Ultrafast structural changes within a photosynthetic reaction centre.

Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.

Modelling the Encapsulation of 3-Hydroxyflavone with Cyclodextrin and Octa Acid and Comparing Their Differences.

The 3-hydroxyflavone (3-HF) is one of the common fluorescence probes. It has two distinct fluorescence bands: normal form and tautomer form. However, 3-hydroxyflavone has poor performance in water because of hydrogen bonding perturbation. The utilization of supramolecular chemistry would improve the fluorescence performance of 3-hydroxyflavone in water. In this paper, it reviews supramolecular chemistry of 3-hydroxyflavone with cyclodextrin and octa acid. Past research has found that the addition of ß-cyclodextrin to 3-hydroxyflavone in water would slightly improve the fluorescence intensity of the tautomer form. When adding γ-cyclodextrin to 3-hydroxyflavone in water, the green fluorescence intensity would be enhanced. Finally, the addition of octa acid creates a dry environment for the 3-hydroxyflavone, and it would only have a tautomer form. The ONIOM calculation shows the ways of self-assembly of ß- and γ-cyclodextrin. It can explain the difference in ratio between the tautomer form and normal form after understanding the interaction.

Anti-Kasha Behavior of 3-Hydroxyflavone and Its Derivatives.

Excited state intramolecular proton transfer (ESIPT) in 3-hydroxyflavone (3HF) has been known for its dependence on excitation wavelength. Such a behavior violates Kasha's rule, which states that the emission and photochemistry of a compound would only take place from its lowest excited state. The photochemistry of 3HF was studied using femtosecond transient absorption spectroscopy at a shorter wavelength excitation (266 nm), and these new experimental findings were interpreted with the aid of computational studies. These new results were compared with those from previous studies that were obtained with a longer wavelength excitation and show that there exists a pathway of proton transfer that bypasses the normal first excited state from the higher excited state to the tautomer from first excited state. The experimental data correlate with the electron density difference calculations such that the proton transfer process is faster on the longer excitation wavelength than compared to the shorter excitation wavelength.

Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores.

Ultrafast processes in light-absorbing proteins have been implicated in the primary step in the light-to-energy conversion and the initialization of photoresponsive biological functions. Theory and computations have played an instrumental role in understanding the molecular mechanism of such processes, as they provide a molecular-level insight of structural and electronic changes at ultrafast time scales that often are very difficult or impossible to obtain from experiments alone. Among theoretical strategies, the application of hybrid quantum mechanics and molecular mechanics (QM/MM) models is an important approach that has reached an evident degree of maturity, resulting in several important contributions to the field. This review presents an overview of state-of-the-art computational studies on subnanosecond events in rhodopsins, photoactive yellow proteins, phytochromes, and some other photoresponsive proteins where photoinduced double-bond isomerization occurs. The review also discusses current limitations that need to be solved in future developments.

Reactivity of Hydroxyl Radical in Nonaqueous Phases: Addition Reactions.

The effect of ring substitution on the kinetics of reaction of arenes, heterocycles, and alkenes with hydroxyl radical is investigated in terms of reactivity and selectivity, using laser flash photolysis (LFP) in acetonitrile solution. The LFP data indicate that charge-transfer contributions in the transition state play an important role in dictating reactivity, and there is a correlation between the experimental and calculated ionization potentials of the arenes and alkenes and their respective reactivities. The reactivity observed for arenes in acetonitrile exhibits a much greater sensitivity toward substitution on the ring than in water, and therefore aqueous data cannot be used to predict reactivity in nonaqueous environments. Nonaqueous solution data may be predictable from gas phase data, and vice versa.

Molecular bases for the selection of the chromophore of animal rhodopsins.

