Archaerhodopsin 3 is an ideal template for the engineering of highly fluorescent optogenetic reporters

Archaerhodopsin-3 (AR-3) variants stand out among other rhodopsins in that they display a weak, but voltage-sensitive, near-infrared fluorescence emission. This has led to their application in optogenetics both in cell cultures and small animals. However, in the context of improving the fluorescence characteristics of the next generation of AR-3 reporters, an understanding of their ultrafast light-response in light-adapted conditions, is mandatory. To this end, we present a combined experimental and computational investigation of the excited state dynamics and quantum yields of AR-3 and its DETC and Arch-5 variants. The latter always display a mixture of all-trans/15-anti and 13-cis/15-syn isomers, which leads to a bi-exponential excited state decay. The isomerisation quantum yield is reduced more than 20 times as compared to WT AR-3 and proves that the steady-state fluorescence is induced by a single absorption photon event. In wild-type AR-3, we show that a 300 fs, barrier-less and vibrationally coherent isomerization is driven by an unusual covalent electronic character of its all-trans retinal chromophore leading to a metastable twisted diradical (TIDIR), in clear contrast to the standard charge-transfer scenario established for other microbial rhodopsins. We discuss how the presence of TIDIR makes AR-3 an ideal candidate for the design of variants with a one-photon induced fluorescence possibly reaching the emission quantum yield of the top natural emitter neorhodopsin (NeoR).

Ultrafast transient absorption spectra and kinetics of human blue cone visual pigment at room temperature

The ultrafast photochemical reaction mechanism, transient spectra, and transition kinetics of the human blue cone visual pigment have been recorded at room temperature. Ultrafast time-resolved absorption spectroscopy revealed the progressive formation and decay of several metastable photo-intermediates, corresponding to the Batho to Meta-II photo-intermediates previously observed with bovine rhodopsin and human green cone opsin, on the picosecond to millisecond timescales following pulsed excitation. The experimental data reveal several interesting similarities and differences between the photobleaching sequences of bovine rhodopsin, human green cone opsin, and human blue cone opsin. While Meta-II formation kinetics are comparable between bovine rhodopsin and blue cone opsin, the transition kinetics of earlier photo-intermediates and qualitative characteristics of the Meta-I to Meta-II transition are more similar for blue cone opsin and green cone opsin. Additionally, the blue cone photo-intermediate spectra exhibit a high degree of overlap with uniquely small spectral shifts. The observed variation in Meta-II formation kinetics between rod and cone visual pigments is explained based on key structural differences.

Analytic Nuclear Gradients for Complete Active Space Linearized Pair-Density Functional Theory

Accurately modeling photochemical reactions is difficult due to the presence of conical intersections and locally avoided crossings, as well as the inherently multiconfigurational character of excited states. As such, one needs a multistate method that incorporates state interaction in order to accurately model the potential energy surface at all nuclear coordinates. The recently developed linearized pair-density functional theory (L-PDFT) is a multistate extension of multiconfiguration PDFT, and it has been shown to be a cost-effective post-MCSCF method (as compared to more traditional and expensive multireference many-body perturbation methods or multireference configuration interaction methods) that can accurately model potential energy surfaces in regions of strong nuclear-electronic coupling in addition to accurately predicting Franck-Condon vertical excitations. In this paper, we report the derivation of analytic gradients for L-PDFT and their implementation in the PySCF-forge software, and we illustrate the utility of these gradients for predicting ground- and excited-state equilibrium geometries and adiabatic excitation energies for formaldehyde, s-trans-butadiene, phenol, and cytosine.

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.

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.

Linearized Pair-Density Functional Theory

Multiconfiguration pair-density functional theory (MC-PDFT) is a post-SCF multireference method that has been successful at computing ground- and excited-state energies. However, MC-PDFT is a single-state method in which the final MC-PDFT energies do not come from diagonalization of a model-space Hamiltonian matrix, and this can lead to inaccurate topologies of potential energy surfaces near locally avoided crossings and conical intersections. Therefore, in order to perform physically correct ab initio molecular dynamics with electronically excited states or to treat Jahn-Teller instabilities, it is necessary to develop a PDFT method that recovers the correct topology throughout the entire nuclear configuration space. Here we construct an effective Hamiltonian operator, called the linearized PDFT (L-PDFT) Hamiltonian, by expanding the MC-PDFT energy expression to first order in a Taylor series of the wave function density. Diagonalization of the L-PDFT Hamiltonian gives the correct potential energy surface topology near conical intersections and locally avoided crossings for a variety of challenging cases including phenol, methylamine, and the spiro cation. Furthermore, L-PDFT outperforms MC-PDFT and previous multistate PDFT methods for predicting vertical excitations from a variety of representative organic chromophores.

Quantum Kinetic Rates within the Nonequilibrium Steady State

The nonequilibrium steady state (NESS) of a quantum network is central to a host of physical and biological scenarios. Examples include natural processes such as vision and photosynthesis as well as technical devices such as photocells, both activated by incoherent light (e.g., sunlight) and leading to quantum transport. Assessing time scales of the relevant chemical processes in the steady state is thus of utmost interest and is our goal in this paper. Here, a completely general approach to defining components of a quantum network in the NESS and obtaining rates of processes between these components is provided. Quantum effects are explicitly included throughout, both in (a) defining network components via projection operators and (b) determining the role of coherences in rate processes. As examples, the methodology is applied to model cases, two versions of the V-level system, and to the spin-boson model, wherein the roles of the environment and of internal system properties in determining the rates are examined. In addition, the role of Markovian vs non-Markovian contributions is quantified, exposing conditions under which NESS rates can be obtained by perturbing the nonequilibrium steady state.

