Multiple retinal isomerizations during the early phase of the bestrhodopsin photoreaction.

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.

Visible-Light-Activated Carbon Monoxide Release from Porphyrin-Flavonol Hybrids.

We report on porphyrin-flavonol hybrids consisting of a porphyrin antenna and four covalently bound 3-hydroxyflavone (flavonol) groups, which act as highly efficient photoactivatable carbon monoxide (CO)-releasing molecules (photoCORMs). These bichromophoric systems enable activation of the UV-absorbing flavonol chromophore by visible light up to 650 nm and offer precise spatial and temporal control of CO administration. The physicochemical properties of the porphyrin antenna system can also be tuned by inserting a metal cation. Our computational study revealed that the process occurs via endergonic triplet-triplet energy transfer from porphyrin to flavonol and may become feasible thanks to flavonol energy stabilization upon intramolecular proton transfer. This mechanism was also indirectly supported by steady-state and transient absorption spectroscopy techniques. Additionally, the porphyrin-flavonol hybrids were found to be biologically benign. With four flavonol CO donors attached to a single porphyrin chromophore, high CO release yields, excellent uncaging cross sections, low toxicity, and CO therapeutic properties, these photoCORMs offer exceptional potential for their further development and future biological and medical applications.

Experimental Assessment of the Electronic and Geometrical Structure of a Near-Infrared Absorbing and Highly Fluorescent Microbial Rhodopsin.

The recently discovered Neorhodopsin (NeoR) exhibits absorption and emission maxima in the near-infrared spectral region, which together with the high fluorescence quantum yield makes it an attractive retinal protein for optogenetic applications. The unique optical properties can be rationalized by a theoretical model that predicts a high charge transfer character in the electronic ground state (S0) which is otherwise typical of the excited state S1 in canonical retinal proteins. The present study sets out to assess the electronic structure of the NeoR chromophore by resonance Raman (RR) spectroscopy since frequencies and relative intensities of RR bands are controlled by the ground and excited state's properties. The RR spectra of NeoR differ dramatically from those of canonical rhodopsins but can be reliably reproduced by the calculations carried out within two different structural models. The remarkable agreement between the experimental and calculated spectra confirms the consistency and robustness of the theoretical approach.

Nonresonant coherent two-dimensional spectroscopy.

Coherent electronic two-dimensional spectroscopy is nowadays a matured experimental technique that monitors the time evolution of the studied sample after its resonant optical excitation. However, the experimental experience shows that even nonresonant interactions can provide detectable spectral contributions. These are often present as a weak parasitic signals originating in the solvent and/or cuvette walls underlying the resonant spectrum of the actual sample and as such they are usually discarded from the analysis. In this work, we adapt the formalism of double-sided Feynman diagrams for the needs of coherent two-dimensional spectroscopy in the nonresonant regime. We analytically calculate the third-order polarization of a two-level and several variants of three-level systems. As a result, we demonstrate the typical appearance of the optical Kerr-effect, cross-phase modulation, excited-state coherence, two-photon absorption and stimulated Raman scattering in the 2D spectrum. This provides a framework for studying these effects by means of coherent two-dimensional spectroscopy.

Interplay between coherence-time undersampling and scattered light in two-dimensional electronic spectroscopy.

Scanning pulse delays in multi-pulse non-linear optical spectroscopy experiments is a major contributor to lengthy data acquisition. Using large steps for the scan can significantly speed up the experiment. However, an improper choice of step length can cause distortions to the resulting spectra, especially if the light scattered on the sample is mixed into the signal. In this work, we identify potential sources of such distortions and suggest appropriate countermeasures to avoid them while maintaining a faster data collection.

Bayesian approach for analysis of time-to-event data in plant biology.

