The role of the correlated motion(s) of the chromophore in photoswitching of green and red forms of the photoconvertible fluorescent protein mSAASoti.

Wild-type SAASoti and its monomeric variant mSAASoti can undergo phototransformations, including reversible photoswitching of the green form to a nonfluorescent state and irreversible green-to-red photoconversion. In this study, we extend the photochemistry of mSAASoti variants to enable reversible photoswitching of the red form. This result is achieved by rational and site-saturated mutagenesis of the M163 and F177 residues. In the case of mSAASoti it is M163T substitution that leads to the fastest switching and the most photostable variant, and reversible photoswitching can be observed for both green and red forms when expressed in eukaryotic cells. We obtained a 13-fold increase in the switching efficiency with the maximum switching contrast of the green form and the appearance of comparable switching of the red form for the C21N/M163T mSAASoti variant. The crystal structure of the C21N mSAASoti in its green on-state was obtained for the first time at 3.0 Å resolution, and it is in good agreement with previously calculated 3D-model. Dynamic network analysis reveals that efficient photoswitching occurs if motions of the 66H residue and phenyl fragment of chromophore are correlated and these moieties belong to the same community.

Selective enhancement of (6-4) photoproduct formation in dithymine dinucleotides driven by specific sugar puckering.

Four dinucleotide analogs of thymidylyl(3'-5')thymidine (TpT) have been designed and synthesized with a view to increase the selectivity, with respect to CPD, of efficient UV-induced (6-4) photoproduct formation. The deoxyribose residues of these analogs have been modified to increase north and south conformer populations at 5'- and 3'-ends, respectively. Dinucleotides whose 5'-end north population exceeds ca. 60% and whose 3'-end population is almost completely south display a three-fold selective enhancement in (6-4) adduct production when exposed to UV radiation, compared to TpT. These experimental results undoubtedly provide robust foundations for studying the singular ground-state proreactive species involved in the (6-4) photoproduct formation mechanism.

Reassessing the Quantum Yield and Reactivity of Triplet-State Dissolved Organic Matter via Global Kinetic Modeling.

Measuring the quantum yield and reactivity of triplet-state dissolved organic matter (3DOM*) is essential for assessing the impact of DOM on aquatic photochemical processes. However, current 3DOM* quantification methods require multiple fitting steps and rely on steady-state approximations under stringent application criteria, which may introduce certain inaccuracies in the estimation of DOM photoreactivity parameters. Here, we developed a global kinetic model to simulate the reaction kinetics of the hv/DOM system using four DOM types and 2,4,6-trimethylphenol as the probe for 3DOM*. Analyses of residuals and the root-mean-square error validated the exceptional precision of the new model compared to conventional methods. 3DOM* in the global kinetic model consistently displayed a lower quantum yield and higher reactivity than those in local regression models, indicating that the generation and reactivity of 3DOM* have often been overestimated and underestimated, respectively. The global kinetic model derives parameters by simultaneously fitting probe degradation kinetics under different conditions and considers the temporally increasing concentrations of the involved reactive species. It minimizes error propagation and offers insights into the interactions of different species, thereby providing advantages in accuracy, robustness, and interpretability. This study significantly advances the understanding of 3DOM* behavior and provides a valuable kinetic model for aquatic photochemistry research.

Photocobilins integrate B12 and bilin photochemistry for enzyme control.

Photoreceptor proteins utilise chromophores to sense light and trigger a biological response. The discovery that adenosylcobalamin (or coenzyme B12) can act as a light-sensing chromophore heralded a new field of B12-photobiology. Although microbial genome analysis indicates that photoactive B12-binding domains form part of more complex protein architectures, regulating a range of molecular-cellular functions in response to light, experimental evidence is lacking. Here we identify and characterise a sub-family of multi-centre photoreceptors, termed photocobilins, that use B12 and biliverdin (BV) to sense light across the visible spectrum. Crystal structures reveal close juxtaposition of the B12 and BV chromophores, an arrangement that facilitates optical coupling. Light-triggered conversion of the B12 affects quaternary structure, in turn leading to light-activation of associated enzyme domains. The apparent widespread nature of photocobilins implies involvement in light regulation of a wider array of biochemical processes, and thus expands the scope for B12 photobiology. Their characterisation provides inspiration for the design of broad-spectrum optogenetic tools and next generation bio-photocatalysts.

