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 B2 cat2 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.

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.

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.

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.

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.

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.

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.

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.

Modulation of thermal noise and spectral sensitivity in Lake Baikal cottoid fish rhodopsins.

Lake Baikal is the deepest and one of the most ancient lakes in the world. Its unique ecology has resulted in the colonization of a diversity of depth habitats by a unique fauna that includes a group of teleost fish of the sub-order Cottoidei. This relatively recent radiation of cottoid fishes shows a gradual blue-shift in the wavelength of the absorption maximum of their visual pigments with increasing habitat depth. Here we combine homology modeling and quantum chemical calculations with experimental in vitro measurements of rhodopsins to investigate dim-light adaptation. The calculations, which were able to reproduce the trend of observed absorption maxima in both A1 and A2 rhodopsins, reveal a Barlow-type relationship between the absorption maxima and the thermal isomerization rate suggesting a link between the observed blue-shift and a thermal noise decrease. A Nakanishi point-charge analysis of the electrostatic effects of non-conserved and conserved amino acid residues surrounding the rhodopsin chromophore identified both close and distant sites affecting simultaneously spectral tuning and visual sensitivity. We propose that natural variation at these sites modulate both the thermal noise and spectral shifting in Baikal cottoid visual pigments resulting in adaptations that enable vision in deep water light environments.

Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology.

We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their mutants. In the present implementation the information required for the construction of each model is essentially a crystallographic structure or a comparative model complemented with information on the protonation state of ionizable side chains and distributions of external counterions. Starting with such information, a model formed by a fixed environment system, a flexible cavity system, and a chromophore system is automatically generated. The results of the predicted vertical excitation energy for 27 different rhodopsins including vertebrate, invertebrate, and microbial pigments indicate that such basic models could be employed for predicting trends in spectral changes and/or correlate the spectral changes with structural variations in large sets of proteins.

Probing the Photodynamics of Rhodopsins with Reduced Retinal Chromophores.

While the light-induced population dynamics of different photoresponsive proteins has been investigated spectroscopically, systematic computational studies have not yet been possible due to the phenomenally high cost of suitable high level quantum chemical methods and the need of propagating hundreds, if not thousands, of nonadiabatic trajectories. Here we explore the possibility of studying the photodynamics of rhodopsins by constructing and investigating quantum mechanics/molecular mechanics (QM/MM) models featuring reduced retinal chromophores. In order to do so we use the sensory rhodopsin found in the cyanobacterium Anabaena PCC7120 (ASR) as a benchmark system. We find that the basic mechanistic features associated with the excited state dynamics of ASR QM/MM models are reproduced using models incorporating a minimal (i.e., three double-bond) chromophore. Furthermore, we show that ensembles of nonadiabatic ASR trajectories computed using the same abridged models replicate, at both the CASPT2 and CASSCF levels of theory, the trends in spectroscopy and lifetimes estimated using unabridged models and observed experimentally at room temperature. We conclude that a further expansion of these studies may lead to low-cost QM/MM rhodopsin models that may be used as effective tools in high-throughput in silico mutant screening.

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.

Excited-state hydroxide ion transfer from a model xanthenol photobase.

This article reports a study of excited-state hydroxide ion release from a model xanthenol photobase, XanOH. The driving force for the reaction was tuned using solvent mixtures with varying water/acetonitrile ratios, and the kinetics of the reaction was monitored using ultrafast pump-probe spectroscopy. The intrinsic barrier for the heterolysis was evaluated using Marcus and bond-energy bond-order (BEBO) models. The obtained value (ΔG(o)(#) = 10.17-10.80 kcal/mol) is significantly higher than the intrinsic barriers found for the proton release from previously studied photoacids. These results were discussed in terms of the difference in structures of solvated H(+) and OH(-) ions.

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.

Toward organic photohydrides: excited-state behavior of 10-methyl-9-phenyl-9,10-dihydroacridine.

The excited-state hydride release from 10-methyl-9-phenyl-9,10-dihydroacridine (PhAcrH) was investigated using steady-state and time-resolved UV/vis absorption spectroscopy. Upon excitation, PhAcrH is oxidized to the corresponding iminium ion (PhAcr(+)), while the solvent (acetonitrile/water mixture) is reduced (52% of PhAcr(+) and 2.5% of hydrogen is formed). The hydride release occurs from the triplet excited state by a stepwise electron/hydrogen-atom transfer mechanism. To facilitate the search for improved organic photohydrides that exhibit a concerted mechanism, a computational methodology is presented that evaluates the thermodynamic parameters for the hydride ion, hydrogen atom, and electron release from organic hydrides.

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.

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 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).