Photoisomerization Quantum Yield Research Articles

Reaction dynamics of the chimeric channelrhodopsin C1C2

Channelrhodopsin (ChR) is a key protein of the optogenetic toolkit. C1C2, a functional chimeric protein of Chlamydomonas reinhardtii ChR1 and ChR2, is the only ChR whose crystal structure has been solved, and thus uniquely suitable for structure-based analysis. We report C1C2 photoreaction dynamics with ultrafast transient absorption and multi-pulse spectroscopy combined with target analysis and structure-based hybrid quantum mechanics/molecular mechanics calculations. Two relaxation pathways exist on the excited (S1) state through two conical intersections CI1 and CI2, that are reached via clockwise and counter-clockwise rotations: (i) the C13=C14 isomerization path with 450 fs via CI1 and (ii) a relaxation path to the initial ground state with 2.0 ps and 11 ps via CI2, depending on the hydrogen-bonding network, hence indicating active-site structural heterogeneity. The presence of the additional conical intersection CI2 rationalizes the relatively low quantum yield of photoisomerization (30 ± 3%), reported here. Furthermore, we show the photoreaction dynamics from picoseconds to seconds, characterizing the complete photocycle of C1C2.

Time-Resolved Energetics of Photoprocesses in Prokaryotic Phytochrome-Related Photoreceptors.

Time-resolved photoacoustics (PA) is uniquely able to explore the energy landscape of photoactive proteins and concomitantly detects light-induced volumetric changes (ΔV) accompanying the formation and decay of transient species in a time window between ca. 20ns and 5μs. Here, we report PA measurements on diverse photochromic bilin-binding photoreceptors of prokaryotic origin: (1) the chromophore-binding GAF3 domain of the red (R)/green (G) switching cyanobacteriochrome 1393 (Slr1393g3) from Synechocystis; (2) the red/far red (R/FR) Synechocystis Cph1 phytochrome; (3) full-length and truncated constructs of Xanthomonas campestris bacteriophytochrome (XccBphP), absorbing up to the NIR spectral region. In almost all cases, photoisomerization results in a large fraction of energy dissipated as heat (up to 90%) on the sub-ns scale, reflecting the low photoisomerization quantum yield (<0.2). This "prompt" step is accompanied by a positive ΔV1 =5-12.5mLmol-1 . Formation of the first intermediate is the sole process accessible to PA, with the notable exception of Slr1393g3-G for which ΔV1 = +4.5mLmol-1 is followed by a time-resolved, energy-conserving contraction ΔV2 =-11.4mLmol-1 , τ2 =180ns at 2.4°C. This peculiarity is possibly due to a larger solvent occupancy of the chromophore cavity for Slr1393g3-G.

Temperature-Dependent Photoisomerization Quantum Yields for Azobenzene-Modified DNA

We study the photoisomerization quantum yield of azobenzene-modified DNA as a function of temperature for various DNA sequences. We find that even though the photoisomerization quantum yield of free azobenzene is essentially temperature-independent, the trans-to-cis photoisomerization quantum yield depends strongly on temperature when the azobenzene is incorporated into DNA. We show that this temperature dependence is DNA-sequence-dependent and closely linked to the melting temperature of the host DNA. While the trans-to-cis isomerization quantum yield is sequence- and temperature-dependent, in contrast, the thermal cis-to-trans isomerization of azobenzene embedded in DNA is sequence-independent and exhibits Arrhenius-like behavior with an activation energy of 88.8 ± 0.693 kJ/mol and a smaller pre-exponential factor than free azobenzene, yielding first-order cis-to-trans kinetics with a rate constant of (2.08 ± 0.00952) × 10–6 s–1 at 25 °C. These results provide an understanding of the azobenzene isomeriz...

Optomechanical Control of Quantum Yield in Trans-Cis Ultrafast Photoisomerization of a Retinal Chromophore Model.

