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We present a methodology that provides a complete parametric description of the time evolution of the electronically and vibrationally excited states as detected by ultrafast transient absorption (TA). Differently from previous approaches, which started fitting the data after ≈100 fs, no data are left out in our methodology, and the "coherent artifact" and the instrument response function are fully taken into account. In case studies, the method is applied to solvents, the dye Nile blue, and all-trans β-carotene in cyclohexane solution. The estimated Damped Oscillation Associated Spectra (DOAS) and phases express the most important vibrational frequencies present in the molecular system. By global fit alone of the experimental data, it is difficult to interpret in detail the underlying dynamics. Since it is unfeasible to directly fit the data by a theoretical simulation, our enhanced DOAS methodology thus provides a useful "middle ground" where the theoretical description and the fit of the experimental data can meet. β-carotene in cyclohexane was complementarily studied with femtosecond stimulated Raman spectroscopy (FSRS). The fs–ps dynamics of β-carotene in cyclohexane in TA and FSRS experiments can be described by a sequential scheme S2 → hot S1 → S1′ → S1 → S0 with lifetimes of 167 fs (fixed), 0.35, 1.1, and 9.6 ps. The correspondence of DOAS decaying concomitantly with hot S1 and the Species Associated Difference Spectra of hot S1 in TA and FSRS suggest that we observe here features of the vibrational relaxation and nuclear reorganization responsible for the hot S1 to S1 transition. [ABSTRACT FROM AUTHOR]

Abstract: Femtosecond stimulated Raman spectroscopy (FSRS) is a promising multiple-pulse ultrafast spectroscopic tool whose simplest form utilizes an actinic pump, a Raman pump and a continuum probe. Here, we report that the transient absorption generated by the actinic pulse modulates the overall magnitude of the Raman signals of the photoactivated sample. As a consequence, the traditional transient FSRS signal is distorted by artifacts, which were observed in the past but left without interpretation. We propose a simple model to calculate the correct transient FSRS signals from the knowledge of transient absorption signal. The model was verified by application to experimental data. [Copyright &y& Elsevier]

A series of phthalocyanine-carotenoid dyads in which a phenylamino group links a phthalocyanine to carotenoids having 8-11 backbone double bonds were examined by visible and near-infrared femtosecond pump -probe spectroscopy combined with global fitting analysis. The series of molecules has permitted investigation of the role of carotenoids in the quenching of excited states of cyclic tetrapyrroles. The transient behavior varied dramatically with the length of the carotenoid and the solvent environment. Clear spectroscopic signatures of radical species revealed photoinduced electron transfer as the main quenching mechanism for all dyads dissolved in a polar solvent (THF), and the quenching rate was almost independent of carotenoid length. However, in a nonpolar solvent (toluene), quenching rates displayed a strong dependence on the conjugation length of the carotenoid and the mechanism did not include charge separation. The lack of any rise time components of a carotenoid S1 signature in all experiments in toluene suggests that an excitonic coupling between the carotenoid S1 state and phthalocyanine Q state, rather than a conventional energy transfer process, is the major mechanism of quenching. A pronounced inhomogeneity of the system was observed and attributed to the presence of a phenyl-amino linker between phthalocyanine and carotenoids. On the basis of accumulated work on various caroteno-phthalocyanine dyads and triads, we have now identified three mechanisms of tetrapyrrole singlet excited state quenching by carotenoids in artificial systems: (i) Car-Pc electron transfer and recombination; (ii) 1Pc to CarS1 energy transfer and fast internal conversion to the Car ground state; (iii) excitonic coupling between 1Pc and CarS1 and ensuing internal conversion to the ground state of the carotenoid. The dominant mechanism depends upon the exact molecular architecture and solvent environment. These synthetic systems are providing a deeper understanding of structural and environmental effects on the interactions between carotenoids and tetrapyrroles and thereby better defining their role in controlling natural photosynthetic systems. [ABSTRACT FROM AUTHOR]

