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Ultraviolet-induced photodissociation and photo-isomerization of the three most stable conformers (SSC, GAC, and AAT) of glycolic acid are investigated in a low-temperature solid argon matrix using FTIR spectroscopy and employing laser radiation with wavelengths of 212 nm, 226 nm, and 230 nm. The present work broadens the wavelength range of photochemical studies of glycolic acid, thus extending the understanding of the overall photochemistry of the compound. The proposed kinetic model for the photodissociation of glycolic acid proceeds from the lowest energy conformer (SSC). The model suggests that ultraviolet light induces isomerization only between the SSC and GAC conformers and between the SSC and AAT conformers. The relative reaction rate coefficients are reported for all proposed reactions. These results suggest that the direct photodissociation of GAC and AAT conformer does not occur in an argon matrix. The main photodissociation channel via the SSC conformer produces formaldehyde–water complexes. The proposed photodissociation mechanism emphasizes that the conformers’ relative abundancies can significantly affect the photodissociation rate of the molecule. For example, in the case of high relative GAC and AAT concentrations, the ultraviolet photodissociation of glycolic acid requires the proceeding photo-isomerization of GAC and AAT to SSC.

Chromophore cis/trans photoisomerization is a fundamental process in chemistry and in the activation of many photosensitive proteins. A major task is understanding the effect of the protein environment on the efficiency and direction of this reaction compared to what is observed in the gas and solution phases. In this study, we set out to visualize the hula twist (HT) mechanism in a fluorescent protein, which is hypothesized to be the preferred mechanism in a spatially constrained binding pocket. We use a chlorine substituent to break the twofold symmetry of the embedded phenolic group of the chromophore and unambiguously identify the HT primary photoproduct. Through serial femtosecond crystallography, we then track the photoreaction from femtoseconds to the microsecond regime. We observe signals for the photoisomerization of the chromophore as early as 300 fs, obtaining the first experimental structural evidence of the HT mechanism in a protein on its femtosecond-to-picosecond timescale. We are then able to follow how chromophore isomerization and twisting lead to secondary structure rearrangements of the protein β-barrel across the time window of our measurements. peerReviewed

In red-light sensing phytochromes, isomerization of the bilin chromophore triggers structural and dynamic changes across multiple domains, ultimately leading to control of the output module (OPM) activity. In between, a hairpin structure, "arm", extends from an interconnecting domain to the chromophore region. Here, by removing this protein segment in a bacteriophytochrome from Deinococcus radiodurans (DrBphP), we show that the arm is crucial for signal transduction. Crystallographic, spectroscopic, and biochemical data indicate that this variant maintains the properties of DrBphP in the resting state. Spectroscopic data also reveal that the armless systems maintain the ability to respond to light. However, there is no subsequent regulation of OPM activity without the arms. Thermal denaturation reveals that the arms stabilize the DrBphP structure. Our results underline the importance of the structurally flexible interconnecting hairpin extensions and describe their central role in the allosteric coupling of phytochromes. peerReviewed

Signal propagation in photosensory proteins is a complex and multidimensional event. Unraveling such mechanisms site-specifically in real time is an eligible but a challenging goal. Here, we elucidate the site-specific events in a red-light sensing phytochrome using the unnatural amino acid azidophenylalanine, vibrationally distinguishable from all other protein signals. In canonical phytochromes, signal transduction starts with isomerization of an excited bilin chromophore, initiating a multitude of processes in the photosensory unit of the protein, which eventually control the biochemical activity of the output domain, nanometers away from the chromophore. By implementing the label in prime protein locations and running two-color step-scan FTIR spectroscopy on the Deinococcus radiodurans bacteriophytochrome, we track the signal propagation at three specific sites in the photosensory unit. We show that a structurally switchable hairpin extension, a so-called tongue region, responds to the photoconversion already in microseconds and finalizes its structural changes concomitant with the chromophore, in milliseconds. In contrast, kinetics from the other two label positions indicate that the site-specific changes deviate from the chromophore actions, even though the labels locate in the chromophore vicinity. Several other sites for labeling resulted in impaired photoswitching, low structural stability, or no changes in the difference spectrum, which provides additional information on the inner dynamics of the photosensory unit. Our work enlightens the multidimensionality of the structural changes of proteins under action. The study also shows that the signaling mechanism of phytochromes is accessible in a time-resolved and site-specific approach by azido probes and demonstrates challenges in using these labels. peerReviewed

Photoactivation of bacteriophytochrome involves a cis–trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail. In our simulations the photoisomerization of the D ring occurs in the counterclockwise direction. On a subpicosecond time scale, the photoexcited chromophore adopts a short-lived intermediate with a highly twisted configuration stabilized by an extended hydrogen-bonding network. Within tens of picoseconds, these hydrogen bonds break, allowing the chromophore to adopt a more planar configuration, which we assign to the early Lumi-R state. The isomerization process is completed via helix inversion of the biliverdin chromophore to form the late Lumi-R state. The mechanistic insights into the photoisomerization process are essential to understand how bacteriophytochrome has evolved to mediate photoactivation and to engineer this protein for new applications. peerReviewed