State averaged CASSCF in AMOEBA polarizable water model for simulating nonadiabatic molecular dynamics with nonequilibrium solvation effects

This paper presents a state-averaged complete active space self-consistent field (SA-CASSCF) in the atomic multipole optimized energetics for biomolecular application (AMOEBA) polarizable water model, which enables rigorous simulation of non-adiabatic molecular dynamics with nonequilibrium solvation effects. The molecular orbital and configuration interaction coefficients of the solute wavefunction, and the induced dipoles on solvent atoms, are solved by minimizing the state averaged energy variationally. In particular, by formulating AMOEBA water models and the polarizable continuum model (PCM) in a unified way, the algorithms developed for computing SA-CASSCF/PCM energies, analytical gradients, and non-adiabatic couplings in our previous work can be generalized to SA-CASSCF/AMOEBA by properly substituting a specific list of variables. Implementation of this method will be discussed with the emphasis on how the calculations of different terms are partitioned between the quantum chemistry and molecular mechanics codes. We will present and discuss results that demonstrate the accuracy and performance of the implementation. Next, we will discuss results that compare three solvent models that work with SA-CASSCF, i.e., PCM, fixed-charge force fields, and the newly implemented AMOEBA. Finally, the new SA-CASSCF/AMOEBA method has been interfaced with the ab initio multiple spawning method to carry out non-adiabatic molecular dynamics simulations. This method is demonstrated by simulating the photodynamics of the model retinal protonated Schiff base molecule in water.

The involvement of triplet states in the isomerization of retinaloids

Rhodopsins form a family of photoreceptor proteins which utilize the retinal chromophore for light energy conversion. Upon light absorption the retinal chromophore undergoes a photoisomerization. This reaction involves a non-radiative relaxation through a conical intersection between the singlet excited state and the ground state. In this work we studied the possible involvement of triplet states in the photoisomerization of retinaloids using the extended multistate (XMS) version of CASPT2. To this end, truncated models of three retinaloids were considered: protonated Schiff base, deprotonated Schiff base and the aldehyde form. The optimized geometries of the reactant, the product and the conical intersection were connected by a linear interpolation of internal coordinates to describe the isomerization. The energetic position of the low-lying singlet and triplet states as well as their spin-orbit coupling matrix elements (SOCME) were calculated along the isomerization profile. The SOCME values peaked in vicinity of the conical intersection for all the retinaloids. Furthermore, the magnitude of SOCME is invariant to the number of double bonds in the model. The SOCME for the protonated Schiff base is negligible (1.5 cm^-1) which renders the involvement of the triplet state as improbable. However, the largest SOCME value of 30 cm^-1 was found for the aldehyde form, followed by 15 cm^-1 for the deprotonated Schiff base.

E/Z photoisomerization pathway in pristine and fluorinated di(3-furyl)ethenes

We report an XMCQDPT2 study of the E/Z photoisomerization in a series of fluorinated di(3-furyl)ethenes (3DFEs). Upon excitation, pristine and low-fluorinated 3DFE show conventional behavior of many diarylethenes: unhindered twisting motion toward the pyramidalized zwitterionic state where relaxation to the ground state occurs. However, deep fluorination of 3DFEs can hamper E-to-Z isomerization by giving rise to an alternative excited-state relaxation pathway: an out-of-plane motion of a ring fluorine atom. Importantly, the case of fluorinated 3DFEs reveals serious deficiencies of the popular TDDFT approach. With some commonly used exchange-correlation functionals, the alternative relaxation pathway is not reproduced and, moreover, an irrelevant ring rotation coordinate is predicted instead. Nevertheless, TDDFT remains qualitatively adequate for the E-to-Z twisting coordinate taken alone.

Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.

Steady State Photoisomerization Quantum Yield of Model Rhodopsin: Insights from Wavepacket Dynamics?

We simulate the nonequilibrium steady state cis-trans photoisomerization of retinal chromophore in rhodopsin on the basis of a two-state, two-mode model coupled to a thermal environment. By analyzing the systematic trends within an inhomogeneously broadened ensemble of systems, we find that the steady state reaction quantum yield (QY) correlates strongly with the excess energy above the crossing point of the system, in agreement with the prediction of the short-time dynamical wavepacket picture. However, the nontrivial dependence of the QY on the system-environment interaction indicates that a pure dynamical picture is insufficient and that environment-induced partial internal energy redistribution takes place before the reaction concludes. These results imply that a proper treatment of the photoisomerization reaction, particularly its high QY, must account for the redistribution and dissipation of energy beyond the dynamical wavepacket motion that is typically employed in the literature and that is appropriate only in the transient regime.

A Unified View on Varied Ultrafast Dynamics of the Primary Process in Microbial Rhodopsins

All-trans to 13-cis photoisomerization of the protonated retinal Schiff base (PRSB) chromophore is the primary step that triggers various biological functions of microbial rhodopsins. While this ultrafast primary process has been extensively studied, it has been recognized that the relevant excited-state relaxation dynamics differ significantly from one rhodopsin to another. To elucidate the origin of the complicated ultrafast dynamics of the primary process in microbial rhodopsins, we studied the excited-state dynamics of proteorhodopsin, its D97N mutant, and bacteriorhodopsin by femtosecond time-resolved absorption (TA) spectroscopy in a wide pH range. The TA data showed that their excited-state relaxation dynamics drastically change when pH approaches the pKa of the counterion residue of the PRSB chromophore in the ground state. This result reveals that the varied excited-state relaxation dynamics in different rhodopsins mainly originate from the difference of the ground-state heterogeneity (i.e., protonation/deprotonation of the PRSB counterion).

Multiphoton Control of 6π Photocyclization via State-Dependent Reactant-Product Correlations

Multiphoton excitation promises opportunities for opening new photochemical reaction pathways and controlling photoproduct distributions. We demonstrate photonic control of the 6π photocyclization of ortho-terphenyl to make 4a,4b-dihydrotriphenylene (DHT). Using pump-repump-probe spectroscopy we show that 1 + 1' excitation to a high-lying reactant electronic state generates a metastable species characterized by a red absorption feature that accompanies a repump-induced depletion in the one-photon trans-dihydro product (trans-DHT); signatures of the new photoproduct are clearer for a structural analogue of the reactant that is sterically inhibited against one-photon cyclization. Quantum-chemical computations support assignment of this species to cis-DHT, which is accessible photochemically along a disrotatory coordinate from high-lying electronic states reached by 1 + 1' excitation. We use time-resolved spectroscopy to track photochemical dynamics producing cis-DHT. In total, we demonstrate that selective multiphoton excitation opens a new photoreaction channel in these photocyclizing reactants by taking advantage of state-dependent correlations between reactant and product electronic states.