Couple-close construction of polycyclic rings from diradicals.

Heteroarenes are ubiquitous motifs in bioactive molecules, conferring favourable physical properties when compared to their arene counterparts1-3. In particular, semisaturated heteroarenes possess attractive solubility properties and a higher fraction of sp3 carbons, which can improve binding affinity and specificity. However, these desirable structures remain rare owing to limitations in current synthetic methods4-6. Indeed, semisaturated heterocycles are laboriously prepared by means of non-modular fit-for-purpose syntheses, which decrease throughput, limit chemical diversity and preclude their inclusion in many hit-to-lead campaigns7-10. Herein, we describe a more intuitive and modular couple-close approach to build semisaturated ring systems from dual radical precursors. This platform merges metallaphotoredox C(sp2)-C(sp3) cross-coupling with intramolecular Minisci-type radical cyclization to fuse abundant heteroaryl halides with simple bifunctional feedstocks, which serve as the diradical synthons, to rapidly assemble a variety of spirocyclic, bridged and substituted saturated ring types that would be extremely difficult to make by conventional methods. The broad availability of the requisite feedstock materials allows sampling of regions of underexplored chemical space. Reagent-controlled radical generation leads to a highly regioselective and stereospecific annulation that can be used for the late-stage functionalization of pharmaceutical scaffolds, replacing lengthy de novo syntheses.

Photochemistry in Medicinal Chemistry and Chemical Biology.

Photochemistry has emerged as a transformative force in organic chemistry, significantly expanding the chemical space accessible for medicinal chemistry. Light-induced reactions enable the efficient synthesis of intricate organic structures and have found applications throughout the different stages of the drug discovery and development processes. Moreover, photochemical techniques provide innovative solutions in chemical biology, allowing precise spatiotemporal drug activation and targeted delivery. In this Perspective, we highlight the already numerous remarkable applications and the even more promising future of photochemistry in medicinal chemistry and chemical biology.

Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct.

Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as "K". We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics.

Crystal structure reveals the binding mode and selectivity of a photoswitchable ligand for the adenosine A2A receptor.

Rational synthetic expansion of photoresponsive ligands is important for photopharmacological studies. Adenosine A2A receptor (A2AR) is stimulated by adenosine and related in Parkinson's disease and other diseases. Here, we report the crystal structure of the A2AR in complex with the novel photoresponsive ligand photoNECA (blue) at 3.34 Å resolution. PhotoNECA (blue) was designed for this structural study and the cell-based assay showed a photoresponsive and receptor selective characteristics of photoNECA (blue) for A2AR. The crystal structure explains the binding mode, photoresponsive mechanism and receptor selectivity of photoNECA (blue). Our study would promote not only the rational design of photoresponsive ligands but also dynamic structural studies of A2AR.

How electron tunneling and uphill excitation energy transfer support photochemistry in Halomicronema hongdechloris.

Halomicronema hongdechloris, the first cyanobacterium reported to produce the red-shifted chlorophyll f (Chl f) upon acclimation to far-red light, demonstrates remarkable adaptability to diverse light conditions. The photosystem II (PS II) of this organism undergoes reversible changes in its Chl f content, ranging from practically zero under white-light culture conditions to a Chl f: Chl a ratio of up to 1:8 when exposed to far-red light (FRL) of 720-730 nm for several days. Our ps time- and wavelength-resolved fluorescence data obtained after excitation of living H. hongdechloris cells indicate that the Soret band of a far-red (FR) chlorophyll involved in charge separation absorbs around 470 nm. At 10 K, the fluorescence decay at 715-720 nm is still fast with a time constant of 165 ps indicating an efficient electron tunneling process. There is efficient excitation energy transfer (EET) from 715-720 nm to 745 nm with the latter resulting from FR Chl f, which mainly functions as light-harvesting pigment upon adaptation to FRL. From there, excitation energy reaches the primary donor in the reaction center of PS II with an energetic uphill EET mechanism inducing charge transfer. The fluorescence data are well explained with a secondary donor PD1 represented by a red-shifted Chl a molecule with characteristic fluorescence around 715 nm and a more red-shifted FR Chl f with fluorescence around 725 nm as primary donor at the ChlD1 or PD2 position.

Modeling pH-Dependent Biomolecular Photochemistry.