Phytochromes are ubiquitous photosensor proteins, which control the growth, reproduction and movement in plants, fungi and bacteria. Phytochromes switch between two photophysical states depending on the light conditions. In analogy to molecular machines, light absorption induces a series of structural changes that are transduced from the bilin chromophore, through the protein, and to the output domains. Recent progress towards understanding this structural mechanism of signal transduction has been manifold. We describe this progress with a focus on bacteriophytochromes. We describe the mechanism along three structural tiers, which are the chromophore-binding pocket, the photosensory module, and the output domains. We discuss possible interconnections between the tiers and conclude by presenting future directions and open questions. We hope that this review may serve as a compendium to guide future structural and spectroscopic studies designed to understand structural signaling in phytochromes.

Photoactivation in the Photoactive Yellow Protein, a bacterial blue light photoreceptor, proceeds via photo-isomerization of the double C=C bond in the covalently attached chromophore. Quantum chemistry calculations, however, have suggested that in addition to double bond photo-isomerization, the isolated chromophore and many of its analogues, can isomerize around a single C-C bond as well. Whereas double bond photo-isomerization has been observed with x-ray crystallography, experimental evidence for single bond photo-isomerization is currently lacking. Therefore, we have synthesized a chromophore analogue, in which the formal double bond is covalently locked in a cyclopentenone ring and carried out transient absorption spectroscopy experiments in combination with non-adiabatic molecular dynamics simulations to reveal that the locked chromophore isomerizes around the single bond upon photo-activation. Our work thus provides experimental evidence for single bond photo-isomerization in a photoactive yellow protein chromophore analogue and suggests that photo-isomerization is not restricted to the double bonds in conjugated systems. This insight may be useful for designing light-driven molecular switches or motors. peerReviewed

Phytochromes sense red/far-red light and control many biological processes in plants, fungi, and bacteria. Although crystal structures of dark and light adapted states have been determined, the molecular mechanisms underlying photoactivation remains elusive. Here we demonstrate that the conserved tongue region of the PHY domain of a 57kDa photosensory module of Deinococcus radiodurans phytochrome, changes from a structurally heterogeneous dark state to an ordered light activated state. The results were obtained in solution by utilizing a laser-triggered activation approach detected on the atomic level with high-resolution protein NMR spectroscopy. The data suggest that photosignaling of phytochromes relies on careful modulation of structural heterogeneity of the PHY tongue. peerReviewed

Solar radiation initiates photochemical oxidation of dissolved organic carbon (DOC) to dissolved inorganic carbon (DIC) in inland waters, contributing to their carbon dioxide emissions to the atmosphere. Models can determine photochemical DIC production over large spatiotemporal scales and assess its role in aquatic C cycling. The apparent quantum yield (AQY) spectrum for photochemical DIC production, defined as mol DIC produced per mol chromophoric dissolved organic matter-absorbed photons, is a critical model parameter. In previous studies, the principle for the determination of AQY spectra is the same but methodological specifics differ, and the extent to which these differences influence AQY spectra and simulated aquatic DIC photoproduction is unclear. Here, four laboratories determined AQY spectra from water samples of eight inland waters that are situated in Alaska, Finland, and Sweden and span a nearly 10-fold range in DOM absorption coefficients. All AQY values fell within the range previously reported for inland waters. The inter-laboratory coefficient of variation (CV) for wavelength-integrated AQY spectra (300–450 nm) averaged 38% ± 3% SE, and the inter-water CV averaged 63% ± 1%. The inter-laboratory CV for simulated photochemical DIC production (conducted for the five Swedish lakes) averaged 49% ± 12%, and the inter-water CV averaged 77% ± 10%. This uncertainty is not surprising given the complexities and methodological choices involved in determining DIC AQY spectra and needs to be considered when applying photochemical rate modeling. Thus, we also highlight current methodological limitations and suggest future improvements for DIC AQY determination to reduce inter-laboratory uncertainty. peerReviewed

The excited-state properties of an amphiphilic porphyrin–fullerene dyad and of its porphyrin analogue adsorbed at the dodecane/water interface are investigated by using surface second-harmonic generation. Although the porphyrin is formally centrosymmetric, the second-harmonic spectra of both compounds are dominated by the intense Soret band of the porphyrin. Polarization-selective measurements and molecular dynamics simulations suggest an angle of about 45° between the donor–acceptor axis and the interfacial plane, with the porphyrin interacting mostly with the nonpolar phase. Time-resolved measurements reveal a marked concentration dependence of the dynamics of both compounds upon Q-band excitation, indicating the occurrence of intermolecular quenching processes. The significant differences in dynamics and spectra between the dyad and the porphyrin analogue are explained by a self-quenching of the excited dyad via an intermolecular electron transfer. peerReviewed