Capturing photochemical and photophysical transformations in iron complexes with ultrafast X-ray spectroscopy and scattering

Light-driven chemical transformations provide a compelling approach to understanding chemical reactivity with the potential to use this understanding to advance solar energy and catalysis applications. Capturing the non-equilibrium trajectories of electronic excited states with precision, particularly for transition metal complexes, would provide a foundation for advancing both of these objectives. Of particular importance for 3d metal compounds is characterizing the population dynamics of charge-transfer (CT) and metal-centered (MC) electronic excited states and understanding how the inner coordination sphere structural dynamics mediate the interaction between these states. Recent advances in ultrafast X-ray laser science has enabled the electronic excited state dynamics in 3d metal complexes to be followed with unprecedented detail. This review will focus on simultaneous X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS) studies of iron coordination and organometallic complexes. These simultaneous XES-XSS studies have provided detailed insight into the mechanism of light-induced spin crossover in iron coordination compounds, the interaction of CT and MC excited states in iron carbene photosensitizers, and the mechanism of Fe-S bond dissociation in cytochrome c.

Extreme Parametric Sensitivity in the Steady-State Photoisomerization of Two-Dimensional Model Rhodopsin

We computationally studied the photoisomerization reaction of the retinal chromophore in rhodopsin using a two-state two-mode model coupled to thermal baths. Reaction quantum yields at the steady state (10 ps and beyond) were found to be considerably different than their transient values, suggesting a weak correlation between transient and steady-state dynamics in these systems. Significantly, the steady-state quantum yield was highly sensitive to minute changes in system parameters, while transient dynamics was nearly unaffected. Correlation of such sensitivity with standard level spacing statistics of the nonadiabatic vibronic system suggests a possible origin in quantum chaos. The significance of this observation of quantum yield parametric sensitivity in biological models of vision has profound conceptual and fundamental implications.

Absorption and Emission Spectroscopic Investigation of the Thermal Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor Archon2

Archon2 is a fluorescent voltage sensor derived from Archaerhodopsin 3 (Arch) of Halorubrum sodomense using robotic multidimensional directed evolution approach. Here we report absorption and emission spectroscopic studies of Archon2 in Tris buffer at pH 8. Absorption cross-section spectra, fluorescence quantum distributions, fluorescence quantum yields, and fluorescence excitation spectra were determined. The thermal stability of Archon2 was studied by long-time attenuation coefficient measurements at room temperature (21 ± 1 °C) and at refrigerator temperature (3 ± 1 °C). The apparent melting temperature was determined by stepwise sample heating up and cooling down (obtained apparent melting temperature: 63 ± 3 °C). In the protein melting process protonated retinal Schiff base (PRSB) with absorption maximum at 586 nm converted to de-protonated retinal Schiff base (RSB) with absorption maximum at 380 nm. Storage of Archon2 at room temperature and refrigerator temperature caused absorption coefficient decrease because of partial protein clustering to aggregates at condensation nuclei and sedimentation. At room temperature an onset of light scattering was observed after two days because of the beginning of protein unfolding. During the period of observation (18 days at 21 °C, 22 days at 3 °C) no change of retinal isomer composition was observed indicating a high potential energy barrier of S₀ ground-state isomerization.

Optical properties of 3-substituted indoles

The optical properties of various donor or acceptor p-phenyl substituted ethenyl indoles were studied in solvents of varying polarity using absorption, fluorescence and TDDFT methods. Ethenyl indole exhibits non-linear optical properties (NLO) in a substituent dependent manner. Compound with a strong electron-attracting substituent, shows large NLO properties with charge transfer behavior, whereas ethenyls with moderate electron withdrawing or electron donating substituent exhibit lower NLO properties with non polar excited state. A highly dipolar excited state for p-nitro phenyl substituted ethenyl indoles (μ _e: 18.2-27.1 debye; Δμ: 9.4-17.8 debye) is observed as compared to other ethenyls (μ _e: 6.6-9.5 debye; Δμ: 4.2-6.2 debye). From TDDFT study, it is shown that the HOMO-LUMO energy of ethenyl is increased with increasing the electron donating ability of the p-phenyl substitution. The optical band gap of ethenyl 3 without substitution, is decreased upon p-phenyl substitution either with an electron withdrawing (Cl, NO₂) or an electron donating (OCH₃, OH, NH₂) substituent. The compound with a strong electron accepting, p-nitrophenyl ethenyl indole 1 shows 12 times better NLO response as compared to the reference ethenyl indole 3 (β: 1: 115 × 10^-30 esu^-1 cm⁵, 3: 9 × 10^-30 esu^-1 cm⁵). Ethenyls 2-6 bearing a weak or moderately electron withdrawing or electron accepting substituent, exhibit lower NLO response. The β of ethenyl is increased with increasing the order of electron withdrawing nature of phenyl ring. Overall, a correlation of β with the optical band gap, ground state dipole moment, % of charge transfer in the ground and excited state is found.