The quantum yield of a photochemical reaction is one of the most fundamental quantities in photochemistry, as it measures the efficiency of the transduction of light energy into chemical energy. Nature has evolved photoreceptors in which the reactivity of a chromophore is enhanced by its molecular environment to achieve high quantum yields. The retinal chromophore sterically constrained inside rhodopsin proteins represents an outstanding example of such a control. In a more general framework, mechanical forces acting on a molecular system can strongly modify its reactivity. Herein, we show that the exertion of tensile forces on a simplified retinal chromophore model provokes a substantial and regular increase in the trans-to-cis photoisomerization quantum yield in a counterintuitive way, as these extension forces facilitate the formation of the more compressed cis photoisomer. A rationale for the mechanochemical effect on this photoisomerization mechanism is also proposed.

Optomechanical Control of Quantum Yield in Trans–Cis Ultrafast Photoisomerization of a Retinal Chromophore Model

AbstractThe quantum yield of a photochemical reaction is one of the most fundamental quantities in photochemistry, as it measures the efficiency of the transduction of light energy into chemical energy. Nature has evolved photoreceptors in which the reactivity of a chromophore is enhanced by its molecular environment to achieve high quantum yields. The retinal chromophore sterically constrained inside rhodopsin proteins represents an outstanding example of such a control. In a more general framework, mechanical forces acting on a molecular system can strongly modify its reactivity. Herein, we show that the exertion of tensile forces on a simplified retinal chromophore model provokes a substantial and regular increase in the trans‐to‐cis photoisomerization quantum yield in a counterintuitive way, as these extension forces facilitate the formation of the more compressed cis photoisomer. A rationale for the mechanochemical effect on this photoisomerization mechanism is also proposed.

Determining the Photoisomerization Quantum Yield of Photoswitchable Molecules in Solution and in the Solid State

Photoswitchable molecules are able to isomerize between two metastable forms through light stimuli. Originally being studied by photochemists, this type of molecule has now found a wide range of applications within physics, chemistry and biology. The extensive usage of photochromic molecules is due to the two isomers having fundamentally different physical and chemical properties. The most important attribute of a photoswitch is the photoisomerization quantum yield, which defines the efficiency of the photoisomerization event. Here we show how to determine the photoisomerization quantum yield in the solid state and in solution when taking thermal processes into account. The described method together with provided software allows for rapid and accurate determination of the isomerization process for this important class of molecules.

Spectral and photochemical properties of hybrid organic—inorganic nanosystems based on CdS quantum dots and a styrylquinoline ligand

The kinetics of photolysis of a styrylquinoline (SQ) derivative as the photochromic ligand in organic—inorganic hybrid nanosystems (HNSs) with the core composed of CdS quantum dots (QDs) has been studied for the first time as a function of the number of ligand molecules in the HNS shell, which varied from 1 to 10. The hybrid nanosystems have been synthesized in the microwave-assisted mode according to the single-step injection-free procedure. It has been shown that high quantum yields of photoisomerization of the SQ ligand are conserved in the HNS. In the early stages of the photolysis, regardless of the number of SQ ligand molecules in the HNS shell, the kinetics obeys the equation for the photolysis of the monomolecular system (model SQ photochrome) with allowance for the absorption due to QDs as an inert shutter. During the course of long-term photolysis, the quantum dots undergo photodegradation to be completely decomposed. According to the principal component analysis data, several photoproducts with different absorption spectra are formed at the intermediate times of the HNS photolysis.

Synthesis and Photoisomerization of Substituted Dibenzofulvene Molecular Rotors.

The synthesis, spectral and structural characterization, and photoisomerization of a family of 2-substituted dibenzofulvene molecular actuators based on (2,2,2-triphenylethylidene)fluorene (TEF) are reported. The 2-substituted species investigated are nitro (NTEF), cyano (CTEF), and iodo (ITEF). X-ray structures of these three compounds and three intermediates were determined to assign alkene configuration and investigate the effects of the 2-substituents on steric gearing. The addition-elimination reaction of Z-9 with trityl anion to form Z-10 proceeded with complete retention of configuration. Rates of photoisomerization were measured at irradiation wavelengths between 266-355 nm in acetonitrile/dioxane solutions at room temperature. Photoisomerization quantum yields (φ) were calculated by means of a mathematical model that accounts for a certain degree of photodecomposition in the cases of CTEF and ITEF. Quantum yields vary significantly with substituent, having maximum values of φ=0.26 for NTEF, 0.39 for CTEF, and 0.50 for ITEF. NTEF is photochemically robust and has a large quantum yield for photoisomerization in the near-UV, making it a particularly promising drive rotor moiety for light-powered molecular devices.

