Blind instrument response function identification from fluorescence decays

Time-resolved fluorescence spectroscopy plays a crucial role when studying dynamic properties of complex photochemical systems. Nevertheless, the analysis of measured time decays and the extraction of exponential lifetimes often requires either the experimental assessment or the modeling of the instrument response function (IRF). However, the intrinsic nature of the IRF in the measurement process, which may vary across measurements due to chemical and instrumental factors, jeopardizes the results obtained by reconvolution approaches. In this paper, we introduce a novel methodology, called blind instrument response function identification (BIRFI), which enables the direct estimation of the IRF from the collected data. It capitalizes on the properties of single exponential signals to transform a deconvolution problem into a well-posed system identification problem. To delve into the specifics, we provide a step-by-step description of the BIRFI method and a protocol for its application to fluorescence decays. The performance of BIRFI is evaluated using simulated and time-correlated single-photon counting data. Our results demonstrate that the BIRFI methodology allows an accurate recovery of the IRF, yielding comparable or even superior results compared with those obtained with experimental IRFs when they are used for reconvolution by parametric model fitting.

Dynamics of the energy transfer involved in a diarylethene-perylenebisimide dyad: comparison between the molecule and the nanoparticle level

Photochromic materials are widely used to achieve fluorescence photoswitching. Understanding the energy transfer processes occurring in these systems would be an advantage for their use and better optimization of their properties. In this scope, we studied a diarylethene-perylenebisimide (DAE-PBI) dyad that presents a bright red emission and a large ON-OFF contrast, both in solution and in an aqueous suspension of nanoparticles (NPs). Using ultrafast transient absorption spectroscopy, the excited state dynamics was characterized for this dyad in THF solution and compared to its behavior in NPs state. An efficient energy transfer process between the PBI fluorophore and the DAE photochromic unit in its closed form was demonstrated, occurring in a few hundreds of femtoseconds.

Cloning and structural basis of fluorescent protein color variants from identical species of sea anemone, Diadumene lineata

Diadumene lineata is a colorful sea anemone with orange stripe tissue of the body column and plain tentacles with red lines. We subjected Diadumene lineata to expression cloning and obtained genes encoding orange (OFP: DiLiFP561) and red fluorescent proteins (RFPs: DiLiFP570 and DiLiFP571). These proteins formed obligatory tetramers. All three proteins showed bright fluorescence with the brightness of 58.3 mM^-1·cm^-1 (DiLiFP561), 43.9 mM^-1·cm^-1 (DiLiFP570), and 31.2 mM^-1·cm^-1 (DiLiFP571), which were equivalent to that of commonly used red fluorescent proteins. Amplitude-weighted average fluorescence lifetimes of DiLiFP561, DiLiFP570 and DiLiFP571 were determined as 3.7, 3.6 and 3.0 ns. We determined a crystal structure of DiLiFP570 at 1.63 Å resolution. The crystal structure of DiLiFP570 revealed that the chromophore has an extended π-conjugated structure similar to that of DsRed. Most of the amino acid residues surrounding the chromophore were common between DiLiFP570 and DiLiFP561, except M159 of DiLiFP570 (Lysine in DiLiFP561), which is located close to the chromophore hydroxyl group. Interestingly, a similar K-to-M substitution has been reported in a red-shifted variant of DsRed (mRFP1). It is a striking observation that the naturally evolved color-change variants are consistent with the mutation induced via protein engineering processes. The newly cloned proteins are promising as orange and red fluorescent markers for imaging with long fluorescence lifetime.

Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement

Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, one of the key parameters that dictate the achievable resolution in nanoscopy applications, and chromophore conformation in the non-fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off-state conformations, trans1 and trans2, located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off-state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high-level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue- and red-shifts of the absorption bands associated to trans1 and trans2, respectively. Thus, due to elimination of trans2, the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two-fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2-V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications.

Structure-function-dynamics relationships in the peculiar Planktothrix PCC7805 OCP1: Impact of his-tagging and carotenoid type

The orange carotenoid protein (OCP) is a photoactive protein involved in cyanobacterial photoprotection. Here, we report on the functional, spectral and structural characteristics of the peculiar Planktothrix PCC7805 OCP (Plankto-OCP). We show that this OCP variant is characterized by higher photoactivation and recovery rates, and a stronger energy-quenching activity, compared to other OCP studied thus far. We characterize the effect of the functionalizing carotenoid and of his-tagging on these reactions, and identify the time scales on which these modifications affect photoactivation. The presence of a his-tag at the C-terminus has a large influence on photoactivation, thermal recovery and PBS-fluorescence quenching, and likewise for the nature of the carotenoid that additionally affects the yield and characteristics of excited states and the ns-s dynamics of photoactivated OCP. By solving the structures of Plankto-OCP in the ECN- and CAN-functionalized states, each in two closely-related crystal forms, we further unveil the molecular breathing motions that animate Plankto-OCP at the monomer and dimer levels. We finally discuss the structural changes that could explain the peculiar properties of Plankto-OCP.