Phytochrome proteins detect red/far-red light to guide the growth, motion, development and reproduction in plants, fungi, and bacteria. Bacterial phytochromes commonly function as an entrance signal in two-component sensory systems. Despite the availability of three-dimensional structures of phytochromes and other two-component proteins, the conformational changes, which lead to activation of the protein, are not understood. We reveal cryo electron microscopy structures of the complete phytochrome from Deinoccocus radiodurans in its resting and photoactivated states at 3.6 Å and 3.5 Å resolution, respectively. Upon photoactivation, the photosensory core module hardly changes its tertiary domain arrangement, but the connector helices between the photosensory and the histidine kinase modules open up like a zipper, causing asymmetry and disorder in the effector domains. The structures provide a framework for atom-scale understanding of signaling in phytochromes, visualize allosteric communication over several nanometers, and suggest that disorder in the dimeric arrangement of the effector domains is important for phosphatase activity in a two-component system. The results have implications for the development of optogenetic applications.

Funding Information: This work was supported by Academy of Finland grants 285461 (H.T.), 330678 (H.T., J.R.), 277194 (H.L.), and 290677 (S.M.). We acknowledge the European Synchrotron Radiation Facility (ESRF) for providing synchrotron access for crystal data collection. We thank Prof. Janne Ihalainen (University of Jyväskylä) for all the help in all aspects of the paper, Prof. Gerrit Groenhof (University of Jyväskylä) for support, and Prof. Nikolai V. Tkachenko (Tampere University) for help and facilities for time-resolved absorption spectroscopy. We also thank M.Sc. Alli Liukkonen (University of Jyväskylä) and Dr. Heikki Häkkänen (University of Jyväskylä) for the assistance in laboratory and spectroscopy, respectively. Funding Information: This work was supported by Academy of Finland grants 285461 (H.T.), 330678 (H.T., J.R.), 277194 (H.L.), and 290677 (S.M.). We acknowledge the European Synchrotron Radiation Facility (ESRF) for providing synchrotron access for crystal data collection. We thank Prof. Janne Ihalainen (University of Jyväskylä) for all the help in all aspects of the paper, Prof. Gerrit Groenhof (University of Jyväskylä) for support, and Prof. Nikolai V. Tkachenko (Tampere University) for help and facilities for time-resolved absorption spectroscopy. We also thank M.Sc. Alli Liukkonen (University of Jyväskylä) and Dr. Heikki Häkkänen (University of Jyväskylä) for the assistance in laboratory and spectroscopy, respectively. Publisher Copyright: © 2022, The Author(s). Phytochromes are red light-sensing photoreceptor proteins that bind a bilin chromophore. Here, we investigate the role of a conserved histidine (H260) and tyrosine (Y263) in the chromophore-binding domain (CBD) of Deinococcus radiodurans phytochrome (DrBphP). Using crystallography, we show that in the H260A variant, the missing imidazole side chain leads to increased water content in the binding pocket. On the other hand, Y263F mutation reduces the water occupancy around the chromophore. Together, these changes in water coordination alter the protonation and spectroscopic properties of the biliverdin. These results pinpoint the importance of this conserved histidine and tyrosine, and the related water network, for the function and applications of phytochromes.

When photoactive molecules interact strongly with confined light modes in optical cavities, new hybrid light–matter states form. They are known as polaritons and correspond to coherent superpositions of excitations of the molecules and of the cavity photon. The polariton energies and thus potential energy surfaces are changed with respect to the bare molecules, such that polariton formation is considered a promising paradigm for controlling photochemical reactions. To effectively manipulate photochemistry with confined light, the molecules need to remain in the polaritonic state long enough for the reaction on the modified potential energy surface to take place. To understand what determines this lifetime, we have performed atomistic molecular dynamics simulations of room-temperature ensembles of rhodamine chromophores strongly coupled to a single confined light mode with a 15 fs lifetime. We investigated three popular experimental scenarios and followed the relaxation after optically pumping (i) the lower polariton, (ii) the upper polariton, or (iii) uncoupled molecular states. The results of the simulations suggest that the lifetimes of the optically accessible lower and upper polaritons are limited by (i) ultrafast photoemission due to the low cavity lifetime and (ii) reversible population transfer into the “dark” state manifold. Dark states are superpositions of molecular excitations but with much smaller contributions from the cavity photon, decreasing their emission rates and hence increasing their lifetimes. We find that population transfer between polaritonic modes and dark states is determined by the overlap between the polaritonic and molecular absorption spectra. Importantly, excitation can also be transferred ”upward” from the lower polariton into the dark-state reservoir due to the broad absorption spectra of the chromophores, contrary to the common conception of these processes as a ”one-way” relaxation from the dark states down to the lower polariton. Our results thus suggest that polaritonic chemistry relying on modified dynamics taking place within the lower polariton manifold requires cavities with sufficiently long lifetimes and, at the same time, strong light–matter coupling strengths to prevent the back-transfer of excitation into the dark states, This work was supported by the Academy of Finland (Grants 289947 to JJT, 290677 to GG, and 285481 to DM) as well as the European Research Council (ERC-2016-StG-714870 to JF) and the Spanish Ministry for Science, Innovation, and Universities − AEI (RTI2018-099737-B-I00 to JF). We thank the Center for Scientific Computing (CSC-IT Center for Science) for computational resources and Fredrik Robertsen in particular ́ for his help with running our simulations on GPUs. We also acknowledge PRACE for awarding us access to resource Curie based in France at GENCI

The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that in both states the protonated form of the chromophore dominates, we also find that a minor population with a deprotonated D-ring could contribute to the red-shifted tail in the absorption spectra.

