molecular dynamics simulations of an isolated photo-excited protonated Schiff base (C1-N2=C3-C4=C5-C6) to search for mechanisms that control its photoisomerization outcome, such as the bond selectivity and (trans, cis) conformation. We observe that the photo-excited molecule twists around the N2C3 bond (∼80% cases of the thermal ensemble) or the C4C5 bond, and relaxes back to the ground electronic state with either a trans or cis outcome. First, we show that a significant initial distortion of several selected dihedral angles can preferentially guide the excited-state dynamics towards twisting of the C4C5 bond. Next, we examine if the bond selectivity can be controlled by the vibrational pre-excitation of the molecule along individual normal modes. We find that pre-excitation of only one of the modes, which contains a prominent propelling motion of the C4C5 bond with respect to the neighboring C3C4 single bond, leads to twisting of the C4C5 bond. Normal mode decomposition of the ground state thermal ensemble shows that in starting structures in which this same mode is pre-excited by 1-2 kBT thermal energy, the twisting of C4C5 occurs with a 30-50% probability. Finally, we find that the (trans, cis) outcome of the reaction can be controlled by selective pre-twisting of several dihedral angles, while keeping other degrees of freedom thermally excited. This choice was justified by the observed pre-twisting of retinal chromophore in rhodopsin, which exhibits 65% cis to trans transition. In the thermal ensemble with such pre-twisted dihedrals, we observe on the excited state potential energy surface synchronized twisting of CN2C3C and HN2C3H torsional angles surrounding the isomerizing N2C3 bond, which significantly increases the fraction of reactive (cis to trans) trajectories. These observations provide crucial understanding of natural photoisomerization mechanisms and their potential use in synthetic molecules.