The tuning mechanism of pH can be extremely challenging to model computationally in complex biological systems, especially with respect to the photochemical properties. This article reports a protocol aimed at modeling pH-dependent photodynamics using a combination of constant-pH molecular dynamics and semiclassical nonadiabatic molecular dynamics simulations. With retinal photoisomerization in Anabaena sensory rhodopsin (ASR) as a testbed, we show that our protocol produces pH-dependent photochemical properties, such as the isomerization quantum yield or decay rates. We decompose our results into single-titrated residue contributions, identifying some key tuning amino acids. Additionally, we assess the validity of the single protonation state picture to represent the system at a given pH and propose the most populated protein charge state as a compromise between cost and accuracy.

Rolling circle amplification assisted CRISPR/Cas12a dual-cleavage photoelectrochemical biosensor for highly sensitive detection of miRNA-21.

BACKGROUND: MicroRNA-21 has been determined to be the only microRNA overexpressed in 11 types of solid tumors, making it an excellent candidate as a biomarker for disease diagnosis and therapy. Photoelectrochemical (PEC) biosensors have been widely used for quantification of microRNA-21. However, most PEC biosensing processes still suffer from some problems, such as the difficulty of avoiding the influence of interferents in complex matrices and the false-positive signals. There is a pressing need for establishing a sensitive and stable PEC method to detect microRNA-21. RESULTS: Herein, a nicking endonuclease-mediated rolling circle amplification (RCA)-assisted CRISPR/Cas12a PEC biosensor was fabricated for ultrasensitive detection of microRNA-21. The p-p type heterojunction PbS QDs/Co3O4 polyhedra were prepared as the quencher, thus the initial PEC signal attained the "off" state. Furthermore, the target was specifically identified and amplified by the RCA process. Then, its product single-stranded DNA S1 activated the cis- and trans-cleavage abilities of CRISPR/Cas12a, leading to almost all of the PbS QDs/Co3O4 polyhedra to leave the electrode surface, the p-n semiconductor quenching effect to be disrupted, and the signal achieving the "super-on" state. This pattern of PEC signal changed from "off" to "on" eliminated the interference of false-positive signals. The proposed PEC biosensor presented a satisfactory linear relationship ranging from 1 fM to 10 nM with a detection limit of 0.76 fM (3 Sb/N). SIGNIFICANCE AND NOVELTY: With innovatively synthesized PbS QDs/Co3O4 polyhedra as the effective quencher for PEC signal, the CRISPR/Cas12a dual-cleavage PEC biosensor possessed excellent selectivity, stability and repeatability. Furthermore, the detection of various miRNAs can be realized by changing the relevant base sequences in the constructed PEC biosensor. It also provides a powerful strategy for early clinical diagnosis and biomedical research.

Combining PSII photochemistry and hydraulics improves predictions of photosynthesis and water use from mild to lethal drought.

Rising temperatures and increases in drought negatively impact the efficiency and sustainability of both agricultural and forest ecosystems. Although hydraulic limitations on photosynthesis have been extensively studied, a solid understanding of the links between whole plant hydraulics and photosynthetic processes at the cellular level under changing environmental conditions is still missing, hampering our predictive power for plant mortality. Here, we examined plant hydraulic traits and CO2 assimilation rate under progressive water limitation by implementing Photosystem II (PSII) dynamics with a whole plant process model (TREES). The photosynthetic responses to plant water status were parameterized based on measurements of chlorophyll a fluorescence, gas exchange and water potential for Brassica rapa (R500) grown in a greenhouse under fully watered to lethal drought conditions. The updated model significantly improved predictions of photosynthesis, stomatal conductance and leaf water potential. TREES with PSII knowledge predicted a larger hydraulic safety margin and a decrease in percent loss of conductivity. TREES predicted a slower decrease in leaf water potential, which agreed with measurements. Our results highlight the pressing need for incorporating PSII drought photochemistry into current process models to capture cross-scale plant water dynamics from cell to whole plant level.

Multimodal Carbon Monoxide Photorelease from Flavonoids.

Photooxygenation of flavonoids leads to the release of carbon monoxide (CO). Our structure-photoreactivity study, employing several structurally different flavonoids, including their 13C-labeled analogs, revealed that CO can be produced via two completely orthogonal pathways, depending on their hydroxy group substitution pattern and the reaction conditions. While photooxygenation of the enol 3-OH group has previously been established as the CO liberation channel, we show that the catechol-type hydroxy groups of ring B can predominantly participate in photodecarbonylation.