Unravelling the Kinetic Model of Photochemical Reactions via Deep Learning

Time-resolved spectroscopies have been playing an essential role in the elucidation of the fundamental mechanisms of light-driven processes, particularly in exploring relaxation models for electronically excited molecules. However, the determination of such models from experimentally obtained time-resolved and spectrally resolved data still demands a high degree of intuition, frequently poses numerical challenges, and is often not free from ambiguities. Here, we demonstrate the analysis of time-resolved laser spectroscopy data via a deep learning network to obtain the correct relaxation kinetic model. In its current design, the presented Deep Spectroscopy Kinetic Analysis Network (DeepSKAN) can predict kinetic models (involved states and relaxation pathways) consisting of up to five states, which results in 103 possible different classes, by estimating the probability of occurrence of a given kinetic model class. DeepSKAN was trained with synthetic time-resolved spectra spanning over 4 orders of magnitude in time with a unitless time axis, thereby demonstrating its potential as a universal approach for analyzing data from various time-resolved spectroscopy techniques in different time ranges. By adding the probabilities of each pathway of the top-k models normalized by the total probability, we can determine the relaxation pathways for a given data set with high certainty (up to 99%). Due to its architecture and training, DeepSKAN is robust against experimental noise and typical preanalysis errors like time-zero corrections. Application of DeepSKAN to experimental data is successfully demonstrated for three different photoinduced processes: transient absorption of the retinal isomerization, transient IR spectroscopy of the relaxation of the photoactivated DRONPA, and transient absorption of the dynamics in lycopene. This approach delivers kinetic models and could be a unifying asset in several areas of spectroscopy.

Spectroscopy and excited state dynamics of nearly infinite polyenes

Steady-state and transient absorption spectra with <50 fs time resolution were obtained for two conjugated polymers, both with ≈200 conjugated double bonds (N), constrained in planar, stable, polyene frameworks. Solutions of the polymers exhibit the same S2 → S1 → S* → S0 decay pathway observed for the N = 11-19 polyene oligomers and for zeaxanthin homologues with N = 11-23. Comparisons with the excited state dynamics of polydiactylene and a much longer, more disordered polyene polymer (poly(DEDPM)) show that the S2, S1, and S* lifetimes of the four polymers are almost identical. The S* signals in the polymers are assigned to absorption from vibrationally excited ground states. In spite of significant heterogeneities and variations in conjugation lengths in these long polyenes, their S0 → S2 absorptions are vibronically-resolved in room temperature solutions with electronic origins at ≈600 nm. The limiting wavelength for the S0 → S2 transitions is consistent with the persistence of bond length alternation in the electronic ground states and a HOMO-LUMO band gap in polyenes with N ≈ 200. The coincidence of the well-resolved S0 → S2 electronic origins and the convergence of the excited state lifetimes in the four polymers point to a common, "nearly infinite" polyene limit.

Effect of point mutations on the ultrafast photo-isomerization of Anabaena sensory rhodopsin

Anabaena sensory rhodopsin (ASR) is a particular microbial retinal protein for which light-adaptation leads to the ability to bind both the all-trans, 15-anti (AT) and the 13-cis, 15-syn (13C) isomers of the protonated Schiff base of retinal (PSBR). In the context of obtaining insight into the mechanisms by which retinal proteins catalyse the PSBR photo-isomerization reaction, ASR is a model system allowing to study, within the same protein, the protein-PSBR interactions for two different PSBR conformers at the same time. A detailed analysis of the vibrational spectra of AT and 13C, and their photo-products in wild-type ASR obtained through femtosecond (pump-) four-wave-mixing is reported for the first time, and compared to bacterio- and channelrhodopsin. As part of an extensive study of ASR mutants with blue-shifted absorption spectra, we present here a detailed computational analysis of the origin of the mutation-induced blue-shift of the absorption spectra, and identify electrostatic interactions as dominating steric effects that would entail a red-shift. The excited state lifetimes and isomerization reaction times (IRT) for the three mutants V112N, W76F, and L83Q are studied experimentally by femtosecond broadband transient absorption spectroscopy. Interestingly, in all three mutants, isomerization is accelerated for AT with respect to wild-type ASR, and this the more, the shorter the wavelength of maximum absorption. On the contrary, the 13C photo-reaction is slightly slowed down, leading to an inversion of the ESLs of AT and 13C, with respect to wt-ASR, in the blue-most absorbing mutant L83Q. Possible mechanisms for these mutation effects, and their steric and electrostatic origins are discussed.

Intrinsic photoisomerization dynamics of protonated Schiff-base retinal

The retinal protonated Schiff-base (RPSB) in its all-trans form is found in bacterial rhodopsins, whereas visual rhodopsin proteins host 11-cis RPSB. In both cases, photoexcitation initiates fast isomerization of the retinal chromophore, leading to proton transport, storage of chemical energy or signaling. It is an unsolved problem, to which degree this is due to protein interactions or intrinsic RPSB quantum properties. Here, we report on time-resolved action-spectroscopy studies, which show, that upon photoexcitation, cis isomers of RPSB have an almost barrierless fast 400 fs decay, whereas all-trans isomers exhibit a barrier-controlled slow 3 ps decay. Moreover, formation of the 11-cis isomer is greatly favored for all-trans RPSB when isolated. The very fast photoresponse of visual photoreceptors is thus directly related to intrinsic retinal properties, whereas bacterial rhodopsins tune the excited state potential-energy surface to lower the barrier for particular double-bond isomerization, thus changing both the timescale and specificity of the photoisomerization.

The primary photoresponse of protonated Schiff-base retinal in visual and bacterial rhodopsins is fast sub-ps isomerisation. Here, the authors show that the fast photoisomerization of rhodopsin is related to an intrinsic retinal property, whereas bacterial rhodopsins tune the excited-state potential-energy surface and improve the isomerization timescale and specificity.