The functions of microbial and animal rhodopsins are triggered by the isomerization of their all-trans and 11-cis retinal chromophores, respectively. To lay the molecular basis driving the evolutionary transition from the all-trans to the 11-cis chromophore, multiconfigurational quantum chemistry is used to compare the isomerization mechanisms of the sensory rhodopsin from the cyanobacterium Anabaena PCC 7120 (ASR) and of the bovine rhodopsin (Rh). It is found that, despite their evolutionary distance, these eubacterial and vertebrate rhodopsins start to isomerize via distinct implementations of the same bicycle-pedal mechanism originally proposed by Warshel [Warshel A (1976) Nature 260:678-683]. However, by following the electronic structure changes of ASR (featuring the all-trans chromophore) during the isomerization, we find that ASR enters a region of degeneracy between the first and second excited states not found in Rh (featuring the 11-cis chromophore). We show that such degeneracy is modulated by the preorganized structure of the chromophore and by the position of the reactive double bond. It is argued that the optimization of the electronic properties of the chromophore, which affects the photoisomerization efficiency and the thermal isomerization barrier, provided a key factor for the emergence of the striking amino acid sequence divergence observed between the microbial and animal rhodopsins.

A Computational Study of Photoinduced Borylation for Selected Boron Sources.

This research article uses density functional theory (DFT) to study photoinduced borylation. This work examined the electron donor-acceptor complex (EDA) of bis(catecholato)diboron with different redox-active leaving groups and bis(pinacol)diboron with aryl N-hydroxyphthalimide. The results of these DFT studies show the complex ratio of B2cat2 and N, N-dimethylacetamide (DMA) should be 1 : 2 which is consistent with the experimental results in the literature. We further proposed a reaction mechanism and calculated the energies associated with each step.

Macrocyclic porphyrin photocatalysts without metal chelation: A novel pathway for complete degradation of tough halophenols with longwave visible LED light source.

Halophenols are toxic and persistent pollutants in water environments which poses harm to various organisms. Due to their high stability and long residence time, ultraviolet radiation, heavy metals and oxidizing agents have been largely adopted on treating these compounds. However, these treatment methods could pose toxicity or hazardous risks to the marine environment and plant operators. In this study, a water-soluble porphyrin photocatalyst was synthesized and introduced for halophenol treatment using UV-free LED white light. The porphyrin catalyst is a macrocyclic ring consisting of pyrroles linked with methine bridges, the highly conjugated ring provided the superior functionality of visible light absorption. Surprisingly, over 99 % degradation of halophenols and over 90 % dehalogenation have been achieved without metal chelation, even higher than those of transition metal porphyrins with inclusion of Fe3+, Zn2+, Cu2+, Co2+, Ni2+, and Mn2+. Ring-opening reactions were confirmed with the formation of carboxylic acids; dicarboxylic acids like acrylic acid, and malonic acid; while fumaric acid was the main product. Total organic carbon results indicated no CO2 produced during the reaction. Triplet absorbance and scavenger studies also indicated that singlet oxygen and conduction band electrons are the main radical species for halophenol degradation. The 100-fold singlet emission quenching over triplet absorption quenching indicated that the excited electrons tend to be transferred via singlet state. This concept brings along new approaches detoxifying halophenol-related wastewater without UV, metals and other additives, which is more environmentally-friendly and sheds light to the conversion of toxic materials into useful chemical precursors.

Mechanistic aspects of ketene formation deduced from femtosecond photolysis of diazocyclohexadienone, o-phenylene thioxocarbonate, and 2-chlorophenol.

The photochemistry of diazocyclohexadienone (1), o-phenylene thioxocarbonate (2), and 2-chlorophenol (3) in solution was studied using time-resolved UV-vis and IR transient absorption spectroscopies. In these three cases, the same product cyclopentadienyl ketene (5) is formed, and two different mechanistic pathways leading to this product are discussed: (a) rearrangement in the excited state (RIES) and (b) a stepwise route involving the intermediacy of vibrationally excited or relaxed carbene. Femtosecond UV-vis detection allows observation of an absorption band assigned to singlet 2-oxocyclohexa-3,5-dienylidene (4), and this absorption feature decays with an ∼30 ps time constant in hexane and acetonitrile. The excess vibrational energy present in nascent carbenes results in the ultrafast Wolff rearrangement of the hot species. IR detection shows that photoexcited o-phenylene thioxocarbonate (2) and 2-chlorophenol (3) efficiently form the carbene species while diazocyclohexadienone (1) photochemistry proceeds mainly by a concerted process.