The electrophilic borylation of 2,5-diarylpyrazines results in the formation of boron–nitrogen doped dihydroindeno[1,2-b]fluorene which can be synthesized using standard Schlenk techniques and worked up and handled readily under atmospheric conditions. Through transmetallation via diarylzinc reagents a series of derivatives were synthesized which show broad visible to near-IR light absorption profiles that highlight the versatility of this BN substituted core for use in optoelectronic devices. The synthesis is efficient, scalable and allows for tuning through changes in substituents on the planar heterocyclic core and at boron. Exploratory evaluation in organic solar cell devices as non-fullerene acceptors gave power conversion efficiencies of 2%. peerReviewed

Methylene bridged 2,2′-dipyridylamine (dpa) derivatives and their metal complexes possess outstanding properties due to their inherent structural flexibility. Synthesis of such complexes typically involves derivatization of dpa followed by coordination on metals, and may not always be very efficient. In this work, an alternative synthetic approach, involving the derivatization step after – rather than prior to – coordination of dpa on metal center, is proposed and applied to synthesis of a number of platinum(II) complexes with substituted benzyldi(2-pyridyl)amines. Comparison with the more conventional synthetic route reveals greater efficiency and versatility of the proposed approach. The obtained complexes are not luminescent in solution at room temperature, but display blue phosphorescence emission (ca. 415 nm) with the lifetimes of μs order in glassy matrix at 77 K, with additional green (ca. 485 nm) and relatively long living (τ = 3.7 ms) emission in the case of iodine substituted derivative. peerReviewed

Solvent access to the protein interior plays an important role in the function of many proteins. Phytochromes contain a specific structural feature, a hairpin extension that appears to relay structural information from the chromophore to the rest of the protein. The extension interacts with amino acids near the chromophore, and hence shields the chromophore from the surrounding solvent. We envision that the detachment of the extension from the protein surface allows solvent exchange reactions in the vicinity of the chromophore. This can facilitate for example, proton transfer processes between solvent and the protein interior. To test this hypothesis, the kinetics of the protonation state of the biliverdin chromophore from Deinococcus radiodurans bacteriophytchrome, and thus, the pH of the surrounding solution, is determined. The observed absorbance changes are related to the solvent access of the chromophore binding pocket, gated by the hairpin extension. We therefore propose a model with an “open” (solvent-exposed, deprotonation-active on a (sub)second time-scale) state and a “closed” (solvent-gated, deprotonation inactive) state, where the hairpin fluctuates slowly between these conformations thereby controlling the deprotonation process of the chromophore on a minute time scale. When the connection between the hairpin and the biliverdin surroundings is destabilized by a point mutation, the amplitude of the deprotonation phase increases considerably. In the absence of the extension, the chromophore deprotonates essentially without any “gating”. Hence, we introduce a straightforward method to study the stability and fluctuation of the phytochrome hairpin in its photostationary state. This approach can be extended to other chromophore-protein systems where absorption changes reflect dynamic processes of the protein.

The photochemistry of matrix-isolated glycolic acid, induced by UV light, was studied by FTIR spectroscopy and B3LYPD3/6-311++G(3df,3pd) calculations. Several decomposition pathways were found to take place upon 212 nm and 226 nm wavelengths irradiation. A number of complexes formed between photoproducts were identified, among them those of formaldehyde with water, carbon monoxide and carbon dioxide as well as the H2O-CO complexes. The structure and spectroscopic assignment of the photoproducts were made comparing the experimental results with the theoretical predictions and available literature data. The observed formation of different complexes indicates various pathways for their formation resulting from UV-induced photodecomposition of different precursor isomers. peerReviewed

We demonstrate the first example of bidirectional reversible electronic energy transfer (REET) between the mechanically bonded components of a rotaxane. Our prototypical system was designed such that photoexcitation of a chromophore in the axle results in temporary storage of electronic energy in a quasi-isoenergetic “reservoir” chromophore in the macrocycle. Over time, the emissive state of the axle is repopulated from this reservoir, resulting in long-lived, delayed luminescence. Importantly, we show that cation binding in the cavity formed by the mechanical bond perturbs the axle chromophore energy levels, modulating the REET process, and ultimately providing a luminescence read-out of cation binding. Modulation of REET processes represents an unexplored mechanism in luminescent molecular sensor development., Delayed emission due to reversible electronic energy transfer (REET) between chromophores in the axle and macrocycle components of a rotaxane is demonstrated. The REET process can be modulated by metal ion binding in the cavity of the rotaxane.