BACKGROUND: Plants, like all living organisms, metamorphose their bodies during their lifetime. All the developmental and growth events in a plant's life are connected to specific points in time, be it seed germination, seedling emergence, the appearance of the first leaf, heading, flowering, fruit ripening, wilting, or death. The onset of automated phenotyping methods has brought an explosion of such time-to-event data. Unfortunately, it has not been matched by an explosion of adequate data analysis methods. RESULTS AND DISCUSSION: In this paper, we introduce the Bayesian approach towards time-to-event data in plant biology. As a model example, we use seedling emergence data of maize under control and stress conditions but the Bayesian approach is suitable for any time-to-event data (see the examples above). In the proposed framework, we are able to answer key questions regarding plant emergence such as these: (1) Do seedlings treated with compound A emerge earlier than the control seedlings? (2) What is the probability of compound A increasing seedling emergence by at least 5 percent? CONCLUSION: Proper data analysis is a fundamental task of general interest in life sciences. Here, we present a novel method for the analysis of time-to-event data which is applicable to many plant developmental parameters measured in field or in laboratory conditions. In contrast to recent and classical approaches, our Bayesian computational method properly handles uncertainty in time-to-event data and it is capable to reliably answer questions that are difficult to address by classical methods.

Correction: From wavelike to sub-diffusive motion: exciton dynamics and interaction in squaraine copolymers of varying length.

[This corrects the article DOI: 10.1039/C9SC04367E.].

From wavelike to sub-diffusive motion: exciton dynamics and interaction in squaraine copolymers of varying length.

Exciton transport and exciton-exciton interactions in molecular aggregates and polymers are of great importance in natural photosynthesis, organic electronics, and related areas of research. Both the experimental observation and theoretical description of these processes across time and length scales, including the transition from the initial wavelike motion to the following long-range exciton transport, are highly challenging. Therefore, while exciton dynamics at small scales are often treated explicitly, long-range exciton transport is typically described phenomenologically by normal diffusion. In this work, we study the transition from wavelike to diffusive motion of interacting exciton pairs in squaraine copolymers of varying length. To this end we use a combination of the recently introduced exciton-exciton-interaction two-dimensional (EEI2D) electronic spectroscopy and microscopic theoretical modelling. As we show by comparison with the model, the experimentally observed kinetics include three phases, wavelike motion dominated by immediate exciton-exciton annihilation (10-100 fs), sub-diffusive behavior (0.1-10 ps), and excitation relaxation (0.01-1 ns). We demonstrate that the key quantity for the transition from wavelike to diffusive dynamics is the exciton delocalization length relative to the length of the polymer: while in short polymers wavelike motion of rapidly annihilating excitons dominates, in long polymers the excitons become locally trapped and exhibit sub-diffusive behavior. Our findings indicate that exciton transport through conjugated systems emerging from the excitonic structure is generally not governed by normal diffusion. Instead, to characterize the material transport properties, the diffusion presence and character should be determined.

Direct observation of exciton-exciton interactions.

Natural light harvesting as well as optoelectronic and photovoltaic devices depend on efficient transport of energy following photoexcitation. Using common spectroscopic methods, however, it is challenging to discriminate one-exciton dynamics from multi-exciton interactions that arise when more than one excitation is present in the system. Here we introduce a coherent two-dimensional spectroscopic method that provides a signal only in case that the presence of one exciton influences the behavior of another one. Exemplarily, we monitor exciton diffusion by annihilation in a perylene bisimide-based J-aggregate. We determine quantitatively the exciton diffusion constant from exciton-exciton-interaction 2D spectra and reconstruct the annihilation-free dynamics for large pump powers. The latter enables for ultrafast spectroscopy at much higher intensities than conventionally possible and thus improves signal-to-noise ratios for multichromophore systems; the former recovers spatio-temporal dynamics for a broad range of phenomena in which exciton interactions are present.

Solvent-Templated Folding of Perylene Bisimide Macrocycles into Coiled Double-String Ropes with Solvent-Sensitive Optical Signatures.

A series of semirigid perylene bisimide (PBI) macrocycles with varied ring size containing two to nine PBI chromophores were synthesized in a one-pot reaction and their photophysical properties characterized by fluorescence, steady-state, and transient absorption spectroscopy as well as femtosecond stimulated Raman spectroscopy. These macrocycles show solvent-dependent conformational equilibria and excited-state properties. In dichloromethane, the macrocycles prevail in wide-stretched conformations and upon photoexcitation exhibit symmetry-breaking charge separation followed by charge recombination to triplet states, which photosensitize singlet oxygen formation. In contrast, in aromatic solvents folding of the macrocycles with a distinct odd-even effect regarding the number of PBI chromophore units was observed in steady-state and time-resolved absorption and fluorescence spectroscopy as well as femtosecond stimulated Raman spectroscopy. These distinctive optical properties are attributable to the folding of the even-membered macrocycles into exciton-vibrational coupled dimer pairs in aromatic solvents. Studies in a variety of aromatic solvents indicate that these solvents embed between PBI dimer pairs and accordingly template the folding of even-membered PBI macrocycles into ropelike folded conformations that give rise to solvent-specific exciton-vibrational couplings in UV-vis absorption spectra. As a consequence of the embedding of solvent molecules in the coiled double-string rope architecture, highly solvent specific intensity ratios are observed for the two lowest-energy exciton-vibrational bands, enabling assignment of the respective solvent simply based on the absorption spectra measured for the tetramer macrocycle.