A light-sensitive protein-based wearable pH biometer.

Bacteriorhodopsin is a biological material with excellent photosensitivity properties. It can directly convert optical signals into electrical signals and is widely used in various biosensors. Here, we present a bR-based wearable pH biometer that can be used to monitor wound infection. The mechanism of the pH-sensitive effect of the bR electrode is explained, which generates a transient photovoltage under light irradiation and a negative photovoltage when the lamp is turned off. Since the photoelectric signal of bR is affected by different pH values, the photovoltage is changed by adjusting the pH value. The ratio (Vn/Vp) of negative photovoltage (Vn) to positive photovoltage (Vp) has a good linear relationship (R2 = 0.9911) in the pH range of 4.0-10.0. In vitro experiments using rats as a model confirmed that this wearable pH biometer can monitor pH changes that occur in wound infection.

pH-Dependent Aqueous-Phase Brown Carbon Formation: Rate Constants and Implications for Solar Absorption and Atmospheric Photochemistry.

Aqueous-phase reactions of α-dicarbonyls with amines or ammonium have been identified as important sources of secondary brown carbon (BrC). However, the kinetics of BrC formation and the effects of pH are still not very clear. In this study, the kinetics of BrC formation by aqueous reactions of α-dicarbonyls (glyoxal and methylglyoxal) with ammonium, amino acids, or alkylamines in bulk solution at different pH values are investigated. Our results reveal pH-parameterized BrC production rate constants, kBrCII (m-1 [M]-2 s-1), based on the light absorption between 300 and 500 nm: log10(kBrCII) = (1.0 ± 0.1) × pH - (7.4 ± 1.0) for reactions with glyoxal and log10(kBrCII) = (1.0 ± 0.1) × pH - (6.3 ± 0.9) for reactions with methylglyoxal. The linear slopes closing to 1.0 indicate that BrC formation is governed by the nitrogen nucleophilic addition pathway. Consequently, the absorptivities of the produced BrC increase exponentially with the increase of pH. BrC from reactions with methylglyoxal at higher pH (≥6.5) exhibits optical properties comparable to BrC from biomass burning or coal combustion, categorized as the "weakly" absorbing BrC, while BrC from reactions with methylglyoxal at lower pH (<6.0) or reactions with glyoxal (pH 5.0-7.0) falls into the "very weakly" absorbing BrC. The pH-dependent BrC feature significantly affects the solar absorption ability of the produced BrC and thus the atmospheric photochemical processes, e.g., BrC produced at pH 7.0 absorbs 14-16 times more solar power compared to that at pH 5.0, which in turn could lead to a decrease of 1 order of magnitude in the photolysis rate constants of O3 and NO2.

Dysphania ambrosioides (L.) Mosyakin and Clemants: bridging traditional knowledge, photochemistry, preclinical investigations, and toxicological validation for health benefits.

Dysphania ambrosioides L. (Chenopodiaceae) is a Moroccan medicinal plant known locally as "M'Khinza." It is widely used in traditional medicine to treat numerous ailments, such as diabetes, digestive disorders, fever, fertility problems, immune disorders, hypertension, bronchitis, respiratory conditions, pharyngitis, cough, and flu. As part of this review, comprehensive preclinical investigations, including in vitro, in vivo, and in silico studies, were conducted to better understand the mechanisms of action of D. ambrosioides. Additionally, the phytochemical profile of the plant was examined, highlighting the presence of certain bioactive secondary metabolites. The information was gathered from electronic data sources such as Web of Science, PubMed, Science Direct, Scopus, Springer Link, and Google Scholars. Numerous studies have mentioned the pharmacological properties of D. ambrosioides, including its antioxidant, anti-inflammatory, antiparasitic, antiviral, antibacterial, and antifungal activities. Furthermore, research has also suggested its potential as an anticancer, antidiabetic, and vasorelaxant agent. Phytochemical characterization of D. ambrosioides has revealed the presence of over 96 major bioactive compounds, including terpenoids, polyphenols, flavonoids, alkaloids, and fatty acids. As for the toxicity of this plant, it is dose-dependent. Furthermore, more in-depth pharmacological studies are needed to establish the mechanisms of action of this plant more accurately before considering clinical trials. In conclusion, this review highlights the traditional use of D. ambrosioides in Moroccan medicine and emphasizes its potential pharmacological properties. However, to fully harness its therapeutic potential, further research, both in terms of chemistry and pharmacology, is necessary. These future studies could help identify new active compounds and provide a better understanding of the mechanisms of action of this plant, thus opening new prospects for its pharmaceutical application.