Photochemistry of the 1,4-Diphenyl-1,3-butadienes in Ethanol. Trapping Conical Intersections.

We report photoisomerization and photoaddition quantum yields in ethanol starting from each 1,4-diphenyl-1,3-butadiene, DPB, isomer. Despite the fact that the trans,trans isomer, tt-DPB, has a significant fluorescence quantum yield and lifetime, whereas no fluorescence is observed from the cis isomers, ether formation occurs with similar efficiency from tt-DPB and ct-DPB and less efficiently from cc-DPB. Photoaddition is about 72 times slower than photoisomerization to the ct- and tt-DPB isomers starting from tt- and ct-DPB, respectively. The results are consistent with addition of alcohol to the common zwitterionic trans-phenallyl cation/benzyl anion intermediate that leads to photoisomerization through a conical intersection. Ether formation from cc-DPB tracks inefficient formation of tt-DPB indicating that the small bicycle pedal cc-DPB → tt-DPB component proceeds stepwise through the same zwitterionic trans-phenallyl cation/benzyl anion intermediate. Previous results concerning the addition of methanol to the stilbenes are similarly interpreted. In contrast to trans-stilbene, the fluorescence and photoisomerization quantum yields of tt-DPB are inconsistent with the assumption of strict complementarity between radiative and torsional relaxation channels of tt-DPB in alcohols.

Tuning the Activation Wavelength of Photochromic Oxazines.

The activation wavelength of a photochromic oxazine can be shifted bathochromically with the introduction of a methoxy substituent on the chromophore responsible for initiating the photochemical transformation. This structural modification permits switching under mild illumination conditions, enhances the photoisomerization quantum yield and ensures outstanding fatigue resistance. Thus, these results can guide the design of new members of this family of photoresponsive molecular switches with improved photochemical and photophysical properties.

Local Compressibility: Ground-State Predictions of Quantum Yield Trends in Azobenzene-Modified DNA

Azobenzene incorporated into DNA has a photoisomerization quantum yield that varies as a function of the local DNA sequence and base pairing near the azobenzene attachment site. We use Molecular Dynamics computer simulations to study the effects of local free volume on photoswitching in azobenzene-modified DNA, and we find that the azobenzene quantum yield correlates strongly with the sequence-dependent variance of the local free volume. We infer that differences in quantum yield are controlled by the free energy cost of emptying the volume surrounding the azobenzene. We use our simulations to correctly predict the quantum yields for azobenzenes in several sequences not previously measured. These results will be useful in the development of a wide range of applications of photoresponsive DNA nanotechnology, ranging from controlled gene expression to DNA sensing and nanoparticle assembly.

Can Azobenzene Photoisomerize When Chemisorbed on a Gold Surface? An Analysis of Steric Effects Based on Nonadiabatic Dynamics Simulations

Through a combined quantum mechanics/molecular mechanics (QM/MM) approach, we evaluate the photodynamics of the mono- and dithiolated azobenzenes when they are chemisorbed on a gold surface. The analysis of steric effects suggests that the presence of the surface influences the photoisomerization process of the chemisorbed monothiolated azobenzene. In particular, the trans → cis quantum yields decrease, and the nπ* state lifetimes become longer. The approach to the twisted conical intersection needed for the isomerization is hindered when the molecule is attached to a substrate because of the van der Waals interactions with the surface. For the cis isomer, the cis → trans photoisomerization quantum yield is almost unaffected, since this isomer is not flat, and thus the interaction with the surface is less remarkable. Dithiolated azobenzene can photoisomerize both trans → cis and cis → trans, also when doubly linked to the surface, preserving the two bonds with the gold atoms: the flexibility of the centra...

The effect of ring size on the optical behavior of novel photochromic push-pull dyes.