Is orange carotenoid protein photoactivation a single-photon process?

In all published photoactivation mechanisms of orange carotenoid protein (OCP), absorption of a single photon by the orange dark state starts a cascade of red-shifted OCP ground-state intermediates that subsequently decay within hundreds of milliseconds, resulting in the formation of the final red form OCP^R, which is the biologically active form that plays a key role in cyanobacteria photoprotection. A major challenge in deducing the photoactivation mechanism is to create a uniform description explaining both single-pulse excitation experiments, involving single-photon absorption, and continuous light irradiation experiments, where the red-shifted OCP intermediate species may undergo re-excitation. We thus investigated photoactivation of Synechocystis OCP using stationary irradiation light with a biologically relevant photon flux density coupled with nanosecond laser pulse excitation. The kinetics of photoactivation upon continuous and nanosecond pulse irradiation light show that the OCP^R formation quantum yield increases with photon flux density; thus, a simple single-photon model cannot describe the data recorded for OCP in vitro. The results strongly suggest a consecutive absorption of two photons involving a red intermediate with ≈100 millisecond lifetime. This intermediate is required in the photoactivation mechanism and formation of the red active form OCP^R.

Selective population of triplet excited states in heavy-atom-free BODIPY-C60 based molecular assemblies

Photophysical studies on a BODIPY-fullerene-distyryl BODIPY triad (BDP-C₆₀-DSBDP) and its reference dyads (BODIPY-fullerene; BDP-C₆₀ and distyryl BODIPY-fullerene; DSBDP-C₆₀) are presented herein. In the triad, the association of the two chromophore units linked by a fullerene moiety leads to strong near UV-Visible light absorption from 300 to 700 nm. The triplet-excited state was observed upon visible excitation in all these assemblies, and shown to be localized on the C₆₀ or BODIPY moieties. Using quantitative nanosecond transient absorption, we provide a complete investigation on the lifetime and formation quantum yield of the triplet-excited state. In the BDP-C₆₀ dyad, the triplet excited state of C₆₀ (τ = 7 ± 1 μs) was obtained with a quantum yield of 40 ± 8%. For the DSBDP-C₆₀ dyad and BDP-C₆₀-DSBDP triad, a longer-lived triplet excited state with a lifetime of around 250 ± 20 μs centered on the DSBDP moiety was formed, with respective quantum yields of 37 ± 8 and 20 ± 4%. Triplet-triplet annihilation up-conversion is characterized in the BDP-C₆₀ dyad and the bichromophoric triad in the presence of perylene and DSBDP-monomer as respective annihilators. The photo-induced formation of a long-lived ³DSBDP* in the triad coupled with panchromatic light absorption offers potential applications as a heavy-atom-free organic triplet photosensitizer.

Unifying Perspective of the Ultrafast Photodynamics of Orange Carotenoid Proteins from Synechocystis: Peril of High-Power Excitation, Existence of Different S* States, and Influence of Tagging

A substantial number of Orange Carotenoid Protein (OCP) studies have aimed to describe the evolution of singlet excited states leading to the formation of a photoactivated form, OCP^R. The most recent one suggests that 3 ps-lived excited states are formed after the sub-100 fs decay of the initial S₂ state. The S* state, which has the longest reported lifetime of a few to tens of picoseconds, is considered to be the precursor of the first red photoproduct P₁. Here, we report the ultrafast photodynamics of the OCP from Synechocystis PCC 6803 carried out using visible-near infrared femtosecond time-resolved absorption spectroscopy as a function of the excitation pulse power and wavelength. We found that a carotenoid radical cation can form even at relatively low excitation power, obscuring the determination of photoactivation yields for P₁. Moreover, the comparison of green (540 nm) and blue (470 nm) excitations revealed the existence of an hitherto uncharacterized excited state, denoted as S^∼, living a few tens of picoseconds and formed only upon 470 nm excitation. Because neither the P₁ quantum yield nor the photoactivation speed over hundreds of seconds vary under green and blue continuous irradiation, this S^∼ species is unlikely to be involved in the photoactivation mechanism leading to OCP^R. We also addressed the effect of His-tagging at the N- or C-termini on the excited-state photophysical properties. Differences in spectral signatures and lifetimes of the different excited states were observed at a variance with the usual assumption that His-tagging hardly influences protein dynamics and function. Altogether our results advocate for the careful consideration of the excitation power and His-tag position when comparing the photoactivation of different OCP variants and beg to revisit the notion that S* is the precursor of photoactivated OCP^R.

