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Low-temperature persistent and transient hole-burning (HB) spectra are presented for the triple hydrogen-bonded L131LH + M160LH + M197FH mutant of Rhodobacter sphaeroides. These spectra expose the heterogeneous nature of the P-, B-, and H-bands, consistent with a distribution of electron transfer (ET) times and excitation energy transfer (EET) rates. Transient P+Q − holes are observed for A fast (tens of picoseconds or faster) ET times and reveal strong coupling to phonons and marker mode(s), while the persistent holes are bleached in a fraction of reaction centers with long-lived excited states characterized by much weaker electron−phonon coupling. Exposed differences in electron−phonon coupling strength, as well as a different coupling to the marker mode(s), appear to affect the ET times. Both resonantly and nonresonantly burned persistent HB spectra show weak blue- (∼150 cm−1) and large, red-shifted (∼300 cm−1) antiholes of the P band. Slower EET times from the H- and B-bands to the special pair dimer provide new insight on the influence of hydrogen bonds on mutation-induced heterogeneity.