The photochemistry of 4,5-carbomethoxy-1,2,3-thiadiazole: direct observation of thiirene formation and its decay in solution.

The photochemistry of 4,5-carbomethoxy-1,2,3-thiadiazole in solution was studied at room temperature with use of UV-vis and IR transient absorption spectroscopies (λ(ex) = 266 nm). Ultrafast time-resolved techniques demonstrate that there is a very fast rise (<0.4 ps) of bis(carbomethoxy)thiirene in acetonitrile, and that it is the only intermediate formed. The lifetime of the thiirene is limited by dimerization to eventually form tetra(carbomethoxy)thiophene.

Direct observation of a sulfonyl azide excited state and its decay processes by ultrafast time-resolved IR spectroscopy.

The photochemistry of 2-naphthylsulfonyl azide (2-NpSO(2)N(3)) was studied by femtosecond time-resolved infrared (TR-IR) spectroscopy and with quantum chemical calculations. Photolysis of 2-NpSO(2)N(3) with 330 nm light promotes 2-NpSO(2)N(3) to its S(1) state. The S(1) excited state has a prominent azide vibrational band. This is the first direct observation of the S(1) state of a sulfonyl azide, and this vibrational feature allows a mechanistic study of its decay processes. The S(1) state decays to produce the singlet nitrene. Evidence for the formation of the pseudo-Curtius rearrangement product (2-NpNSO(2)) was inconclusive. The singlet sulfonylnitrene (1)(2-NpSO(2)N) is a short-lived species (τ ≈ 700 ± 300 ps in CCl(4)) that decays to the lower-energy and longer-lived triplet nitrene (3)(2-NpSO(2)N). Internal conversion of the S(1) excited state to the ground state S(0) is an efficient deactivation process. Intersystem crossing of the S(1) excited state to the azide triplet state contributes only modestly to deactivation of the S(1) state of 2-NpSO(2)N(3).

Mechanistic study of the photochemical hydroxide ion release from 9-hydroxy-10-methyl-9-phenyl-9,10-dihydroacridine.

The excited-state behavior of 9-hydroxy-10-methyl-9-phenyl-9,10-dihydroacridine and its derivative, 9-methoxy-10-methyl-9-phenyl-9,10-dihydroacridine (AcrOR, R = H, Me), was studied via femtosecond and nanosecond UV-vis transient absorption spectroscopy. The solvent effects on C-O bond cleavage were clearly identified: a fast heterolytic cleavage (τ = 108 ps) was observed in protic solvents, while intersystem crossing was observed in aprotic solvents. Fast heterolysis generates 10-methyl-9-phenylacridinium (Acr(+)) and (-)OH, which have a long recombination lifetime (no signal decay was observed within 100 µs). AcrOH exhibits the characteristic behavior needed for its utilization as a chromophore in the pOH jump experiment.

Ultrafast infrared and UV-vis studies of the photochemistry of methoxycarbonylphenyl azides in solution.