Structural Information about the trans-to-cis Isomerization Mechanism of the Photoswitchable Fluorescent Protein rsEGFP2 Revealed by Multiscale Infrared Transient Absorption

RsEGFP2 is a reversibly photoswitchable fluorescent protein used in super-resolved optical microscopies, which can be toggled between a fluorescent On state and a nonfluorescent Off state. Previous time-resolved ultraviolet-visible spectroscopic studies have shown that the Off-to-On photoactivation extends over the femto- to millisecond time scale and involves two picosecond lifetime excited states and four ground state intermediates, reflecting a trans-to-cis excited state isomerization, a millisecond deprotonation, and protein structural reorganizations. Femto- to millisecond time-resolved multiple-probe infrared spectroscopy (TRMPS-IR) can reveal structural aspects of intermediate species. Here we apply TRMPS-IR to rsEGFP2 and implement a Savitzky-Golay derivative analysis to correct for baseline drift. The results reveal that a subpicosecond twisted excited state precursor controls the trans-to-cis isomerization and the chromophore reaches its final position in the protein pocket within 100 ps. A new step with a time constant of 42 ns is reported and assigned to structural relaxation of the protein that occurs prior to the deprotonation of the chromophore on the millisecond time scale.

Multivariate Curve Resolution Slicing of Multiexponential Time-Resolved Spectroscopy Fluorescence Data

Time-resolved fluorescence spectroscopy (TRFS), i.e., measurement of fluorescence decay curves for different excitation and/or emission wavelengths, provides specific and sensitive local information on molecules and on their environment. However, TRFS relies on multiexponential data fitting to derive fluorescence lifetimes from the measured decay curves and the time resolution of the technique is limited by the instrumental response function (IRF). We propose here a multivariate curve resolution (MCR) approach based on data slicing to perform tailored and fit-free analysis of multiexponential fluorescence decay curves. MCR slicing, taking as a basic framework the multivariate curve resolution-alternating least-squares (MCR-ALS) soft-modeling algorithm, relies on a hybrid bilinear/trilinear data decomposition. A key feature of the method is that it enables the recovery of individual components characterized by decay profiles that are only partially describable by monoexponential functions. For TRFS data, not only pure multiexponential tail information but also shorter time delay information can be decomposed, where the signal deviates from the ideal exponential behavior due to the limited time resolution. The accuracy of the proposed approach is validated by analyzing mixtures of three commercial dyes and characterizing the mixture composition, lifetimes, and associated contributions, even in situations where only ternary mixture samples are available. MCR slicing is also applied to the analysis of TRFS data obtained on a photoswitchable fluorescent protein (rsEGFP2). Three fluorescence lifetimes are extracted, along with the profile of the IRF, highlighting that decomposition of complex systems, for which individual isomers are characterized by different exponential decays, can also be achieved.

Mechanism and dynamics of fatty acid photodecarboxylase

Fatty acid photodecarboxylase (FAP) is a photoenzyme with potential green chemistry applications. By combining static, time-resolved, and cryotrapping spectroscopy and crystallography as well as computation, we characterized Chlorella variabilis FAP reaction intermediates on time scales from subpicoseconds to milliseconds. High-resolution crystal structures from synchrotron and free electron laser x-ray sources highlighted an unusual bent shape of the oxidized flavin chromophore. We demonstrate that decarboxylation occurs directly upon reduction of the excited flavin by the fatty acid substrate. Along with flavin reoxidation by the alkyl radical intermediate, a major fraction of the cleaved carbon dioxide unexpectedly transformed in 100 nanoseconds, most likely into bicarbonate. This reaction is orders of magnitude faster than in solution. Two strictly conserved residues, R451 and C432, are essential for substrate stabilization and functional charge transfer.

Photoactive Organic/Inorganic Hybrid Materials with Nanosegregated Donor-Acceptor Arrays

The synthesis of the first mesogenic donor-acceptor polyoxometalate (POM)-based hybrid is herein described. The structural and electronic properties of the hybrid compound were evaluated through combination of small- and wide-angle X-ray scattering, optical microscopy, electrochemistry and photoluminescence. In the solid state, the compound behaves as a birefringent solid, displaying a lamellar organization in which double-layers of POMs and bis(thiophene)thienothiophene organic donors alternate regularly. Noticeably, the sub-unit organizations in the composite are similar to that observed for the individual POM and organic donor precursors. Photophysical studies show that in the hybrid, the fluorescence of the organic donor unit is considerably quenched both in solution and in the solid state, which is attributed to occurrence of intramolecular charge-separated state.

Control of the Photo-Isomerization Mechanism in 3H-Naphthopyrans to Prevent Formation of Unwanted Long-Lived Photoproducts

In the photochromic reactions of 3H-naphthopyrans, two colored isomers TC (transoid-cis) and TT (transoid-trans) are formed. In terms of optimized photo-switchable materials, synthetic efforts are nowadays evolving toward developing 3H-naphthopyran derivatives that would not be able to photoproduce the long-living transoid-trans, TT, photoproduct. The substitution with a methoxy group at position 10 results in significant reduction of the TT isomer formation yield. The TC photophysics responsible for TT suppression were revealed here using a combination of multi-scale time resolved absorption UV-vis spectroscopy and ab initio calculations. The substitution changes the TC excited-state potential energy landscape, the bicycle-pedal isomerization path is favored over the rotation around a single double bond. The bicycle-pedal path is aborted in halfway to TT formation due to S₁→S₀ internal conversion populating back the TC species in the ground electronic state. This is validated by a shorter TC S₁ state lifetime for methoxy derivative in comparison to that of the parent-unsubstituted compound (0.47 ± 0.05 ps vs. 0.87 ± 0.09 ps) in cyclohexane.

