In this study we have investigated binding of the fluorescent hydrophobicity probe Nile Red to the photoactive yellow protein (PYP), to characterize the exposure and accessibility of hydrophobic surface upon formation of the signaling state of this photoreceptor protein. Binding of Nile Red, reflected by a large blue shift and increase in fluorescence quantum yield of the Nile Red emission, is observed exclusively when PYP resides in its signaling state. N-terminal truncation of the protein allows assignment of the region surrounding the chromophore as the site where Nile Red binds to PYP. We also observed a pH dependence of the affinity of Nile Red for pB, which we propose is caused by pH dependent differences of the structure of the signaling state. From a comparative analysis of the kinetics of Nile Red binding and transient absorption changes in the visible region we can conclude that protonation of the chromophore precedes the exposure of a hydrophobic surface near the chromophore binding site, upon formation of the signaling state. Furthermore, the data presented here favor the view that the signaling state is structurally heterogeneous.

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Triplet-sensitized generation of a long-lived intramolecular charge-separated excited state is described in an electron donor-acceptor molecule with a short distance between the donor and the acceptor. Time-resolved UV-Vis optical absorption spectroscopy shows that the lifetime of this triplet excited state is 1.4 micros in acetonitrile at 298 K, i.e. five orders of magnitude greater than that of the corresponding singlet charge-separated state. In slightly less polar alkane nitrile solvents, the local and CT triplet states coexist, which allows determination of their relative energies.

A long-lived intramolecular charge-separated state in an electron-donor-acceptor molecule is characterized by time-resolved visible and infrared absorption spectroscopy. Bands that can be assigned to the negatively charged acceptor chromophore can be clearly observed in the time-resolved IR spectrum. In contrast, the electronic absorption spectrum of the radical anion lacks characteristic absorption bands. The IR spectra can be interpreted on the basis of harmonic vibrational frequencies and intensities calculated using B3LYP ab initio methods for model systems of the separate electron donor and acceptor units. This result indicates that the charge-separated state, in spite of the small distance between electron donor and acceptor, can be represented well as an intramolecular radical ion pair.

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