Tuning of optical properties of p-phenyl ethenyl-E-furans: A Solvatochromism and Density functional theory

p-Phenyl ethenyl-E-furans (1-6) with varied electron donor and acceptor substituent (NO₂, CN, Cl, H, OCH₃, NH₂) were synthesized and studied the substituent induced optical properties (dipole moment, transition dipole moment, oscillator strength, optical band gap, hyperpolarizability) using Solvatochromism and Density functional theory. It is shown that furan acts as a weak electron donor in presence of an electron withdrawing p‑phenyl substituent (NO₂, CN, Cl), whereas furan acts as a weak electron acceptor in presence of an electron donating p‑phenyl substituent (OCH₃, NH₂). In comparison to ethenylfuran 4, the HOMO-LUMO energy band gap is decreased upon increasing the electron donating or electron withdrawing nature of the phenyl ring. Calculation of excited state dipole moment and polarizability of 1-6 in solvent of varying polarity suggest that the nitro and amino compounds (1, 6) exhibit charge transfer excited state, whereas excited state of compounds 3-5 is non-polar in nature. As compared to the ethenylfuran (4), the first hyperpolarizability (β) is increased in presence of a strong electron withdrawing or strong electron donating p‑phenyl substituent. The higher β value is found for ethenylfuran with p‑nitrophenyl and p‑amino phenyl substitution. Overall, these studies provide useful information in tuning the optical properties of p‑phenyl substituted heterocyclic ethenyl systems.

Excited State Vibrational Spectra of All- trans Retinal Derivatives in Solution Revealed By Pump-DFWM Experiments

The ultrafast structural changes during the photoinduced isomerization of the retinal-protonated Schiff base (RPSB) is still a poorly understood aspect in the retinal's photochemistry. In this work, we apply pump-degenerate four-wave mixing (pump-DFWM) to all- trans retinal (ATR) and retinal Schiff bases (RSB) to resolve coherent high- and low-frequency vibrational signatures from excited electronic states. We show that the vibrational spectra of excited singlet states in these samples exhibit pronounced differences compared to the relaxed ground state. Pump-DFWM results indicate three major features for ATR and RSB. (i) Excited state vibrational spectra of ATR and RSB consist predominately of low-frequency modes in the energetic range 100-500 cm^-1. (ii) Excited state vibrational spectra show distinct differences for excitation in specific regions of electronic transitions of excited state absorption and emission. (iii) Low-frequency modes in ATR and RSB are inducible during the entire lifetime of the excited electronic states. This latter effect points to a transient molecular structure that, following initial relaxation between different excited electronic states, does not change anymore over the lifetime of the finally populated excited electronic state.

Mapping the ultrafast vibrational dynamics of all-trans and 13-cis retinal isomerization in Anabaena Sensory Rhodopsin

Discrepancies in the isomerization dynamics and quantum yields of the trans and cis retinal protonated Schiff base is a well-known issue in the context of retinal photochemistry. Anabaena Sensory Rhodopsin (ASR) is a microbial retinal protein that comprises a retinal chromophore in two ground state (GS) conformations: all-trans, 15-anti (AT) and 13-cis, 15-syn (13C). In this study, we applied impulsive vibrational spectroscopic techniques (DFWM, pump-DFWM and pump-IVS) to ASR to shed more light on how the structural changes take place in the excited state within the same protein environment. Our findings point to distinct features in the ground state structural conformations as well as to drastically different evolutions in the excited state manifold. The ground state vibrational spectra show stronger Raman activity of the C14-H out-of-plane wag (at about 805 cm-1) for the 13C isomer than that for the AT isomer, which hints at a pre-distortion of 13C in the ground state. Evolution of the Raman frequency after interaction with the actinic pulse shows a blue-shift for the C[double bond, length as m-dash]C stretching and CH3 rocking mode for both isomers. For AT, however, the blue-shift is not instantaneous as observed for the 13C isomer, rather it takes more than 200 fs to reach the maximum frequency shift. This frequency blue-shift is rationalized by a decrease in the effective conjugation length during the isomerization reaction, which further confirms a slower formation of the twisted state for the AT isomer and corroborates the presence of a barrier in the excited state trajectory previously predicted by quantum chemical calculations.

Substituent Dependent Optical Properties of p-phenyl Substituted ethenyl-E-thiophenes

Various electron donor and acceptor substituted (NO₂, CN, Cl, H, OCH₃, NH₂) p-phenyl ethenyl-E- thiophenes (1-6) were synthesized and substituent dependent optical properties (dipole moment, transition dipole moment, oscillator strength, optical band gap, hyperpolarizability) were studied using Solvatochromism and Density functional theory. It is shown that thiophene acts as a weak electron donor in presence of an electron withdrawing p-phenyl substituent (NO₂, CN, Cl), whereas thiophene acts as a weak electron acceptor in presence of an electron donating p-phenyl substituent (OCH₃, NH₂). In comparison to ethenyl thiophene 4, the HOMO-LUMO energy band gap is decreased upon increasing the electron donating or electron withdrawing capacity of p-phenyl substituent. From the excited state dipole moment calculation, it is shown that the excited state is highly dipolar for nitro and amino compounds 1 and 6, whereas compounds 2-5 show a non-polar excited state. As compared to the ethenyl thiophene 4, the first hyperpolarizability (β) increases upon substitution either with a strong electron withdrawing or strong electron donating p-phenyl substituent. A large β value is found for p-nitro phenyl ethenyl-E-thiophene and p-amino phenyl ethenyl-E- thiophene. Overall, these studies provide useful information in understanding the optical properties of phenyl and heterocyclic based ethenyl systems.

Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods

Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.

Proton transfer reactions in the red light-activatable channelrhodopsin variant ReaChR and their relevance for its function

Channelrhodopsins (ChRs) are light-gated ion channels widely used for activating selected cells in large cellular networks. ChR variants with a red-shifted absorption maximum, such as the modified Volvox carteri ChR1 red-activatable channelrhodopsin ("ReaChR," λmax = 527 nm), are of particular interest because longer wavelengths allow optical excitation of cells in deeper layers of organic tissue. In all ChRs investigated so far, proton transfer reactions and hydrogen bond changes are crucial for the formation of the ion-conducting pore and the selectivity for protons versus cations, such as Na+, K+, and Ca2+ (1). By using a combination of electrophysiological measurements and UV-visible and FTIR spectroscopy, we characterized the proton transfer events in the photocycle of ReaChR and describe their relevance for its function. 1) The central gate residue Glu130 (Glu90 in Chlamydomonas reinhardtii (Cr) ChR2) (i) undergoes a hydrogen bond change in D → K transition and (ii) deprotonates in K → M transition. Its negative charge in the open state is decisive for proton selectivity. 2) The counter-ion Asp293 (Asp253 in CrChR2) receives the retinal Schiff base proton during M-state formation. Starting from M, a photocycle branching occurs involving (i) a direct M → D transition and (ii) formation of late photointermediates N and O. 3) The DC pair residue Asp196 (Asp156 in CrChR2) deprotonates in N → O transition. Interestingly, the D196N mutation increases 15-syn-retinal at the expense of 15-anti, which is the predominant isomer in the wild type, and abolishes the peak current in electrophysiological measurements. This suggests that the peak current is formed by 15-anti species, whereas 15-syn species contribute only to the stationary current.