Restriction of the conrotatory motion in photo-induced 6π electrocyclic reaction: formation of the excited state of the closed-ring isomer in the cyclization

The electrocyclic reaction dynamics of a photochromic dithiazolylarylene derivative, 2,3-dithiazolylbenzothiophene (DTA) was investigated by using time-resolved transient absorption and fluorescence spectroscopies. The closed-ring isomer of DTA undergoes cycloreversion through the conical intersection mediating the potential energy surfaces of the excited and ground states, which is in agreement with the Woodward–Hoffmann rules for the electrocyclic reactions of 6π electron systems. On the other hand, a large portion of the open-ring isomer undergoes cyclization along the distinct reaction scheme, in which the cyclization takes place in the excited state manifold leading to the formation of the excited state of the closed-ring isomer. The suppression of the geometrical motion of DTA due to the intramolecular interaction could open a new efficient reaction pathway resulting in the formation of the electronically excited state of the product.

Restriction of the molecular geometry opens up a novel pathway in the cyclization reaction of a photochromic dithiazolylarylene derivative.

Mechanistic Insights into the Triplet Sensitized Photochromism of Diarylethenes

Operating photoswitchable molecules repetitively and reliably is crucial for most of their applications, in particular in (opto)electronic devices, and related to reversibility and fatigue resistance, which both critically depend on the photoisomerization mechanism defined by the substitution pattern. Two diarylethene photoswitches bearing biacetyl triplet sensitizers either at the periphery or at the core were investigated using both stationary as well as transient UV/Vis absorption spectroscopy ranging from the femtosecond to the microsecond time scale. The diarylethene with two biacetyl moieties at the periphery is switching predominantly from the triplet excited state, giving rise to an enhanced fatigue resistance. In contrast, the diarylethene bearing one diketone at the photoreactive inner carbon atom cyclizes from the singlet excited state and shows significantly higher quantum yields for both cyclization and cycloreversion.

All Visible Light Switch Based on the Dimethyldihydropyrene Photochromic Core

Two photoswitchable compounds that can operate under visible light irradiation are prepared and investigated using spectroscopic and computational studies. These all-visible systems are based on the dimethyldihydropyrene (DHP)/cyclophanediene (CPD) photochromic couple connected either to a bipyridine (bpy) unit or to a (tris(bpy)ruthenium(II)) complex through a pyridinium bridge. In these compounds, the DHP to CPD isomerization and the reverse CPD to DHP conversion can be triggered by illumination with red (>630 nm) and blue (460 nm) lights, respectively. The unambiguous and reversible response of these systems triggered by visible light make them potential candidates for biological purposes and electronic devices.

Photoswitching mechanism of a fluorescent protein revealed by time-resolved crystallography and transient absorption spectroscopy

Reversibly switchable fluorescent proteins (RSFPs) serve as markers in advanced fluorescence imaging. Photoswitching from a non-fluorescent off-state to a fluorescent on-state involves trans-to-cis chromophore isomerization and proton transfer. Whereas excited-state events on the ps timescale have been structurally characterized, conformational changes on slower timescales remain elusive. Here we describe the off-to-on photoswitching mechanism in the RSFP rsEGFP2 by using a combination of time-resolved serial crystallography at an X-ray free-electron laser and ns-resolved pump–probe UV-visible spectroscopy. Ten ns after photoexcitation, the crystal structure features a chromophore that isomerized from trans to cis but the surrounding pocket features conformational differences compared to the final on-state. Spectroscopy identifies the chromophore in this ground-state photo-intermediate as being protonated. Deprotonation then occurs on the μs timescale and correlates with a conformational change of the conserved neighbouring histidine. Together with a previous excited-state study, our data allow establishing a detailed mechanism of off-to-on photoswitching in rsEGFP2.

rsEGFP2 is a reversibly photoswitchable fluorescent protein used in super-resolution light microscopy. Here the authors present the structure of an rsEGFP2 ground-state intermediate after excited state-decay that was obtained by nanosecond time-resolved serial femtosecond crystallography at an X-ray free electron laser, and time-resolved absorption spectroscopy measurements complement their structural analysis.