Two-dimensional electronic spectroscopy can fully characterize the population transfer in molecular systems.

Excitation energy transfer in complex systems often proceeds through series of intermediate states. One of the goals of time-resolved spectroscopy is to identify the spectral signatures of all of them in the acquired experimental data and to characterize the energy transfer scheme between them. It is well known that in the case of transient absorption spectra such decomposition is ambiguous even if many simplifying considerations are taken. In contrast to transient absorption, absorptive 2D spectra intuitively resemble population transfer matrices. Therefore, it seems possible to decompose the 2D spectra unambiguously. Here we show that all necessary information is encoded in the combination of absorptive 2D and linear absorption spectra. We set up a simple model describing a broad class of absorptive 2D spectra and prove analytically that they can be inverted uniquely towards physical parameters fully determining the species-associated spectra of individual constituents together with all connecting intrinsic rate constants. Due to the matrix formulation of the model, it is suitable for fast computer calculation necessary to efficiently perform the inversion numerically by fitting the combination of experimental 2D and absorption spectra. Moreover, the model allows for decomposition of the 2D spectrum into its stimulated emission, ground-state bleach, and excited-state absorption components almost unambiguously. The numerical procedure is illustrated exemplarily.

Broadband 7-fs diffractive-optic-based 2D electronic spectroscopy using hollow-core fiber compression.

We demonstrate noncollinear coherent two-dimensional (2D) electronic spectroscopy for which broadband pulses are generated in an argon-filled hollow-core fiber pumped by a 1-kHz Ti:Sapphire laser. Compression is achieved to 7 fs duration (TG-FROG) using dispersive mirrors. The hollow fiber provides a clean spatial profile and smooth spectral shape in the 500-700 nm region. The diffractive-optic-based design of the 2D spectrometer avoids directional filtering distortions and temporal broadening from time smearing. For demonstration we record data of cresyl-violet perchlorate in ethanol and use phasing to obtain broadband absorptive 2D spectra. The resulting quantum beating as a function of population time is consistent with literature data.

In situ mapping of the energy flow through the entire photosynthetic apparatus.

Absorption of sunlight is the first step in photosynthesis, which provides energy for the vast majority of organisms on Earth. The primary processes of photosynthesis have been studied extensively in isolated light-harvesting complexes and reaction centres, however, to understand fully the way in which organisms capture light it is crucial to also reveal the functional relationships between the individual complexes. Here we report the use of two-dimensional electronic spectroscopy to track directly the excitation-energy flow through the entire photosynthetic system of green sulfur bacteria. We unravel the functional organization of individual complexes in the photosynthetic unit and show that, whereas energy is transferred within subunits on a timescale of subpicoseconds to a few picoseconds, across the complexes the energy flows at a timescale of tens of picoseconds. Thus, we demonstrate that the bottleneck of energy transfer is between the constituents.

Exciton Structure and Energy Transfer in the Fenna-Matthews-Olson Complex.

The Fenna-Matthews-Olson (FMO) photosynthetic complex found in green sulfur bacteria has over the last decades been one of the favorite "model" systems for biological energy transfer. However, even after 40 years of studies, quantitative knowledge about its energy-transfer properties is limited. Here, two-dimensional electronic spectroscopy with full polarization control is used to provide an accurate description of the electronic structure and population dynamics in the complex. The sensitivity of the technique has further allowed us to spectroscopically identify the eighth bacterio-chlorophyll molecule recently discovered in the crystal structure. The time evolution of the spectral structure, covering time scales from tens of femtoseconds up to a nanosecond, reflects the energy flow in FMO and enables us to extract an unambiguous energy-transfer scheme.