Five nucleic acid binding cyanine dyes were synthesized and their photophysical properties were evaluated. Changing a single heteroatom in the chromophore causes major differences both in brightness and photostability between the dyes. With such alteration, the brightness of the chromophore increased two-fold compared to the one found in SYBR Green I. peerReviewed

Unravelling the rules of molecular motion is a contemporary challenge that promises to support the development of responsive materials and is likely to enhance the understanding of functional motion. Advances in integrating light‐driven molecular motors in soft matter have led to the design and realization of chiral nematic (cholesteric) liquid crystals that can respond to light with modification of their helical pitch, and also with helix inversion. Under illumination, these chiral liquid crystals convert from one helical geometry to another. Here, a series of light‐driven molecular motors that feature a rich configurational landscape is presented, specifically which involves three stable chiral states. The succession of chiral structures involved in the motor cycle is transmitted at higher structural levels, as the cholesteric liquid crystals that are formed can interconvert between helices of opposite handedness, reversibly. In these materials, the dynamic features of the motors are thus expressed at the near‐macroscopic, functional level, into addressable colors that can be used in advanced materials for tunable optics and photonics. peerReviewed

Phytochromes are photosensory proteins in plants, fungi, and bacteria, which detect red- and far-red light. They undergo a transition between the resting (Pr) and photoactivated (Pfr) states. In bacterial phytochromes, the Pr-to-Pfr transition is facilitated by two intermediate states, called Lumi-R and Meta-R. The molecular structures of the protein in these states are not known and the molecular mechanism of photoconversion is not understood. Here, we apply transient infrared absorption spectroscopy to study the photocycle of the wild-type and Y263F mutant of the phytochrome from Deinococcus radiodurans (DrBphP) from nanoto milliseconds. We identify two sequentially forming Lumi-R states which differ in the local structure surrounding the carbonyl group of the biliverdin D-ring. We also find that the tyrosine at position 263 alters local structure and dynamics around the D-ring and causes an increased rate of Pfr formation. The results shed new light on the mechanism of light-signalling in phytochrome proteins peerReviewed

Halide double perovskites have gained significant attention, owing to their composition of low-toxicity elements, stability in air and long charge-carrier lifetimes. However, most double perovskites, including Cs2AgBiBr6, have wide bandgaps, which limits photoconversion efficiencies. The bandgap can be reduced through alloying with Sb3+, but Sb-rich alloys are difficult to synthesize due to the high formation energy of Cs2AgSbBr6, which itself has a wide bandgap. We develop a solution-based route to synthesize phase-pure Cs2Ag(SbxBi1−x)Br6 thin films, with the mixing parameter x continuously varying over the entire composition range. We reveal that the mixed alloys (x between 0.5 and 0.9) demonstrate smaller bandgaps than the pure Sb- and Bi-based compounds. The reduction in the bandgap of Cs2AgBiBr6 achieved through alloying (170 meV) is larger than if the mixed alloys had obeyed Vegard's law (70 meV). Through in-depth computations, we propose that bandgap lowering arises from the type II band alignment between Cs2AgBiBr6 and Cs2AgSbBr6. The energy mismatch between the Bi and Sb s and p atomic orbitals, coupled with their non-linear mixing, results in the alloys adopting a smaller bandgap than the pure compounds. Our work demonstrates an approach to achieve bandgap reduction and highlights that bandgap bowing may be found in other double perovskite alloys by pairing together materials forming a type II band alignment. peerReviewed

Formation and decomposition of the complex of carbon dioxide and atomic oxygen are characterized by quantum chemistry methods aiming to rationalize experimental studies in solid krypton. The observed FTIR spectra reflected the temporal evolution of the system after irradiation showing the bands of reactants, intermediates and products. Advanced quantum chemistry calculations show that the T-shape complex CO2…O(3P) can be formed in the matrix. Its excitation by the 193 nm light results in the charge-transfer state CO2+…O-, which evolves to the reaction intermediate CO3. The latter species decomposes to CO + O2 following pathways on the excited state energy surfaces. peerReviewed

Photochromic systems have been used to achieve a number of engineering functions such as light energy conversion, molecular motors, pumps, actuators, and sensors. Key to practical applications is a high efficiency in the conversion of light to chemical energy, a rigid structure for the transmission of force to the environment, and directed motion during isomerization. We present a novel type of photochromic system (diindane diazocines) that converts visible light with an efficiency of 18 % to chemical energy. Quantum yields are exceptionally high with >70 % for the cis–trans isomerization and 90 % for the back‐reaction and thus higher than the biochemical system rhodopsin (64 %). Two diastereomers (meso and racemate) were obtained in only two steps in high yields. Both isomers are directional switches with high conversion rates (76–99 %). No fatigue was observed after several thousands of switching cycles in both systems., Azobenzene under lockdown: Photoisomerizable molecules such as azobenzene convert light directly into chemical energy, however, with a low energy efficiency. By systematically reducing the conformational flexibility of azobenzene and thus preventing unproductive photochemical pathways, the energy conversion efficiency was increased from 1.4 % to 18.1 %, which is the largest of any known photochromic compound.