Study of conformational transitions of i-motif DNA using time-resolved fluorescence and multivariate analysis methods

Recently, the presence of i-motif structures at C-rich sequences in human cells and their regulatory functions have been demonstrated. Despite numerous steady-state studies on i-motif at neutral and slightly acidic pH, the number and nature of conformation of this biological structure are still controversial. In this work, the fluorescence lifetime of labelled molecular beacon i-motif-forming DNA sequences at different pH values is studied. The influence of the nature of bases at the lateral loops and the presence of a Watson–Crick-stabilized hairpin are studied by means of time-correlated single-photon counting technique. This allows characterizing the existence of several conformers for which the fluorophore has lifetimes ranging from picosecond to nanosecond. The information on the existence of different i-motif structures at different pH values has been obtained by the combination of classical global decay fitting of fluorescence traces, which provides lifetimes associated with the events defined by the decay of each sequence and multivariate analysis, such as principal component analysis or multivariate curve resolution based on alternating least squares. Multivariate analysis, which is seldom used for this kind of data, was crucial to explore similarities and differences of behaviour amongst the different DNA sequences and to model the presence and identity of the conformations involved in the pH range of interest. The results point that, for i-motif, the intrachain contact formation and its dissociation show lifetimes ten times faster than for the open form of DNA sequences. They also highlight that the presence of more than one i-motif species for certain DNA sequences according to the length of the sequence and the composition of the bases in the lateral loop.

Nonisentropic Release of a Shocked Solid

We present molecular dynamics simulations of shock and release in micron-scale tantalum crystals that exhibit postbreakout temperatures far exceeding those expected under the standard assumption of isentropic release. We show via an energy-budget analysis that this is due to plastic-work heating from material strength that largely counters thermoelastic cooling. The simulations are corroborated by experiments where the release temperatures of laser-shocked tantalum foils are deduced from their thermal strains via in situ x-ray diffraction and are found to be close to those behind the shock.

Importance of the Mixing and High-Temperature Heating Steps in the Controlled Thermal Coprecipitation Synthesis of Sub-5-nm Na(Gd-Yb)F4:Tm

In order to achieve a significant size reduction to get ultrasmall upconverting nanoparticles (UCNPs) following a thermal coprecipitation pathway, we identified two critical points: the UCNP precursor mixing and high-temperature heating steps. Significant differences could be observed according to the way the inorganic sodium and fluoride sources were mixed to the rare-earth oleate before the high-temperature heating step. More interestingly, accurate monitoring of the high-temperature heating step using microwave (MW) dielectric heating yielded major improvement toward ultrasmall UCNPs. Thus, hexagonal, Tm-doped sub-5-nm UCNPs with an unusual Na(Yb-Gd)F₄ matrix with 53% Yb were produced, displaying satisfactory luminescence. Noticeably, MW heating was achieved in a weakly MW-absorbing oleic acid (OA)/octadecene mixture, and the influence of the OA content composition on the MW heating efficiency is discussed in this report.

Photochemical multivariate curve resolution models for the investigation of photochromic systems under continuous irradiation

We propose a multivariate curve resolution approach for the investigation of photochromic systems using UV-Visible spectroscopy. The incorporation of photochemical hard-models as constraints in multivariate curve resolution alternating least squares (MCR-ALS) allows extracting reaction quantum yields in situations where a complete knowledge of the system is not available. We apply this approach to the study of the photochromism of CMTE (cis-1,2-dicyano-1,2-bis(2,4,5-trimethyl-3-thienyl)ethene) under continuous monochromatic irradiation. The mechanism, involving 3 species and 2 reversible reactions, is written and translated into a kinetic constraint that can be applied to the concentration profiles within ALS. First, ambiguity of the solution obtained for photochemical model(s) is calculated and discussed for single set analysis. Multiset analysis is then proposed combining data obtained under different irradiation wavelengths to provide more reliable results. Finally, the photochemical reactivity of CMTE is widely unraveled, and some description of the mechanism observed under irradiation at 365 nm is given.

Study of light-induced formation of photodimers in the i-motif nucleic acid structure by rapid-scan FTIR difference spectroscopy and hybrid hard- and soft-modelling

The i-motif is a DNA structure formed by cytosine-rich sequences, very relevant from a biochemical point of view and potentially useful in nanotechnology as pH-sensitive nanodevices or nanomotors. To provide a different view on the structural changes and dynamics of direct excitation processes involving i-motif structures, the use of rapid-scan FTIR spectroscopy is proposed. Hybrid hard- and soft-modelling based on the Multivariate Curve Resolution by Alternating Least Squares (MCR-ALS) algorithm has been used for the resolution of rapid-scan FTIR spectra and the interpretation of the photochemically induced time-dependent conformational changes of i-motif structures. The hybrid hard- and soft-modelling version of MCR-ALS (HS-MCR), which allows the introduction of kinetic models to describe process behavior, provides also rate constants associated with the transitions modeled. The results show that UV irradiation does not produce degradation of the studied sequences but induces the formation of photodimers. The presence of these affect much more the stability of i-motif structures formed by short sequences than that of those formed by longer sequences containing additional structural stabilizing elements, such as hairpins.

Femtosecond X-Ray Diffraction Studies of the Reversal of the Microstructural Effects of Plastic Deformation during Shock Release of Tantalum

We have used femtosecond x-ray diffraction to study laser-shocked fiber-textured polycrystalline tantalum targets as the 37-253 GPa shock waves break out from the free surface. We extract the time and depth-dependent strain profiles within the Ta target as the rarefaction wave travels back into the bulk of the sample. In agreement with molecular dynamics simulations, the lattice rotation and the twins that are formed under shock compression are observed to be almost fully eliminated by the rarefaction process.