2D spectroscopy study of water-soluble chlorophyll-binding protein from Lepidium virginicum.

Water-soluble chlorophyll-binding proteins (WSCPs) are interesting model systems for the study of pigment-pigment and pigment-protein interactions. While class IIa WSCP has been extensively studied by spectroscopic and theoretical methods, a comprehensive spectroscopic study of class IIb WSCP was lacking so far despite the fact that its structure was determined by X-ray crystallography. In this paper, results of two-dimensional electronic spectroscopy applied to the class IIb WSCP from Lepidium virginicum are presented. Global analysis of 2D data allowed determination of energy levels and excitation energy transfer pathways in the system. Some additional pathways, not present in class IIa WSCP, were observed. The data were interpreted in terms of a model comprising two interacting chlorophyll dimers. In addition, oscillatory signals were observed and identified as coherent beatings of vibrational origin.

Unraveling the nature of coherent beatings in chlorosomes.

Coherent two-dimensional (2D) spectroscopy at 80 K was used to study chlorosomes isolated from green sulfur bacterium Chlorobaculum tepidum. Two distinct processes in the evolution of the 2D spectrum are observed. The first being exciton diffusion, seen in the change of the spectral shape occurring on a 100-fs timescale, and the second being vibrational coherences, realized through coherent beatings with frequencies of 91 and 145 cm(-1) that are dephased during the first 1.2 ps. The distribution of the oscillation amplitude in the 2D spectra is independent of the evolution of the 2D spectral shape. This implies that the diffusion energy transfer process does not transfer coherences within the chlorosome. Remarkably, the oscillatory pattern observed in the negative regions of the 2D spectrum (dominated by the excited state absorption) is a mirror image of the oscillations found in the positive part (originating from the stimulated emission and ground state bleach). This observation is surprising since it is expected that coherences in the electronic ground and excited states are generated with the same probability and the latter dephase faster in the presence of fast diffusion. Moreover, the relative amplitude of coherent beatings is rather high compared to non-oscillatory signal despite the reported low values of the Huang-Rhys factors. The origin of these effects is discussed in terms of the vibronic and Herzberg-Teller couplings.

2D Electronic Spectroscopy Reveals Excitonic Structure in the Baseplate of a Chlorosome.

In green photosynthetic bacteria, the chlorosome baseplate mediates excitation energy transfer from the interior of the light-harvesting chlorosome toward the reaction centers. However, the electronic states of the baseplate remain unexplored, hindering the mechanistic understanding of the baseplate as an excitation energy collector and mediator. Here we use two-dimensional spectroscopy to study the excited state structure and internal energy relaxation in the baseplate of green sulfur bacterium Chlorobaculum tepidum. We resolved an exciton system with four energy states, indicating that the organization of the pigments in the baseplate is more complex than was thought before and constitutes at least four bacteriochlorophyll molecules in a close contact. Based on the finding that the energy of the baseplate states is in the same range as in the adjacent Fenna-Matthews-Olson complex, we propose a "lateral" energy transfer pathway, where excitation energy can flow through the photosynthetic unit via all the states of individual complexes.

Two-dimensional electronic spectroscopy reveals ultrafast energy diffusion in chlorosomes.

Chlorosomes are light-harvesting antennae that enable exceptionally efficient light energy capture and excitation transfer. They are found in certain photosynthetic bacteria, some of which live in extremely low-light environments. In this work, chlorosomes from the green sulfur bacterium Chlorobaculum tepidum were studied by coherent electronic two-dimensional (2D) spectroscopy. Previously uncharacterized ultrafast energy transfer dynamics were followed, appearing as evolution of the 2D spectral line-shape during the first 200 fs after excitation. Observed initial energy flow through the chlorosome is well explained by effective exciton diffusion on a sub-100 fs time scale, which assures efficiency and robustness of the process. The ultrafast incoherent diffusion-like behavior of the excitons points to a disordered energy landscape in the chlorosome, which leads to a rapid loss of excitonic coherences between its structural subunits. This disorder prevents observation of excitonic coherences in the experimental data and implies that the chlorosome as a whole does not function as a coherent light-harvester.