Phytochrome proteins regulate many photoresponses of plants and microorganisms. Light absorption causes isomerization of the biliverdin chromophore, which triggers a series of structural changes to activate the signaling domains of the protein. However, the structural changes are elusive, and therefore the molecular mechanism of signal transduction remains poorly understood. Here, we apply two-color step-scan infrared spectroscopy to the bacteriophytochrome from Deinococcus radiodurans. We show by recordings in H2O and D2O that the hydrogen bonds to the biliverdin D-ring carbonyl become disordered in the first intermediate (Lumi-R) forming a dynamic microenvironment, then completely detach in the second intermediate (Meta-R), and finally reform in the signaling state (Pfr). The spectra reveal via isotope labeling that the refolding of the conserved “PHY-tongue” region occurs with the last transition between Meta-R and Pfr. Additional changes in the protein backbone are detected already within microseconds in Lumi-R. Aided by molecular dynamics simulations, we find that a strictly conserved salt bridge between an arginine of the PHY tongue and an aspartate of the chromophore binding domains is broken in Lumi-R and the arginine is recruited to the D-ring C═O. This rationalizes how isomerization of the chromophore is linked to the global structural rearrangement in the sensory receptor. Our findings advance the structural understanding of phytochrome photoactivation. peerReviewed

When photoactive molecules interact strongly with confined light modes, new hybrid light–matter states may form: the polaritons. These polaritons are coherent superpositions of excitations of the molecules and of the cavity photon. Recently, polaritons were shown to mediate energy transfer between chromophores at distances beyond the Forster limit. Here we explore the potential of strong coupling for light-harvesting applications by means of atomistic molecular dynamics simulations of mixtures of photoreactive and non-photo-reactive molecules strongly coupled to a single confined light mode. These molecules are spatially separated and present at different concentrations. Our simulations suggest that while the excitation is initially fully delocalized over all molecules and the confined light mode, it very rapidly localizes onto one of the photoreactive molecules, which then undergoes the reaction.

Red‐light photosensory proteins, phytochromes, link light activation to biological functions by interconverting between two conformational states. For this, they undergo large‐scale secondary and tertiary changes which follow small‐scale Z to E bond photoisomerization of the covalently bound bilin chromophore. The complex network of amino acid interactions in the chromophore‐binding pocket plays a central role in this process. Highly conserved Y263 and H290 have been found to be important for the photoconversion yield, while H260 has been identified as important for bilin protonation and proton transfer steps. Here, we focus on the roles these amino acids are playing in preserving the chemical properties of bilin in the resting Pr state of the photosensory unit of a bacteriophytochrome from Deinococcus radiodurans. By using pH‐dependent UV‐Vis spectroscopy and spectral decomposition modeling, we confirm the importance of H260 for biliverdin protonation. Further, we demonstrate that in the canonical bacteriophytochromes, the pKa value of the phenol group of the Y263 is uncommonly low. This directly influences the protonation of the bilin molecule and likely the functional properties of the protein. Our study expands the understanding of the tight interplay between the nearby amino acids and bilin in the phytochrome family. peerReviewed

The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that in both states the protonated form of the chromophore dominates, we also find that a minor population with a deprotonated D-ring could contribute to the red-shifted tail in the absorption spectra. peerReviewed

Phytochrome proteins translate light into biochemical signals in plants, fungi and microorganisms. Light cues are absorbed by a bilin chromophore, leading to an isomerization and a rotation of the D-ring. This relays the signal to the protein matrix. A set of amino acids, which is conserved across the phytochrome superfamily, holds the chromophore in the binding pocket. However, the functional role of many of these amino acids is not yet understood. Here, we investigate the hydrogen bonding network which surrounds the D-ring of the chromophore in the resting (Pr) state. We use UV/vis spectroscopy, infrared absorption spectroscopy and X-ray crystallography to compare the photosensory domains from Deinococcus radiodurans, the phytochrome 1 from Stigmatella aurantiaca, and a D. radiodurans H290T mutant. In the latter two, an otherwise conserved histidine next to the D-ring is replaced by a threonine. Our infrared absorption data indicate that the carbonyl of the D-ring is more strongly coordinated by hydrogen bonds when the histidine is missing. This is in apparent contrast with the crystal structure of the PAS–GAF domain of phytochrome 1 from S. aurantiaca (pdb code 4RPW), which did not resolve any obvious binding partners for the D-ring carbonyl. We present a new crystal structure of the H290T mutant of the PAS–GAF from D. radiodurans phytochrome. The 1.4 Å-resolution structure reveals additional water molecules, which fill the void created by the mutation. Two of the waters are significantly disordered, suggesting that flexibility might be important for the photoconversion. Finally, we report a spectral analysis which quantitatively explains why the histidine-less phytochromes do not reach equal Pfr-type absorption in the photoequilibrium compared to the Deinococcus radiodurans wild-type protein. The study highlights the importance of water molecules and the hydrogen bonding network around the chromophore for controlling the isomerization reaction and spectral properties of phytochromes. peerReviewed