Bestrhodopsins constitute a class of light-regulated pentameric ion channels that consist of one or two rhodopsins in tandem fused with bestrophin ion channel domains. Here, we report on the isomerization dynamics in the rhodopsin tandem domains of Phaeocystis antarctica bestrhodopsin, which binds all-trans retinal Schiff-base (RSB) absorbing at 661 nm and, upon illumination, converts to the meta-stable P540 state with an unusual 11-cis RSB. The primary photoproduct P682 corresponds to a mixture of highly distorted 11-cis and 13-cis RSB directly formed from the excited state in 1.4 ps. P673 evolves from P682 in 500 ps and contains highly distorted 13-cis RSB, indicating that the 11-cis fraction in P682 converts to 13-cis. Next, P673 establishes an equilibrium with P595 in 1.2 µs, during which RSB converts to 11-cis and then further proceeds to P560 in 48 µs and P540 in 1.0 ms while remaining 11-cis. Hence, extensive isomeric switching occurs on the early ground state potential energy surface (PES) on the hundreds of ps to µs timescale before finally settling on a metastable 11-cis photoproduct. We propose that P682 and P673 are trapped high up on the ground-state PES after passing through either of two closely located conical intersections that result in 11-cis and 13-cis RSB. Co-rotation of C11=C12 and C13=C14 bonds results in a constricted conformational landscape that allows thermal switching between 11-cis and 13-cis species of highly strained RSB chromophores. Protein relaxation may release RSB strain, allowing it to evolve to a stable 11-cis isomeric configuration in microseconds. [ABSTRACT FROM AUTHOR]

Time-resolved femtosecond-stimulated Raman spectroscopy (FSRS) provides valuable information on the structural dynamics of biomolecules. However, FSRS has been applied mainly up to the nanoseconds regime and above 700 cm−1, which covers only part of the spectrum of biologically relevant time scales and Raman shifts. Here we report on a broadband (~200–2200 cm−1) dual transient visible absorption (visTA)/FSRS set-up that can accommodate time delays from a few femtoseconds to several hundreds of microseconds after illumination with an actinic pump. The extended time scale and wavenumber range allowed us to monitor the complete excited-state dynamics of the biological chromophore flavin mononucleotide (FMN), both free in solution and embedded in two variants of the bacterial light-oxygen-voltage (LOV) photoreceptor EL222. The observed lifetimes and intermediate states (singlet, triplet, and adduct) are in agreement with previous time-resolved infrared spectroscopy experiments. Importantly, we found evidence for additional dynamical events, particularly upon analysis of the low-frequency Raman region below 1000 cm−1. We show that fs-to-sub-ms visTA/FSRS with a broad wavenumber range is a useful tool to characterize short-lived conformationally excited states in flavoproteins and potentially other light-responsive proteins. [ABSTRACT FROM AUTHOR]

The article discusses a study on the electron cryo-microscopy structure of the Gemmatimonas phototrophica photosystem at 2.4 Å. It has a unique, double-ring complex that holds the central type 2 reaction center (RC) which is encircled by an outer 24-subunit antenna ring (LHh) for added light-gathering capacity. It concludes that it has evolved for harvesting and trapping solar energy with compact and robust structure.

Here, we propose a possible photoactivation mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP), suggesting that the reaction involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. Taking advantage of engineering an OCP variant carrying the Y201W mutation, which shows superior spectroscopic and structural properties, it is shown that the presence of Trp201 augments the impact of one critical H-bond between the ketocarotenoid and the protein. This confers an unprecedented homogeneity of the dark-adapted OCP state and substantially increases the yield of the excited photoproduct S*, which is important for the productive photocycle to proceed. A 1.37 Å crystal structure of OCP Y201W combined with femtosecond time-resolved absorption spectroscopy, kinetic analysis, and deconvolution of the spectral intermediates, as well as extensive quantum chemical calculations incorporating the effect of the local electric field, highlighted the role of charge-transfer states during OCP photoconversion. Yaroshevich et al. present a chemical reaction mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP). They find that photoactivation critically involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. This study suggests the role of charge-transfer states during OCP photoconversion. [ABSTRACT FROM AUTHOR]

Near-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes are widely used for structural and functional deep-tissue imaging in vivo. To fluoresce, NIR FPs covalently bind a chromophore, such as biliverdin IXa tetrapyrrole. The efficiency of biliverdin binding directly affects the fluorescence properties, rendering understanding of its molecular mechanism of major importance. miRFP proteins constitute a family of bright monomeric NIR FPs that comprise a Per-ARNT-Sim (PAS) and cGMP-specific phosphodiesterases - Adenylyl cyclases - FhlA (GAF) domain. Here, we structurally analyze biliverdin binding to miRFPs in real time using time-resolved stimulated Raman spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations. Biliverdin undergoes isomerization, localization to its binding pocket, and pyrrolenine nitrogen protonation in <1 min, followed by hydrogen bond rearrangement in ~2 min. The covalent attachment to a cysteine in the GAF domain was detected in 4.3 min and 19 min in miRFP670 and its C20A mutant, respectively. In miRFP670, a second C–S covalent bond formation to a cysteine in the PAS domain occurred in 14 min, providing a rigid tetrapyrrole structure with high brightness. Our findings provide insights for the rational design of NIR FPs and a novel method to assess cofactor binding to light-sensitive proteins. Near-infrared fluorescent proteins engineered from bacterial phytochromes are important for deep-tissue imaging in vivo, but the mechanism through which they bind to chromophores is not fully understood. Here the authors structurally analyze biliverdin binding to miRFP proteins using time-resolved stimulated Raman spectroscopy and quantum mechanical/molecular mechanics calculations. [ABSTRACT FROM AUTHOR]