Submolecular Gates Self-Assemble for Hot-Electron Transfer in Proteins

Redox reactions play key roles in fundamental biological processes. The related spatial organization of donors and acceptors is assumed to undergo evolutionary optimization facilitating charge mobilization within the relevant biological context. Experimental information from submolecular functional sites is needed to understand the organization strategies and driving forces involved in the self-development of structure-function relationships. Here we exploit chemically resolved electrical measurements (CREM) to probe the atom-specific electrostatic potentials (ESPs) in artificial arrays of bacteriochlorophyll (BChl) derivatives that provide model systems for photoexcited (hot) electron donation and withdrawal. On the basis of computations we show that native BChl's in the photosynthetic reaction center (RC) self-assemble at their ground-state as aligned gates for functional charge transfer. The combined computational and experimental results further reveal how site-specific polarizability perpendicular to the molecular plane enhances the hot-electron transport. Maximal transport efficiency is predicted for a specific, ∼5 Å, distance above the center of the metalized BChl, which is in remarkably close agreement with the distance and mutual orientation of corresponding native cofactors. These findings provide new metrics and guidelines for analysis of biological redox centers and for designing charge mobilizing machines such as artificial photosynthesis.

Microbial Rhodopsins: Diversity, Mechanisms, and Optogenetic Applications

Microbial rhodopsins are a family of photoactive retinylidene proteins widespread throughout the microbial world. They are notable for their diversity of function, using variations of a shared seven-transmembrane helix design and similar photochemical reactions to carry out distinctly different light-driven energy and sensory transduction processes. Their study has contributed to our understanding of how evolution modifies protein scaffolds to create new protein chemistry, and their use as tools to control membrane potential with light is fundamental to optogenetics for research and clinical applications. We review the currently known functions and present more in-depth assessment of three functionally and structurally distinct types discovered over the past two years: (a) anion channelrhodopsins (ACRs) from cryptophyte algae, which enable efficient optogenetic neural suppression; (b) cryptophyte cation channelrhodopsins (CCRs), structurally distinct from the green algae CCRs used extensively for neural activation and from cryptophyte ACRs; and

Substituent Dependence Charge Transfer and Photochemical Properties of Donor-Acceptor Substituted Ethenyl Thiophenes

Donor-acceptor conjugated molecules with efficient light induced properties represent interesting material for electronic device application. In this context, we have calculated excited state dipole moment of three ethenyl thiophenes (1-3) bearing varied electron donor-acceptor substituent in p-phenyl unit using Lippert-Mataga, Bakhshiev and Kawski method. It is found that 1 with strong electron-withdrawing nitro substituent, is exhibiting charge transfer and highly dipolar excited state as compared to 2 and 3. Photochemical studies of 1-3, indicate towards the charge transfer dependence trans-cis photoisomerization under direct irradiation condition. Compound 1 exhibits charge transfer and less efficient towards photoisomerization, whereas 2 and 3 undergo efficient photoisomerization. Graphical Abstract Substituent dependence charge transfer and photochemical properties of donor-acceptor substituted ethenyl thiophenes.

The Primary Photochemistry of Vision Occurs at the Molecular Speed Limit

Ultrafast photochemical reactions are initiated by vibronic transitions from the reactant ground state to the excited potential energy surface, directly populating excited-state vibrational modes. The primary photochemical reaction of vision, the isomerization of retinal in the protein rhodopsin, is known to be a vibrationally coherent reaction, but the Franck-Condon factors responsible for initiating the process have been difficult to resolve with conventional time-resolved spectroscopies. Here we employ experimental and theoretical 2D photon echo spectroscopy to directly resolve for the first time the Franck-Condon factors that initiate isomerization on the excited potential energy surface and track the reaction dynamics. The spectral dynamics reveal vibrationally coherent isomerization occurring on the fastest possible time scale, that of a single period of the local torsional reaction coordinate. We successfully model this process as coherent wavepacket motion through a conical intersection on a ∼30 fs time scale, confirming the reaction coordinate as a local torsional coordinate with a frequency of ∼570 cm^-1. As a result of spectral features being spread out along two frequency coordinates, we unambiguously assign reactant and product states following passage through the conical intersection, which reveal the key vibronic transitions that initiate the vibrationally coherent photochemistry of vision.

Mechanism and bottlenecks in strand photodissociation of split green fluorescent proteins (GFPs)

Split GFPs have been widely applied for monitoring protein-protein interactions by expressing GFPs as two or more constituent parts linked to separate proteins that only fluoresce on complementing with one another. Although this complementation is typically irreversible, it has been shown previously that light accelerates dissociation of a noncovalently attached β-strand from a circularly permuted split GFP, allowing the interaction to be reversible. Reversible complementation is desirable, but photodissociation has too low of an efficiency (quantum yield <1%) to be useful as an optogenetic tool. Understanding the physical origins of this low efficiency can provide strategies to improve it. We elucidated the mechanism of strand photodissociation by measuring the dependence of its rate on light intensity and point mutations. The results show that strand photodissociation is a two-step process involving light-activated cis-trans isomerization of the chromophore followed by light-independent strand dissociation. The dependence of the rate on temperature was then used to establish a potential energy surface (PES) diagram along the photodissociation reaction coordinate. The resulting energetics-function model reveals the rate-limiting process to be the transition from the electronic excited-state to the ground-state PES accompanying cis-trans isomerization. Comparisons between split GFPs and other photosensory proteins, like photoactive yellow protein and rhodopsin, provide potential strategies for improving the photodissociation quantum yield.