Comparative photophysical investigation of doubly-emissive photochromic-fluorescent diarylethenes

Diarylethene molecules showing photochromism and fluorescence properties in both open and closed forms, associated with two different emission colors, are very promising for applications involving ratiometric emissive photoswitches. We report here a complete study on the competition between the multiple photophysical processes involved in the excited states for two sulfone derivatives of benzothiophene-based diarylethene molecules, only differing by the substituent groups on their reactive carbon (methyl for DAE-Me and ethyl for DAE-Et). Steady-state and time-resolved spectroscopy, combined with DFT and TD-DFT calculations, allow a complete determination of the kinetic constants leading to fluorescence and photoreaction pathways in different solvents, and enlighten the specific role of the substituent group in the photophysical properties due to a shielding effect against the solvation environment. The predominant role of the non-radiative deactivation processes in such a family of molecules is shown, and a tentative excited state mechanistic scheme is proposed based on femtosecond transient absorption experiments performed on the closed forms.

Frame-Insensitive Expression Cloning of Fluorescent Protein from Scolionema suvaense

Expression cloning from cDNA is an important technique for acquiring genes encoding novel fluorescent proteins. However, the probability of in-frame cDNA insertion following the first start codon of the vector is normally only 1/3, which is a cause of low cloning efficiency. To overcome this issue, we developed a new expression plasmid vector, pRSET-TriEX, in which transcriptional slippage was induced by introducing a DNA sequence of (dT)₁₄ next to the first start codon of pRSET. The effectiveness of frame-insensitive cloning was validated by inserting the gene encoding eGFP with all three possible frames to the vector. After transformation with one of these plasmids, E. coli cells expressed eGFP with no significant difference in the expression level. The pRSET-TriEX vector was then used for expression cloning of a novel fluorescent protein from Scolionema suvaense. We screened 3658 E. coli colonies transformed with pRSET-TriEX containing Scolionema suvaense cDNA, and found one colony expressing a novel green fluorescent protein, ScSuFP. The highest score in protein sequence similarity was 42% with the chain c of multi-domain green fluorescent protein like protein "ember" from Anthoathecata sp. Variations in the N- and/or C-terminal sequence of ScSuFP compared to other fluorescent proteins indicate that the expression cloning, rather than the sequence similarity-based methods, was crucial for acquiring the gene encoding ScSuFP. The absorption maximum was at 498 nm, with an extinction efficiency of 1.17 × 10⁵ M^-1·cm^-1. The emission maximum was at 511 nm and the fluorescence quantum yield was determined to be 0.6. Pseudo-native gel electrophoresis showed that the protein forms obligatory homodimers.

Superhydrophobic polypyrene films to prevent Staphylococcus aureus and Pseudomonas aeruginosa biofilm adhesion on surfaces: high efficiency deciphered by fluorescence microscopy

Superhydrophobic fluorinated-polypyrene proved to be highly efficient to prevent biofilm adhesion.

Ultrafast charge transfer excited state dynamics in trifluoromethyl-substituted iridium(iii) complexes

Ultrafast spectroscopic studies on the excited state interplay in trifluoromethyl-substituted iridium(iii) complexes.

Electrolyte containing lithium cation in squaraine-sensitized solar cells: interactions and consequences for performance and charge transfer dynamics

By optimizing the lithium concentration in an electrolyte to 50 mmol L^-1 and the dye-to-chenodeoxycholic acid ratio in a VG1-based dye solution, we achieved 4.7% power conversion efficiency under standard AM 1.5G conditions. In addition to this performance, we herein discuss the role played by lithium in the electrolyte and its interplay in the charge transfer processes from ms to fs dynamics. Based on electrochemical impedance spectroscopy, photoluminescence and pump-probe transient absorption spectroscopy, we conclude that although lithium increases the electron diffusion length, this has no satisfactory impact on electron injection and even slows dye regeneration. This study provides evidence that lithium is not only specifically adsorbed on the surface of TiO₂ but prompts a molecular reorganization of the self-assembled dye monolayer, forming harmful H-aggregates.

Fusion of Ultraviolet-Visible and Infrared Transient Absorption Spectroscopy Data to Model Ultrafast Photoisomerization

Ultrafast photoisomerization reactions generally start at a higher excited state with excess of internal vibrational energy and occur via conical intersections. This leads to ultrafast dynamics which are difficult to investigate with a single transient absorption spectroscopy technique, be it in the ultraviolet-visible (UV-vis) or infrared (IR) domain. On one hand, the information available in the UV-vis domain is limited as only slight spectral changes are observed for different isomers. On the other hand, the interpretation of vibrational spectra is strongly hindered by intramolecular relaxation and vibrational cooling. These limitations can be circumvented by fusing UV-vis and IR transient absorption spectroscopy data in a multiset multivariate curve resolution analysis. We apply this approach to describe the spectrodynamics of the ultrafast cis-trans photoisomerization around the C-N double bond observed for aromatic Schiff bases. Twisted intermediate states could be elucidated, and isomerization was shown to occur through a continuous complete rotation. More broadly, data fusion can be used to rationalize a vast range of ultrafast photoisomerization processes of interest in photochemistry.