When terrigenous dissolved organic carbon (tDOC) rich in chromophoric dissolved organic matter (tCDOM) enters the ocean, solar radiation mineralizes it partially into dissolved inorganic carbon (DIC). This study addresses the amount and the rates of DIC photoproduction from tDOC and the area of ocean required to photomineralize tDOC. We collected water samples from 10 major rivers, mixed them with artificial seawater, and irradiated them with simulated solar radiation to measure DIC photoproduction and the photobleaching of tCDOM. The linear relationship between DIC photoproduction and tCDOM photobleaching was used to estimate the amount of photoproduced DIC from the tCDOM fluxes of the study rivers. Solar radiation was estimated to mineralize 12.5 +/- 3.7 Tg C yr(-1) (10 rivers)(-1) or 18 +/- 8% of tDOC flux. The irradiation experiments also approximated typical apparent spectral quantum yields for DIC photoproduction (phi(lambda)) over the entire lifetime of the tCDOM. Based on phi(lambda)s and the local solar irradiances in river plumes, the annual areal DIC photoproduction rates from tDOC were calculated to range from 52 +/- 4 (Lena River) to 157 +/- 2 mmol C m(-2) yr(-1) (Mississippi River). When the amount of photoproduced DIC was divided by the areal rate, 9.6 +/- 2.5 x 10(6) km(2) of ocean was required for the photomineralization of tDOC from the study rivers. Extrapolation to the global tDOC flux yields 45 (31-58) Tg of photoproduced DIC per year in the river plumes that cover 34 (25-43) x 10(6) km(2) of the ocean.

When photoactive molecules interact strongly with confined light modes, new hybrid light-matter states may form: the polaritons. These polaritons are coherent superpositions of excitations of the molecules and of the cavity photon. Recently, polaritons were shown to mediate energy transfer between chromophores at distances beyond the Förster limit. Here we explore the potential of strong coupling for light-harvesting applications by means of atomistic molecular dynamics simulations of mixtures of photoreactive and non-photo-reactive molecules strongly coupled to a single confined light mode. These molecules are spatially separated and present at different concentrations. Our simulations suggest that while the excitation is initially fully delocalized over all molecules and the confined light mode, it very rapidly localizes onto one of the photoreactive molecules, which then undergoes the reaction. peerReviewed

Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics in PYP at two excitation wavelengths (435 and 475 nm) with a dual-excitation-wavelength-interleaved pump–probe technique. Multicompartment global analysis of these data demonstrates that the excited-state photochemistry of PYP depends subtly, but convincingly, on excitation wavelength with similar kinetics with distinctly different spectral features, including a shifted ground-state beach and altered stimulated emission oscillator strengths and peak positions. Three models involving multiple excited states, vibrationally enhanced barrier crossing, and inhomogeneity are proposed to interpret the observed excitation-wavelength dependence of the data. Conformational heterogeneity was identified as the most probable model, which was supported with molecular mechanics simulations that identified two levels of inhomogeneity involving the orientation of the R52 residue and different hydrogen bonding networks with the p-coumaric acid chromophore. Quantum calculations were used to confirm that these inhomogeneities track to altered spectral properties consistent with the experimental results. peerReviewed

We report on the complex of a noble-gas hydride HXeOH with carbon monoxide. This species is prepared via the annealing-induced H + Xe + OH···CO reaction in a xenon matrix, the OH···CO complexes being produced by VUV photolysis of the H2O···CO complexes. The H–Xe stretching mode of the HXeOH···CO complex absorbs at 1590.3 cm–1 and it is blue-shifted by 12.7 cm–1 from the H–Xe stretching band of HXeOH monomer. The observed blue shift indicates the stabilization of the H–Xe bond upon complexation, which is characteristic of complexes of noble-gas hydrides. The HXeOH···CO species is the first complex of a noble-gas hydride with carbon monoxide and the second observed complex of HXeOH. On the basis of the MP2/aug-cc-pVTZ-PP calculations, the experimental complex is assigned to the structure, where the carbon atom of CO interacts with the oxygen atom of HXeOH. peerReviewed

In surface waters, solar radiation can photochemically mineralise the dissolved organic carbon (DOC, a measure of dissolved organic matter, DOM) to dissolved inorganic carbon (DIC). This DIC photoproduction constitutes an essential yet vague flux in the aquatic carbon cycling. The present thesis is based on the empirical assessment of the DOC photochemical reactivity, which was determined as the spectral apparent quantum yields (AQY) for DIC photoproduction. First, AQYs were determined in DOM solutions to quantify the impact of pH and DOM-associated iron. Then boreal lake waters were used for assessing the alteration of DOC photoreactivity due to water quality and catchment property. By simulating DIC production, further, AQYs were used to approximate the photomineralisation of terrigenous DOC (tDOC) in coastal waters. Finally, the experimental protocols determining AQY were compared by four laboratories. The results demonstrated the variation of AQYs triggered by the laboratory-specific procedures was less than that across the examined inland waters. Up to 86 % of the DIC photoproduction in DOM solutions can be justified by iron-stimulated photoreactions with acidic pH, while the effect was negligible at pH > 7. This interaction between iron and acidity was similarly influential on DOC photoreactivity in boreal lake waters. Across lakes, the DOC photoreactivity was varied relevant to the water quality and catchment land use patterns. A high DOC photoreactivity can be expected when the contents of DOC and chromophoric DOM are high, more so in small lakes enriched by peaty soils. Although DOC photoreactivity in lakes was higher, the estimates revealed that solar radiation mineralised far more tDOC in marine waters, which may be attributed to the extensive spreading of tDOC during mixing over the coastal ocean.

