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Phytochromes belong to a group of photoreceptor proteins containing a covalently bound biliverdin chromophore that inter-converts between two isomeric forms upon photoexcitation. The existence and stability of the photocycle products are largely determined by the protein sequence and the presence of conserved hydrogen-bonding interactions in the vicinity of the chromophore. The vibrational signatures of biliverdin, however, are often weak and obscured under more intense protein bands, limiting spectroscopic studies of its non-transient signals. In this study, we apply isotope-labeling techniques to isolate the vibrational bands from the protein-bound chromophore of the bacterial phytochrome from Deinococcus radiodurans. We elucidate the structure and ultrafast dynamics of the chromophore with 2D infra-red (IR) spectroscopy and molecular dynamics simulations. The carbonyl stretch vibrations of the pyrrole rings show the heterogeneous distribution of hydrogen-bonding structures, which exhibit distinct ultrafast relaxation dynamics. Moreover, we resolve a previously undetected 1678 cm−1 band that is strongly coupled to the A- and D-ring of biliverdin and demonstrate the presence of complex vibrational redistribution pathways between the biliverdin modes with relaxation-assisted measurements of 2D IR cross peaks. In summary, we expect 2D IR spectroscopy to be useful in explaining how point mutations in the protein sequence affect the hydrogen-bonding structure around the chromophore and consequently its ability to photoisomerize to the light-activated states. [ABSTRACT FROM AUTHOR]

Optical nonlinear spectroscopies carry a high amount of information about the systems under investigation; however, as they report polarization signals, the resulting spectra are often congested and difficult to interpret. To recover the landscape of energy states and physical processes such as energy and electron transfer, a clear interpretation of the nonlinear signals is prerequisite. Here, we focus on the interpretation of the electrochromic band-shift signal, which is generated when an internal electric field is established in the system following optical excitation. Whereas the derivative shape of the band-shift signal is well understood in transient absorption spectroscopy, its emergence in two-dimensional electronic spectroscopy (2DES) has not been discussed. In this work, we employed 2DES to follow the dynamic band-shift signal in reaction centers of purple bacteria Rhodobacter sphaeroides at 77 K. The prominent two-dimensional derivative-shape signal appears with the characteristic formation time of the charge separated state. To explain and characterize the band-shift signal, we use expanded double-sided Feynman diagram formalism. We propose to distinguish two types of Feynman diagrams that lead to signals with negative amplitude: excited state absorption and re-excitation. The presented signal decomposition and modeling analysis allows us to recover precise electrochromic shifts of accessory bacteriochlorophylls, identify additional signals in the B band range, and gain a further insight into the electron transfer mechanism. In a broader perspective, expanded Feynman diagram formalism will allow for interpretation of all 2D signals in a clearer and more intuitive way and therefore facilitate studying the underlying photophysics. [ABSTRACT FROM AUTHOR]

Two-dimensional electronic spectroscopy, and especially the polarization-controlled version of it, is the cutting edge technique for disentangling various types of coherences in molecules and molecular aggregates. In order to evaluate the electronic coherences, which often decay on a 100 fs time scale, the early population times have to be included in the analysis. However, signals in this region are typically plagued by several artifacts, especially in the unavoidable pulse overlap region. In this paper, we show that, in the case of polarization-controlled two-dimensional spectroscopy experiment, the early-time dynamics can be dominated by the "incorrect" pulse ordering signals. These signals can affect kinetics at positive times well beyond the pulse overlap region, especially when the "correct" pulse ordering signals are much weaker. Moreover, the "incorrect" pulse ordering contributions are oscillatory and overlap with the spectral signatures of energy transfer, which may lead to misinterpretation of "incorrect" pulse ordering signals for fast-decaying coherences. [ABSTRACT FROM AUTHOR]

Sensory proteins must relay structural signals from the sensory site over large distances to regulatory output domains. Phytochromes are a major family of red-light-sensing kinases that control diverse cellular functions in plants, bacteria and fungi (1-9). Bacterial phytochromes consist of a photosensory core and a carboxy-terminal regulatory domain (10,11). Structures of photosensory cores are reported in the resting state (12-18) and conformational responses to light activation have been proposed in the vicinity of the chromophore (19-23). However, the structure of the signalling state and the mechanism of downstream signal relay through the photosensory core remain elusive. Here we report crystal and solution structures of the resting and activated states of the photosensory core of the bacteriophytochrome from Deinococcus radiodurans. The structures show an open and closed form of the dimeric protein for the activated and resting states, respectively. This nanometre-scale rearrangement is controlled by refolding of an evolutionarily conserved 'tongue', which is in contact with the chromophore. The findings reveal an unusual mechanism in which atomic-scale conformational changes around the chromophore are first amplified into an angstrom-scale distance change in the tongue, and further grow into a nanometre-scale conformational signal. The structural mechanism isa blueprint for understanding how phytochromes connect to the cellular signalling network., The most common domain architecture of the photosensory core of phytochromes in bacteria, plants and fungi is PAS-GAF-PHY (Per/ Arndt/Sim-cGMP phosphodiesterase/adenylcyclase/FhlA-phytochrome specific) (10). We investigate the PAS-GAF-PHY fragment of the [...]

Femtosecond transient absorption spectroscopy is used to investigate the photoinduced intramolecular electron-transfer (IET) behavior of a perylenebisimide dimmer in a variety of solvents. Findings suggest that IET rates depend on solvent dielectric constant.

A study shows that by using a high-boiling-point solvent, 1,2,4-trichlorobenzene, instead of chloroform for spin-coating, one can typically obtain a threefold increase in solar power conversion efficiency in devices based on CdSe tetrapods and the poly(p-phenylenvinylene) derivative OC1C10-PPV. These results can be explained by the occurrence of vertical phase separation, which leads to an optimal structure for charge collection.