Schizorhodopsin 4 (SzR4) is a microbial rhodopsin that functions as a light-driven inward proton pump, unlike conventional outward proton-pumping rhodopsins. Its characteristic binding-pocket architecture may influence the photophysics of the retinal protonated Schiff base (rPSB).^[1,2] We combine microsecond-scale molecular dynamics (MD) simulations of membrane-embedded SzR4 with QM/MM calculations to characterize binding-pocket hydration and rPSB color tuning. The simulations reveal a persistently partially hydrated pocket, with water molecules near rPSB interacting with the residues R67/D184, polar network. Three regions modulate hydration: the T58/N172 extracellular gate controls water access, R67/D184 regulates hydration around the Schiff base, and Y84/K29/E81 rearrangements influence intracellular solvent exposure. Vibronic absorption spectra were calculated using TD-DFT with M06-2X within the QM/MMPol–cLR3 polarizable embedding framework.^[3] This approach allows us to distinguish the contributions of ground-state polarization, state-specific polarization, linear-response dispersion, and state-specific dispersion to the excitation energy. Relative to fixed-charge embedding (2.47 eV), ground-state polarization produces a blue shift of 0.12 eV, partially offset by state-specifi polarization. Linear-response dispersion provides the dominant red shift (−0.18 eV), whereas state-specific dispersion introduces a configuration-dependent correction. The resulting absorptio maximum of 2.36 eV reduces the deviation from experiment (2.22 eV) to 0.14 eV.^[2] Spectral-density analysis of energy-gap fluctuations sampled by Born–Oppenheimer MD furtherreproduces the asymmetric shape of the experimental absorption band.

_{[1] Urui, T.; Mizutani, Y. Origin of the Difference in Proton Transport Direction between Inward and Outward Proton-Pumping Rhodopsins. Accounts of Chemical Research 2024, 3050–3057.
[2] Higuchi, A.; Shihoya, W.; Konno, M.; Ikuta, T.; Kandori, H.; Inoue, K.; Nureki, O. Crystal structure of schizorhodopsin reveals mechanism of inward proton pumping. Proceedings of the National Academy of Sciences 2021, 118, e2016328118.
[3] Guido, C. A.; Cupellini, L.; Mennucci, B.; Curutchet, C. How Dispersion Interactions at the Excited State Can Tune Photochromism of Embedded Chromophores. Journal of the American Chemical Society 2026, 148,
1847–1857, PMID: 41439643.}