Femtosecond spectroscopic study of photochromic reactions of bacteriorhodopsin and visual rhodopsin

Photochromic ultrafast reactions of bacteriorhodopsin (H. salinarum) and bovine rhodopsin were conducted with a femtosecond two-pump probe pulse setup with the time resolution of 20-25fs. The dynamics of the forward and reverse photochemical reactions for both retinal-containing proteins was compared. It is demonstrated that when retinal-containing proteins are excited by femtosecond pulses, dynamics pattern of the vibrational coherent wave packets in the course of the reaction is different for bacteriorhodopsin and visual rhodopsin. As shown in these studies, the low-frequencies that form a wave packets experimentally observed in the dynamics of primary products formation as a result of retinal photoisomerization have different intensities and are clearer for bovine rhodopsin. Photo-reversible reactions for both retinal proteins were performed from the stage of the relatively stable photointermediates that appear within 3-5ps after the light pulse impact. It is demonstrated that the efficiency of the reverse phototransition K-form→bacteriorhodopsin is almost five-fold higher than that of the Batho-intermediate→visual rhodopsin phototransition. The results obtained indicate that in the course of evolution the intramolecular mechanism of the chromophore-protein interaction in visual rhodopsin becomes more perfect and specific. The decrease in the probability of the reverse chromophore photoisomerization (all-trans→11-cis retinal) in primary photo-induced rhodopsin products causes an increase in the efficiency of the photoreception process.

Effects of Visible-Light Irradiation of Protoporphyrin IX on the Self-Assembly of Tubulin Heterodimers

The formation and the effects of laser irradiation of the complex formed by protoporphyrin IX (PPIX) and tubulin was investigated. We have used tubulin as a model protein to investigate whether docked photoactive ligands can affect the structure and function of polypeptides upon exposure to visible light. We observed that laser irradiation in the Soret band prompts bleaching of the PPIX, which is accompanied by a sharp decrease in the intensity and average fluorescence lifetime of the protein (dominated by the four tryptophan residues of the tubulin monomer). The kinetics indicate non-trivial effects and suggest that the photosensitization of the PPIX bound to tubulin prompts structural alterations of the protein. These modifications were also observed through changes in the energy transfer between Trp residues and PPIX. The results suggest that laser irradiation produces localized partial unfolding of tubulin and that the changes prompt modification of the formation of microtubules in vitro. Measurements of singlet oxygen formation were inconclusive in determining whether the changes are prompted by reactive oxygen species or other excited state mechanisms.

A comprehensive picture of the ultrafast excited-state dynamics of retinal

All-trans retinal is the chromophore of microbial rhodopsins initiating energy conversion and cellular signalling by subpicosecond photoinduced switching. Here, we provide detailed UV-Vis transient absorption experiments to disentangle the complex photochemistry of this polyene, which is governed by its terminal aldehyde group. After photoexcitation to the S2((1)Bu(+)) state, the system exhibits polarity-dependent branching, populating separate S1((1)Ag(-)) and intramolecular charge transfer (ICT) species. In all solvents, population of a singlet nπ* state from S1 is observed which represents the precursor of the T1 triplet state. While triplet formation dominates in nonpolar solvents (67% quantum yield), it is dramatically reduced in polar solvents (4%). The channel closes completely upon replacing the aldehyde by a carboxyl group, due to an energetic up-shift of (1)nπ*. In that case, internal conversion via the ICT species becomes the main pathway, with preferential formation of the initially excited isomer.

Beyond Time-Dependent Density Functional Theory Using Only Single Excitations: Methods for Computational Studies of Excited States in Complex Systems

Single-excitation methods, namely, configuration interaction singles and time-dependent density functional theory (TDDFT), along with semiempirical versions thereof, represent the most computationally affordable electronic structure methods for describing electronically excited states, scaling as [Formula: see text] absent further approximations. This relatively low cost, combined with a treatment of electron correlation, has made TDDFT the most widely used excited-state quantum chemistry method over the past 20+ years. Nevertheless, certain inherent problems (beyond just the accuracy of this or that exchange-correlation functional) limit the utility of traditional TDDFT. For one, it affords potential energy surfaces whose topology is incorrect in the vicinity of any conical intersection (CI) that involves the ground state. Since CIs are the conduits for transitions between electronic states, the TDDFT description of photochemistry (internal conversion and intersystem crossing) is therefore suspect. Second, the [Formula: see text] cost can become prohibitive in large systems, especially those that involve multiple electronically coupled chromophores, for example, the antennae structures of light-harvesting complexes or the conjugated polymers used in organic photovoltaics. In such cases, the smallest realistic mimics might already be quite large from the standpoint of ab initio quantum chemistry. This Account describes several new computational methods that address these problems. Topology around a CI can be rigorously corrected using a "spin-flip" version of TDDFT, which involves an α → β spin-flipping transition in addition to occupied → virtual excitation of one electron. Within this formalism, singlet states are generated via excitation from a high-spin triplet reference state, doublets from a quartet, etc. This provides a more balanced treatment of electron correlation between ground and excited states. Spin contamination is problematic away from the Franck-Condon region, but we describe a "spin-complete" version of the theory in which proper spin eigenstates are obtained by construction. For systems of coupled chromophores, we have developed an ab initio version of the Frenkel-Davydov exciton model in which collective excitations of the system are expanded in a basis of excited states computed for individual chromophores. The monomer calculations are trivially parallelizable, as is computation of the coupling matrix elements needed to construct the exciton Hamiltonian, and systems containing hundreds of chromophores can be tackled on commodity hardware. This enables calculations on organic semiconductors, where even small model systems exhibit a semicontinuum of excited states that renders traditional TDDFT computationally challenging. Despite including only single excitations on each monomer, the exciton model can describe entangled spins on two or more monomers, an effect that is responsible for excitation energy transfer between chromophores, for example, in singlet fission. Excitonic approximations can also be applied to the TDDFT equations themselves, and a particularly promising application is to describe the effects of environment on an excitation that is localized on a single chromophore. This "local excitation approximation" to TDDFT allows an essentially arbitrary number of solvent molecules to be included in the calculation in a highly parallelizable way such that the time-to-solution increases only very slowly as additional solvent molecules are added. It is therefore possible to converge the calculation with respect to describing an ever-larger portion of the environment at a quantum-mechanical level.

