Reply to the ‘Comment on “Mapping photoisomerization dynamics on a three-state model potential energy surface in bacteriorhodopsin using femtosecond stimulated Raman spectroscopy”’ by I. Schapiro, M. Olivucci, K. Heyne and S. Haacke, <i>Chem. Sci.</i

We appreciate the insightful comments by Dr Schapiro <i>et al.</i> on our recent article (<i>Chem. Sci.</i>, 2025, <b>16</b>, 3713). Their comment raises valuable points concerning the excitation regime employed in our femtosecond stimulated Raman spectroscopy (FSRS) experiments, the interpretation of the newly observed 1820 cm^-1 vibronic band, and the electronic-state assignments of the I and J intermediates in the photoisomerization of bacteriorhodopsin (bR). In this reply, we provide detailed clarifications, supplementary analyses, and additional experimental evidence to address these concerns. These results reinforce the validity of our FSRS interpretation of the AT-PSBR photoisomerization dynamics and clarify the photochemical roles of the I and J intermediates in the retinal protein photocycle.