The photochemistry of 4-methoxycarbonylphenyl azide (2a), 2-methoxycarbonylphenyl azide (3a), and 2-methoxy-6-methoxycarbonylphenyl azide (4a) were studied by ultrafast time-resolved infrared (IR) and UV-vis spectroscopies in solution. Singlet nitrenes and ketenimines were observed and characterized for all three azides. Isoxazole species 3g and 4g are generated after photolysis of 3a and 4a, respectively, in acetonitrile. Triplet nitrene 4e formation correlated with the decay of singlet nitrene 4b. The presence of water does not change the chemistry or kinetics of singlet nitrenes 2b and 3b, but leads to protonation of 4b to produce nitrenium ion 4f. Singlet nitrenes 2b and 3b have lifetimes of 2 ns and 400 ps, respectively, in solution at ambient temperature. The singlet nitrene 4b in acetonitrile has a lifetime of about 800 ps, and reacts with water with a rate constant of 1.9 × 10(8) L·mol(-1)·s(-1) at room temperature. These results indicate that a methoxycarbonyl group at either the para or ortho positions has little influence on the ISC rate, but that the presence of a 2-methoxy group dramatically accelerates the ISC rate relative to the unsubstituted phenylnitrene. An ortho-methoxy group highly stabilizes the corresponding nitrenium ion and favors its formation in aqueous solvents. This substituent has little influence on the ring-expansion rate. These results are consistent with theoretical calculations for the various intermediates and their transition states. Cyclization from the nitrene to the azirine intermediate is favored to proceed toward the electron-deficient ester group; however, the higher energy barrier is the ring-opening process, that is, azirine to ketenimine formation, rendering the formation of the ester-ketenimine (4d') to be less favorable than the isomeric MeO-ketenimine (4d).

Direct observation of a carbene-alcohol ylide.

Carboethoxycarbene reacts with methanol-OD to form an ylide. The formation and decay of this ylide was monitored by ultrafast time-resolved IR spectroscopy. The formation and decay of the ylide is linearly dependent on the concentration of methanol-OD in acetonitrile with second-order rate constants of ylide formation (8.4 × 10(9) M(-1) s(-1)) and decay (1.4 × 10(9) M(-1) s(-1)). Similar results were obtained with 1-butanol.

Photochemistry of 2-naphthoyl azide. An ultrafast time-resolved UV-vis and IR spectroscopic and computational study.

The photochemistry of 2-naphthoyl azide was studied in various solvents by femtosecond time-resolved transient absorption spectroscopy with IR and UV-vis detection. The experimental findings were interpreted with the aid of computational studies. Using polar and nonpolar solvents, the formation and decay of the first singlet excited state (S(1)) was observed by both time-resolved techniques. Three processes are involved in the decay of the S(1) excited state of 2-naphthoyl azide: intersystem crossing, singlet nitrene formation, and isocyanate formation. The lifetime of the S(1) state decreases significantly as the solvent polarity increases. In all solvents studied, isocyanate formation correlates with the decay of the azide S(1) state. Nitrene formation correlates with the decay of the relaxed S(1) state only upon 350 nm excitation (S(0) → S(1) excitation). When S(n) (n ≥ 2) states are populated upon excitation (λ(ex) = 270 nm), most nitrene formation takes place within a few picoseconds through the hot S(1) and higher singlet excited states (S(n)) of 2-naphthoyl azide. The data correlate with the results of electron density difference calculations that predict nitrene formation from the higher-energy singlet excited states, in addition to the S(1) state. For all of these experiments, no recovery of the ground state was observed up to 3 ns after photolysis, which indicates that both internal conversion and fluorescence have very low efficiencies.

Time-resolved resonance Raman and computational investigation of the influence of 4-acetamido and 4-N-methylacetamido substituents on the chemistry of phenylnitrene.

A time-resolved resonance Raman (TR(3)) and computational investigation of the photochemistry of 4-acetamidophenyl azide and 4-N-methylacetamidophenyl azide in acetonitrile is presented. Photolysis of 4-acetamidophenyl azide appears to initially produce singlet 4-acetamidophenylnitrene which undergoes fast intersystem crossing (ISC) to form triplet 4-acetamidophenylnitrene. The latter species formally produces 4,4'-bisacetamidoazobenzene. RI-CC2/TZVP and TD-B3LYP/TZVP calculations predict the formation of the singlet nitrene from the photogenerated S(1) surface of the azide excited state. The triplet 4-acetamidophenylnitrene and 4,4'-bisacetamidoazobenzene species are both clearly observed on the nanosecond to microsecond time-scale in TR(3) experiments. In contrast, only one species can be observed in analogous TR(3) experiments after photolysis of 4-N-methylacetamidophenyl azide in acetonitrile, and this species is tentatively assigned to the compound resulting from dimerization of a 1,2-didehydroazepine. The different photochemical reaction outcomes for the photolysis of 4-acetamidophenyl azide and 4-N-methylacetamidophenyl azide molecules indicate that the 4-acetamido group has a substantial influence on the ISC rate of the corresponding substituted singlet phenylnitrene, but the 4-N-methylacetamido group does not. CASSCF analyses predict that both singlet nitrenes have open-shell electronic configurations and concluded that the dissimilarity in the photochemistry is probably due to differential geometrical distortions between the states. We briefly discuss the probable implications of this intriguing substitution effect on the photochemistry of phenyl azides and the chemistry of the related nitrenes.