Disclosing Whole Reaction Pathways of Photochromic 3H-Naphthopyrans with Fast Color Fading

Instantaneous coloration with large absorbance and quick color fading in the dark are desired properties for thermally reversible photochromic compounds. In the case of naphthopyran derivatives, which have been employed to commercial ophthalmic lenses, the quick color fading has been recently achieved by suppression of the generation of the transoid-trans (TT) form by steric hindrance of bulky substituents. However, there are still open questions whether the steric hindrance decreases the photochromic reaction efficiency, which is a crucial problem for industrial applications. Herein, we apply a wide range of electronic and vibrational time-resolved spectroscopies and reveal that the photochromic reaction yields of the naphthopyrans with bulky substituents are almost comparable (∼0.7) to that of nonsubstituted naphthopyran. The suppression of the formation of the TT form and the effect of solvent polarity on the photodynamics are systematically investigated. These findings are important for fundamental photochemistry and developing naphthopyran-based optimal photofunctional materials.

AIE phenomena of a cyanostilbene derivative as a probe of molecular assembly processes

The initial processes of the crystallization of a solute molecule, 1-cyano-trans-1,2-bis-(4′-methylbiphenyl)-ethylene (CN-MBE) in binary solution (water and acetone), were investigated by means of fluorescence spectroscopy as well as scanning electron microscopy (SEM). With an increase in the volume fraction (V_w) of the poor solvent (water) in the solution, a drastic change in the fluorescence spectra and intensity of CN-MBE was observed. This change was attributed to aggregation induced emission (AIE). By analyzing the evolution of AIE by multivariate curve resolution-alternating least squares (MCR-ALS), it was revealed that four main species appeared in the solution depending on the V_w values. On the basis of molecular exciton theory, we assigned these four emissive states to the monomer, H-dimer, J-dimer, and H-aggregates. Interestingly, the J-dimer state was observed only in a V_w range of 40% to 50%, just before the formation of the aggregate. This result suggests that the J-dimer plays an important role as the precursor for larger aggregates leading to crystal formation. By integrating the present results with previous work on the crystallization of CN-MBA through solvent evaporation, we discussed the dynamics of the crystallization from the viewpoint of the sequence of molecular species appearing in the aggregation in solution.

Synthesis, Characterization, and Photocatalytic H2-Evolving Activity of a Family of [Co(N4Py)(X)](n+) Complexes in Aqueous Solution

A series of [Co(III)(N4Py)(X)](ClO4)n (X = Cl(-), Br(-), OH(-), N3(-), NCS(-)-κN, n = 2: X = OH2, NCMe, DMSO-κO, n = 3) complexes containing the tetrapyridyl N5 ligand N4Py (N4Py = 1,1-di(pyridin-2-yl)-N,N-bis(pyridin-2-ylmethyl)methanamine) has been prepared and fully characterized by infrared (IR), UV-visible, and NMR spectroscopies, high-resolution electrospray ionization mass spectrometry (HRESI-MS), elemental analysis, X-ray crystallography, and electrochemistry. The reduced Co(II) and Co(I) species of these complexes have been also generated by bulk electrolyses in MeCN and characterized by UV-visible and EPR spectroscopies. All tested complexes are catalysts for the photocatalytic production of H2 from water at pH 4.0 in the presence of ascorbic acid/ascorbate, using [Ru(bpy)3](2+) as a photosensitizer, and all display similar H2-evolving activities. Detailed mechanistic studies show that while the complexes retain the monodentate X ligand upon electrochemical reduction to Co(II) species in MeCN solution, in aqueous solution, upon reduction by ascorbate (photocatalytic conditions), [Co(II)(N4Py)(HA)](+) is formed in all cases and is the precursor to the Co(I) species which presumably reacts with a proton. These results are in accordance with the fact that the H2-evolving activity does not depend on the chemical nature of the monodentate ligand and differ from those previously reported for similar complexes. The catalytic activity of this series of complexes in terms of turnover number versus catalyst (TONCat) was also found to be dependent on the catalyst concentration, with the highest value of 230 TONCat at 5 × 10(-6) M. As revealed by nanosecond transient absorption spectroscopy measurements, the first electron-transfer steps of the photocatalytic mechanism involve a reductive quenching of the excited state of [Ru(bpy)3](2+) by ascorbate followed by an electron transfer from [Ru(II)(bpy)2(bpy(•-))](+) to the [Co(II)(N4Py)(HA)](+) catalyst. The reduced catalyst then enters into the H2-evolution cycle.