Many linked processes occur concurrently in strongly excited semiconductors, such as interband and intraband absorption, scattering of electrons and holes by the heated lattice, Pauli blocking, bandgap renormalization and the formation of Mahan excitons. In this work, we disentangle their dynamics and contributions to the optical response of a ZnO thin film. Using broadband pump-probe ellipsometry, we can directly and unambiguously obtain the real and imaginary part of the transient dielectric function which we compare with first-principles simulations. We find interband and excitonic absorption partially blocked and screened by the photo-excited electron occupation of the conduction band and hole occupation of the valence band (absorption bleaching). Exciton absorption turns spectrally narrower upon pumping and sustains the Mott transition, indicating Mahan excitons. Simultaneously, intra-valence-band transitions occur at sub-picosecond time scales after holes scatter to the edge of the Brillouin zone. Our results pave new ways for the understanding of non-equilibrium charge-carrier dynamics in materials by reliably distinguishing between changes in absorption coefficient and refractive index, thereby separating competing processes. This information will help to overcome the limitations of materials for high-power optical devices that owe their properties from dynamics in the ultrafast regime. [ABSTRACT FROM AUTHOR]

Photosynthetic organisms protect themselves from high-light stress by dissipating excess absorbed energy as heat in a process called non-photochemical quenching (NPQ). Zeaxanthin is essential for the full development of NPQ, but its role remains debated. The main discussion revolves around two points: where does zeaxanthin bind and does it quench? To answer these questions we have followed the zeaxanthin-dependent quenching from leaves to individual complexes, including supercomplexes. We show that small amounts of zeaxanthin are associated with the complexes, but in contrast to what is generally believed, zeaxanthin binding per se does not cause conformational changes in the complexes and does not induce quenching, not even at low pH. We show that in NPQ conditions zeaxanthin does not exchange for violaxanthin in the internal binding sites of the antennas but is located at the periphery of the complexes. These results together with the observation that the zeaxanthin-dependent quenching is active in isolated membranes, but not in functional supercomplexes, suggests that zeaxanthin is acting in between the complexes, helping to create/participating in a variety of quenching sites. This can explain why none of the antennas appears to be essential for NPQ and the multiple quenching mechanisms that have been observed in plants. [ABSTRACT FROM AUTHOR]

UVR8 is a novel UV-B photoreceptor that regulates a range of plant responses and is already used as a versatile optogenetic tool. Instead of an exogenous chromophore, UVR8 uniquely employs tryptophan side chains to accomplish UV-B photoreception. UV-B absorption by homodimeric UVR8 induces monomerization and hence signaling, but the underlying photodynamic mechanisms are not known. Here, by using a combination of time-resolved fluorescence and absorption spectroscopy from femto- to microseconds, we provide the first experimental evidence for the UVR8 molecular signaling mechanism. The results indicate that tryptophan residues at the dimer interface engage in photoinduced proton coupled electron transfer reactions that induce monomerization. [ABSTRACT FROM AUTHOR]

The orange carotenoid protein (OCP) is a structurally and functionally modular photoactive protein involved in cyanobacterial photoprotection. Recently, based on bioinformatic analysis and phylogenetic relationships, new families of OCP have been described, OCP2 and OCPx. The first characterization of the OCP2 showed both faster photoconversion and back-conversion, and lower fluorescence quenching of phycobilisomes relative to the well-characterized OCP1. Moreover, OCP2 is not regulated by the fluorescence recovery protein (FRP). In this work, we present a comprehensive study combining ultrafast spectroscopy and structural analysis to compare the photoactivation mechanisms of OCP1 and OCP2 from Tolypothrix PCC 7601. We show that despite significant differences in their functional characteristics, the spectroscopic properties of OCP1 and OCP2 are comparable. This indicates that the OCP functionality is not directly related to the spectroscopic properties of the bound carotenoid. In addition, the structural analysis by X-ray footprinting reveals that, overall, OCP1 and OCP2 have grossly the same photoactivation mechanism. However, the OCP2 is less reactive to radiolytic labeling, suggesting that the protein is less flexible than OCP1. This observation could explain fast photoconversion of OCP2. Unlabelled Image • Excited-state dynamics of CAN is comparable in OCP1 and OCP2. • Photoactivation does not alter properties of ICT state of CAN. • CAN S* state identified exclusively in OCP2. • More constrained structure of CAN in OCP2 than in OCP1 • OCP2 is less flexible than OCP1. [ABSTRACT FROM AUTHOR]