This thesis presents a study focused on interactions of femtosecond laser pulses with graphene, a one atom thick carbon membrane. Graphene, which exhibits exceptional electronic and optoelectronic properties, could provide considerable advantage over current silicon-based electronics. Graphene alone, being semi-metal, is not sufficient for electronic applications, but requires modification. For this, a set of methods for modifying and measuring the properties of graphene was developed. With the perspective of making graphene a suitable component for electronics, optoelectronics or photonics, ultrashort laser pulses were used for drawing patterns on graphene. The procedure modifies graphene chemically by photo- oxidation, and physically, by opening a gap to its electronic band structure, changing graphene into a semiconductor. During the process, the band gap can be increased to the extent, where the material becomes an insulator. It was observed in topographic studies that photo-oxidation begins at point-like sources and expands into islands of oxidized graphene, which eventually merge together. This is because the probability that new oxidation occurs in close proximity to an already oxidized area is five orders of magnitude greater than the probability of oxidation elsewhere on graphene. Also, accompanying the oxidation process, a third-order nonlinear signal arising from the graphene, diminishes, providing a contrast mechanism for optical imaging. Additionally, the Raman spectrum shows notable changes in the position of the G-band and increase in intensity of the D-band. Further insight into the patterned structures was obtained with micro--X-ray photoelectron spectroscopy. The initial steps of patterning only change the ratio of sp2/sp3 carbons in the material but the degree of oxidation increases after the islands coalesce. With higher irradiation doses the proportion of hydroxyl and epoxide groups increases, finally reaching the level of ~65 %. The Four-wave mixing (FWM) signal of graphene was monitored during the oxidation process. By utilizing the extraordinarily strong non-linear optical response of graphene FWM spectroscopy was combined with wide-field microscopy, allowing the patterning process to be followed in real-time. Femtosecond wide-field FWM microscopy was proven as fast large area imaging technique for characterization of graphene and observing changes in graphene in real-time. Time-resolved coherent anti-Stokes Raman scattering measurement (CARS) was applied to graphene and a G-mode dephasing time was recorded. Additionally, it was shown that by utilizing BOXCARS excitation geometry various nonlinear optical processes could be unambiguously separated and measured simultaneously. The short dephasing time (T2/2) of the G-mode (325 fs) was explained with dynamically changing G-mode frequency and width accompanied with relaxation of excited charge carrier population, due to non- adiabatic coupling between phonons and electrons in graphene.

Plasmonic oligomers can provide profound Fano resonance in their scattering responses. The sub-radiant mode of Fano resonance can result in significant near-field enhancement due to its light trapping capability into the so-called hotspots. Appearance of these highly localized hotspots at the excitation and/or Stokes wavelengths of the analytes makes such oligomers promising SERS active substrates. In this work, we numerically and experimentally investigate optical properties of two disk-type gold oligomers, which have different strength and origin of Fano resonance. Raman analysis of rhodamine 6G and adenine with the presence of the fabricated oligomers clearly indicates that an increment in the strength of Fano resonance can improve the Raman enhancement of an oligomer significantly. Therefore, by suitable engineering of Fano lineshape, one can achieve efficient SERS active substrates with spatially localized hotspots.

Organic carbon (OC) depleted in 13 C is a widely used tracer for terrestrial organic matter (OM) in aquatic sys- tems. Photochemical reactions can, however, change δ 13 C of dissolved organic carbon (DOC) when chromophoric, aromatic-rich terrestrial OC is selectively mineralized. We assessed the robustness of the δ 13 C signature of DOC ( δ 13 C DOC ) as a tracer for terrestrial OM by estimating its change during the photobleaching of chromophoric DOM (CDOM) from 10 large rivers. These rivers cumulatively ac- count for approximately one-third of the world’s freshwater discharge to the global ocean. Photobleaching of CDOM by simulated solar radiation was associated with the photochem- ical mineralization of 16 to 43 % of the DOC and, by prefer- entially removing compounds depleted in 13 C, caused a 1 to 2.9 ‰ enrichment in δ 13 C in the residual DOC. Such solar- radiation-induced photochemical isotopic shift could bias the calculations of terrestrial OM discharge in coastal oceans to- wards the marine end-member. Shifts in terrestrial δ 13 C DOC should be taken into account when constraining the terres- trial end-member in global calculation of terrestrially derived DOM in the world ocean. peerReviewed

Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light.