The photophysical behaviors of newly synthesized photochromic dyes have been investigated in different solvents of various polarities using steady-state absorption and emission techniques. It was found that, the absorption and emission spectra of these dyes depend on the ring size and the solvent polarity. The higher values of the dipole moments of the investigated dyes in the excited state than those in the ground state suggest that these dyes can serve as good candidate components of nonlinear optical materials. Additionally, the photoisomerization parameters (percentage of composition of cis isomers and quantum yields of photoisomerization) depend on the polarity and the viscosity of the used solvents as well as the ring size. The molecular motion that occurs in the isomerization process has facilitated the development of molecular devices. Finally, the halochromic behaviors of the investigated dyes promise them to act as acid-base indicators.

Photoisomerization dynamics of a rhodopsin-based molecule (potential molecular switch) with high quantum yields

It is worthwhile to explore the detailed reaction dynamics of various candidates for molecular switches, in order to understand, e.g., the differences in quantum yields and switching times. Here we report density-functional-based simulations for the rhodopsin-based molecule 4-[4-methylbenzylidene]-5-p-tolyl-3,4-dihydro-2H-pyrrole (MDP), synthesized by Sampedro et al We find that the photoisomerization quantum yields are remarkably high: 82% for cis-to-trans, and 68% for trans-to-cis. The lifetimes of the S1 excited state in cis-MDP in our calculations are in the range of 900–1800 fs, with a mean value of 1270 fs, while the range of times required for full cis-to-trans isomerization are 1100–2000 fs, with a mean value of 1530 fs. In trans-MDP, the calculated S1 excited state lifetimes are 860–2140 fs, with a mean value of 1330 fs, and with the full trans-to-cis isomerization completed about 200 fs later. In both cases, the dominant reaction mechanism is rotation around the central C=C bond (connected to the pyrroline ring), and de-excitation occurs at an avoided crossing between the ground state and the lowest singlet state, near the midpoint of the rotational pathway. Perhaps remarkably, but apparently because of electrostatic repulsion, the direction of rotation is the same for both reactions.

Spectral and photochemical properties of styrylquinoline-merocyanine dyads based on 2-styrylquinoline

The properties of styrylquinoline-merocyanine dyads, in which the styrylquinoline (SQ) and merocyanine (MC) moieties are linked with a bridge of three (SQ3MC dyad) and eleven (SQ11MC dyad) methylene groups, have been compared with the properties of the model compounds 2-(4-methoxystyryl)quinoline and 1-ethyl-2-(4-methoxystyryl)quinolinium perchlorate, of which the latter is the O-methylated merocyanine derivative. Efficient inductive-resonance energy transfer (FRET) from the SQ to the MC moiety has been revealed, resulting in the quenching of the former and sensitization of the latter. The quenching of the SQ moiety manifests itself in a decrease in the quantum yield of trans-cis photoisomerization and fluorescence, and the sensitization of the MC moiety enhances these parameters. The efficiency of energy transfer decreases from 96 to 87% on passing from the SQ3MC to SQ11MC dyad.

Photochemical properties of 1-(9-Anthryl)-2-(2-Quinolyl)ethylene

Spectral and photochemical properties of 1-(9-anthryl)-2-(2-quinolyl)ethylene (9A2QE) in neutral and protonated forms have been studied experimentally and by quantum-chemical methods. It has been found that the quantum yield of trans-cis photoisomerization (φtc) has values of φtc 0.5, which exceeds the limiting value for the diabatic photoisomerization.

Excitation of Biomolecules with Incoherent Light: Quantum Yield for the Photoisomerization of Model Retinal

Cis-trans isomerization in retinal, the first step in vision, is often computationally studied from a time-dependent viewpoint. Motivation for such studies lies in coherent pulsed laser experiments that explore the isomerization dynamics. However, such biological processes take place naturally in the presence of incoherent light, which is expected to excite a nonevolving mixture of stationary states. Here the isomerization problem is considered from the latter viewpoint and applied to a standard two-state, two-mode linear vibronic coupling model of retinal that explicitly includes a conical intersection between the ground and first excited electronic states. The calculated quantum yield at 500 nm agrees well with both the previous time-dependent calculations of Hahn and Stock (0.63) [ J. Phys. Chem. B 2000, 104, 1146-1149 ] and with experiment (0.65 ± 0.01), as does its wavelength dependence. Significantly, the effects of environmental relaxation on the quantum yield in this well-established model are found to be negligible. The results make clear the connection of the photoisomerization quantum yield to properties of stationary eigenstates, providing alternate insights into conditions for yield optimization.