Photoactive Yellow Protein Chromophore Photoisomerizes around a Single Bond if the Double Bond Is Locked.

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

Excited-State Vibronic Dynamics of Bacteriorhodopsin from Two-Dimensional Electronic Photon Echo Spectroscopy and Multiconfigurational Quantum Chemistry.

Owing to the ultrafast time scale of the photoinduced reaction and high degree of spectral overlap among the reactant, product, and excited electronic states in bacteriorhodopsin (bR), it has been a challenge for traditional spectroscopies to resolve the interplay between vibrational dynamics and electronic processes occurring in the retinal chromophore of bR. Here, we employ ultrafast two-dimensional electronic photon echo spectroscopy to follow the early excited-state dynamics of bR preceding the isomerization. We detect an early periodic photoinduced absorptive signal that, employing a hybrid multiconfigurational quantum/molecular mechanical model of bR, we attribute to periodic mixing of the first and second electronic excited states (S1 and S2, respectively). This recurrent interaction between S1 and S2, induced by a bond length alternation of the retinal chromohore, supports the hypothesis that the ultrafast photoisomerization in bR is initiated by a process involving coupled nuclear and electronic motion on three different electronic states.

Direct observation of acyl azide excited states and their decay processes by ultrafast time resolved infrared spectroscopy.

The photochemistry of three carbonyl azides was studied by ultrafast time-resolved IR spectroscopy. Benzoyl, 2-naphthoyl, and pivavoyl azides are promoted to upper excited states S(n) with 270 nm excitation in chloroform. The S(n) states decay in 300 fs to form both the carbonylnitrenes and the S(1) excited states. The decay of the S(1) states of the carbonyl azides correlates with the growth of isocyanates. Formation of carbonylnitrene from S(1) is at most a minor process if it happens at all. The quantum yields of azide decomposition of these azides with 270 nm light are close to unity in chloroform.

Multiscale Molecular Dynamics Simulations of Polaritonic Chemistry.

When photoactive molecules interact strongly with confined light modes as found in plasmonic structures or optical cavities, new hybrid light-matter states can form, the so-called polaritons. These polaritons are coherent superpositions (in the quantum mechanical sense) of excitations of the molecules and of the cavity photon or surface plasmon. Recent experimental and theoretical works suggest that access to these polaritons in cavities could provide a totally new and attractive paradigm for controlling chemical reactions that falls in between traditional chemical catalysis and coherent laser control. However, designing cavity parameters to control chemistry requires a theoretical model with which the effect of the light-matter coupling on the molecular dynamics can be predicted accurately. Here we present a multiscale quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation model for photoactive molecules that are strongly coupled to confined light in optical cavities or surface plasmons. Using this model we have performed simulations with up to 1600 Rhodamine molecules in a cavity. The results of these simulations reveal that the contributions of the molecules to the polariton are time-dependent due to thermal fluctuations that break symmetry. Furthermore, the simulations suggest that in addition to the cavity quality factor, also the Stokes shift and number of molecules control the lifetime of the polariton. Because large numbers of molecules interacting with confined light can now be simulated in atomic detail, we anticipate that our method will lead to a better understanding of the effects of strong coupling on chemical reactivity. Ultimately the method may even be used to systematically design cavities to control photochemistry.