Light-Activated Reversible Imine Isomerization: Towards a Photochromic Protein Switch

Mutants of cellular retinoic acid-binding protein II (CRABPII), engineered to bind all-trans-retinal as an iminium species, demonstrate photochromism upon irradiation with light at different wavelengths. UV light irradiation populates the cis-imine geometry, which has a high pKa , leading to protonation of the imine and subsequent "turn-on" of color. Yellow light irradiation yields the trans-imine isomer, which has a depressed pKa , leading to loss of color because the imine is not protonated. The protein-bound retinylidene chromophore undergoes photoinduced reversible interconversion between the colored and uncolored species, with excellent fatigue resistance.

Implementation and evaluation of data analysis strategies for time-resolved optical spectroscopy

Time-resolved optical spectroscopy plays a key role in illuminating the mechanisms of many fundamental processes in physics, chemistry, and biology. However, to extract the essential information from the highly complex time-resolved data, advanced data analysis techniques are required. Here we present the implementation strategies and the evaluation of the familiar global lifetime and target analysis as well as the not so widely adopted lifetime distribution analysis (LDA). Furthermore, we demonstrate the implementation of analysis strategies dealing with a number of artifacts inherently present in data from ultrafast optical experiments. The focus of the work is placed on LDA as it allows invaluable exploration depth of the kinetic information contained in the experimental data. We establish a clear regularization procedure for the use of LDA in ultrafast optical spectroscopy and evaluate the performance of a number of factors that play a role in the reliable reconstruction of lifetime distributions. Our results show that the optimal regularization factor can be determined well with the L-curve and the generalized cross-validation techniques. Moreover, the performance evaluations indicate that the most efficient regularization norm is the identity matrix. The analytical procedures described in this work can be readily implemented and used for the analysis of any time-resolved data.

100 fs photo-isomerization with vibrational coherences but low quantum yield in Anabaena Sensory Rhodopsin

Counter-intuitive photochemistry: in Anabaena Sensory Rhodopsin, the retinal 13-cis isomer isomerizes much faster than all-trans ASR, but with a 3-times lower quantum yield.

Tracking the primary photoconversion events in rhodopsins by ultrafast optical spectroscopy

We review the most recent experimental and computational efforts aimed at exposing the very early phases of the ultrafast isomerization in visual Rhodopsins and we discuss future advanced experiments and calculations.

Electron transfer quenching in light adapted and mutant forms of the AppA BLUF domain

The Blue Light Using Flavin (BLUF) domain proteins are an important family of photoreceptors controlling a range of responses in a wide variety of organisms. The details of the primary photochemical mechanism, by which light absorption in the isoalloxazine ring of the flavin is converted into a structure change to form the signalling state of the protein, is unresolved. In this work we apply ultrafast time resolved infra-red (TRIR) spectroscopy to investigate the primary photophysics of the BLUF domain of the protein AppA (AppA_BLUF) a light activated antirepressor. Here a number of mutations at Y21 and W104 in AppA_BLUF are investigated. The Y21 mutants are known to be photoinactive, while W104 mutants show the characteristic spectral red-shift associated with BLUF domain activity. Using TRIR we observed separately the decay of the excited state and the recovery of the ground state. In both cases the kinetics are found to be non-single exponential for all the proteins studied, suggesting a range of ground state structures. In the Y21 mutants an intermediate state was also observed, assigned to formation of the radical of the isoalloxazine (flavin) ring. The electron donor is the W104 residue. In contrast, no radical intermediates were detected in the studies of the photoactive dark adapted proteins, dAppA_BLUF and the dW104 mutants, suggesting a structure change in the Y21 mutants which favours W104 to isoalloxazine electron transfer. In contrast, in the light adapted form of the proteins (lAppA_BLUF, lW104) a radical intermediate was detected and the kinetics were greatly accelerated. In this case the electron donor was Y21 and major structural changes are associated with the enhanced quenching. In AppA_BLUF and the seven mutants studied radical intermediates are readily observed by TRIR spectroscopy, but there is no correlation with photoactivity. This suggests that if a charge separated state has a role in the BLUF photocycle it is only as a very short lived intermediate.

UV-induced isomerization dynamics of N-methyl-2-pyridone in solution

The photoisomerization dynamics of N-methyl-2-pyridone (NMP) dissolved in CH3CN have been interrogated by time-resolved electronic and vibrational absorption spectroscopy. Irradiation at two different wavelengths (330 or 267 nm) prepares NMP(S1) molecules with very different levels of vibrational excitation, which rapidly relax to low vibrational levels of the S1 state. Internal conversion with an associated time constant of 110(4) ps, leading to reformation of NMP(S0) molecules, is identified as the dominant (>90%) decay pathway. Much of the remaining fraction undergoes a photoinitiated rearrangement to yield two ketenes (revealed by their characteristic antisymmetric C═C═O stretching modes at 2110 and 2120 cm(-1)), which are in equilibrium. The rate of ketene formation is found to be pump-wavelength dependent, consistent with ab initio electronic structure calculations which predict a barrier on the S1 potential energy surface en route to a prefulvenic conical intersection, by which isomerization is deduced to occur. Two kinetic models-differentiated by whether product branching occurs in the S1 or S0 electronic states-are presented and used with equal success in the analysis of the experimental data, highlighting the difficulties associated with deducing unambiguous mechanistic information from kinetic data alone.