Competing adiabatic and nonadiabatic pathways in the cis–trans photoisomerization of cis-1,2-di(1-methyl-2-naphthyl)ethene. A zwitterionic twisted intermediate

Identical fluorescence lifetimes and spectra of cis- and trans-1,2-di(1-methyl-2-naphthyl)ethene reveal an adiabatic cis → trans photoisomerization pathway that accounts for a significant fraction of observed cis → trans photoisomerization quantum yields. The fluorescence quantum yields of both isomers decrease as the solvent is changed from methylcyclohexane to the more polarizable toluene or to the more polar acetonitrile and there is a corresponding increase in the photoisomerization quantum yield in the trans → cis direction. The pronounced solvent dependence of the contribution of the adiabatic pathway to cis → trans photoisomerization--methylcyclohexane (70%), toluene (45%), acetonitrile (31%)--is consistent with the participation of a zwitterionic twisted intermediate, (1)p*, on the singlet excited state surface which is stabilized as the polarizability and/or polarity of the solvent is increased. Solvent stabilization of (1)p* favours the nonadiabatic photoisomerization pathways of both isomers and diminishes the cis → trans adiabatic pathway.

Remarkable enhancement of the photoreactivity of a polyfluoroalkyl azobenzene derivative in an organic–inorganic nano-layered microenvironment

Organic-inorganic hybrids composed of polyfluoroalkyl azobenzene surfactant (abbreviated as C3F-Azo-C6H) and inorganic layered compounds are able to undergo reversible three-dimensional morphology changes such as interlayer space changes and nanosheet sliding in a giant scale due to reversible trans-cis isomerization of the azobenzene moiety upon photo-irradiation. In this paper, we have systematically studied the relationship between the layered hybrid microstructures of C3F-Azo-C6H-clay and their photoreactivity for understanding the mechanism of the photo-induced morphology change. The photoreactivity was found to be very much affected by the surrounding microenvironments. As compared with it in solution, the cis-trans photo-isomerization in C3F-Azo-C6H-clay nano-layered film was substantially enhanced with the quantum yield exceeding unity (Φ = 1.9), while the trans-cis isomerization was rather retarded. The corresponding hydrocarbon analogue of the azobenzene surfactant (C3H-Azo-C6H) did not show such an enhancement. The enhancement was discussed in terms of a cooperative effect among adjacent azobenzene moieties along with polyfluoroalkyl chains and the inorganic clay nanosheet to prevent a dissipation of the excess energy being liberated during the photo-isomerization within the nano-layered microenvironment.

Photoisomerization Quantum Yield of Azobenzene-Modified DNA Depends on Local Sequence

Photoswitch-modified DNA is being studied for applications including light-harvesting molecular motors, photocontrolled drug delivery, gene regulation, and optically mediated assembly of plasmonic metal nanoparticles in DNA-hybridization assays. We study the sequence and hybridization dependence of the photoisomerization quantum yield of azobenzene attached to DNA via the popular d-threoninol linkage. Compared to free azobenzene we find that the quantum yield for photoisomerization from trans to cis form is decreased 3-fold (from 0.094 ± 0.004 to 0.036 ± 0.002) when the azobenzene is incorporated into ssDNA, and is further reduced 15-fold (to 0.0056 ± 0.0008) for azobenzene incorporated into dsDNA. In addition, we find that the quantum yield is sensitive to the local sequence including both specific mismatches and the overall sequence-dependent melting temperature (Tm). These results serve as design rules for efficient photoswitchable DNA sequences tailored for sensing, drug delivery, and energy-harvesting applications, while also providing a foundation for understanding phenomena such as photonically controlled hybridization stringency.