Serial Femtosecond Crystallography and Ultrafast Absorption Spectroscopy of the Photoswitchable Fluorescent Protein IrisFP

Reversibly photoswitchable fluorescent proteins find growing applications in cell biology, yet mechanistic details, in particular on the ultrafast photochemical time scale, remain unknown. We employed time-resolved pump-probe absorption spectroscopy on the reversibly photoswitchable fluorescent protein IrisFP in solution to study photoswitching from the nonfluorescent (off) to the fluorescent (on) state. Evidence is provided for the existence of several intermediate states on the pico- and microsecond time scales that are attributed to chromophore isomerization and proton transfer, respectively. Kinetic modeling favors a sequential mechanism with the existence of two excited state intermediates with lifetimes of 2 and 15 ps, the second of which controls the photoswitching quantum yield. In order to support that IrisFP is suited for time-resolved experiments aiming at a structural characterization of these ps intermediates, we used serial femtosecond crystallography at an X-ray free electron laser and solved the structure of IrisFP in its on state. Sample consumption was minimized by embedding crystals in mineral grease, in which they remain photoswitchable. Our spectroscopic and structural results pave the way for time-resolved serial femtosecond crystallography aiming at characterizing the structure of ultrafast intermediates in reversibly photoswitchable fluorescent proteins.

Sparse deconvolution of high-density super-resolution images

In wide-field super-resolution microscopy, investigating the nanoscale structure of cellular processes, and resolving fast dynamics and morphological changes in cells requires algorithms capable of working with a high-density of emissive fluorophores. Current deconvolution algorithms estimate fluorophore density by using representations of the signal that promote sparsity of the super-resolution images via an L1-norm penalty. This penalty imposes a restriction on the sum of absolute values of the estimates of emitter brightness. By implementing an L0-norm penalty--on the number of fluorophores rather than on their overall brightness--we present a penalized regression approach that can work at high-density and allows fast super-resolution imaging. We validated our approach on simulated images with densities up to 15 emitters per μm(-2) and investigated total internal reflection fluorescence (TIRF) data of mitochondria in a HEK293-T cell labeled with DAKAP-Dronpa. We demonstrated super-resolution imaging of the dynamics with a resolution down to 55 nm and a 0.5 s time sampling.

Photoaddition of two guanine bases to single Ru-TAP complexes. Computational studies and ultrafast spectroscopies to elucidate the pH dependence of primary processes

The covalent photoadduct (PA) between [Ru(TAP)3](2+) (TAP = 1,4,5,8-tetraazaphenanthrene) and guanosine monophosphate (GMP) opened the way to interesting photobiological applications. In this context, the PA's capability upon illumination to give rise to the addition of a second guanine base is especially interesting. The origins of these intriguing properties are for the first time thoroughly investigated by an experimental and theoretical approach. The PA's spectroscopic and redox data combined with TDDFT results corroborated with resonance Raman data show that the properties of this PA (pKa around 7) depend on the solution pH. Theoretical results indicate that the acid form PA.H(+) when excited should relax to MLCT (metal-to-ligand charge transfer) excited states, in contrast to the basic form PA whose excited state should have LLCT/ILCT (ligand-to-ligand charge transfer/intra ligand charge transfer) characteristics. Ultrafast excitation of PA.H(+) at pH 5.9 produces continuous dynamic processes in a few hundred picoseconds involving coupled proton-electron transfers responsible for luminescence quenching. Long-lived species of a few microseconds capable of reacting with GMP are produced at that pH, in agreement with the formation of covalent addition of a second GMP to PA, as shown by mass spectrometry results. In contrast, at pH 8 (mainly nonprotonated PA), other ultrafast transient species are detected and no GMP biadduct is formed in the presence of GMP. This pH dependence of photoreaction can be rationalized with the different nature of the excited states, thus at pH 8, unreactive LLCT/ILCT states and at pH 5.9 reactive MLCT states.

From ultrafast events to equilibrium--uncovering the unusual dynamics of ESIPT reaction: the case of dually fluorescent diethyl-2,5-(dibenzoxazolyl)-hydroquinone

The excited state intramolecular proton transfer (ESIPT) reaction of the dually fluorescent 2,5-diethyl-(dibenzoxazolyl)-hydroquinone (DE-BBHQ) was studied with several time resolved techniques. The complementary character of up-conversion and time correlated single photon counting methods was demonstrated. According to the up-conversion experiments, the primary excited dienol form transforms into the monoketo tautomer in a very efficient ultrafast (∼100 fs) proton transfer reaction. The reverse process of proton transfer repopulating the excited dienol form was also observed, whose rate strongly depends on solvent polarity. Both contributions of dienol emission were univocally distinguished. The double-well potential of the S1 state of DE-BBHQ was calculated, and the nature of the phototautomer as the monoketo form was confirmed. This represents an example of how to combine different experimental methods with different temporal resolutions for unravelling ultrafast proton transfer reaction. A similar experimental strategy can be easily adopted for other systems where equilibrium between two states is observed (e.g. photoinduced electron or energy transfer).