Primary processes in photophysics and photochemistry of a potential light-activated anti-cancer dirhodium complex.

Photophysics and photochemistry of a potential light-activated cytotoxic dirhodium complex [Rh2(µ-O2CCH3)2(bpy)(dppz)](O2CCH3)2, where bpy = 2,2'-bipyridine, dppz = dipyrido[3,2-a:2',3'-c]phenazine (Complex 1 or Rh2) in aqueous solutions was studied by means of stationary photolysis and time-resolved methods in time range from hundreds of femtoseconds to microseconds. According to the literature, Complex 1 demonstrates both oxygen-dependent (due to singlet oxygen formation) and oxygen-independent cytotoxicity. Photoexchange of an acetate ligand to a water molecule was the only observed photochemical reaction, which rate was increased by oxygen removal from solutions. Photoexcitation of Complex 1 results in the formation of the lowest triplet electronic excited state, which lifetime is less than 10 ns. This time is too short for diffusion-controlled quenching of the triplet state by dissolved oxygen resulting in 1O2 formation. We proposed that singlet oxygen is produced by photoexcitation of weakly bound van der Waals complexes [Rh2…O2], which are formed in solutions. If this is true, no oxygen-independent light-induced cytotoxicity of Complex 1 exists. Residual cytotoxicity deaerated solutions are caused by the remaining [Rh2…O2] complexes.

Similarities and Differences in Photochemistry of Type I and Type II Rhodopsins.

The diversity of the retinal-containing proteins (rhodopsins) in nature is extremely large. Fundamental similarity of the structure and photochemical properties unites them into one family. However, there is still a debate about the origin of retinal-containing proteins: divergent or convergent evolution? In this review, based on the results of our own and literature data, a comparative analysis of the similarities and differences in the photoconversion of the rhodopsin of types I and II is carried out. The results of experimental studies of the forward and reverse photoreactions of the bacteriorhodopsin (type I) and visual rhodopsin (type II) rhodopsins in the femto- and picosecond time scale, photo-reversible reaction of the octopus rhodopsin (type II), photovoltaic reactions, as well as quantum chemical calculations of the forward photoreactions of bacteriorhodopsin and visual rhodopsin are presented. The issue of probable convergent evolution of type I and type II rhodopsins is discussed.

Visible-Light Mediated Deoxygenation of Carboxylic Acid for Late-Stage Peptide Modification Targeting Dehydroalanine.

A visible-light mediated deoxygenative radical addition of carboxylic acids to dehydroalanines has been disclosed. The method can be used in ß-acyl alanine derivative synthesis, including those chiral and deuterated variants, and late-stage peptide modification with various functional groups, both in the homogeneous phase and on the resin in SPPS. It provides a new tool kit for rapid construction of bioactive peptide analogues, which has been demonstrated by modification of the antimicrobial peptide Feleucin-K3.

Rapid Release of Halocarbons from Saline Water by Iron-Based Photochemistry.

Methyl halides play important roles in stratospheric ozone depletion, but their formation mechanisms are not well defined. This study demonstrated that iron-based photochemistry significantly enhanced alkyl halide production by promoting the reaction of the representative monomer of lignin with halide ions in saline water under solar light irradiation. The methyl chloride (CH3Cl) emission from the light/Fe(III) process was 2 orders of magnitude higher than dark treatment and in the absence of iron. In addition, bromide and iodide showed better reactivity in the formation of the corresponding methyl bromide (CH3Br) and methyl iodide (CH3I). Alkyl halides identified from seawater, brackish water, and salt pan water under sunlight irradiation were positively correlated with the Fe(III) concentrations, indicating that iron-based photochemistry is ubiquitous. This work suggested that the photoinduced formation of methyl radical and redox cycling of iron triggered by the Fenton-like reaction are responsible for the enhanced release of alkyl halides. This study represents an abiotic formation pathway of alkyl halides, which accounts for a portion of the unidentified sources of halocarbons in the ocean.