Thermal Isomerization Rate Research Articles

Mesomorphic and optical properties of azo-ester liquid crystalline reactive mesogens with enhanced thermal stability

A series of azo-ester-linked polymerizable liquid crystalline compounds M1-M3, containing lateral methyl substitution and different terminal alkoxy substituents, e.g., −OCH3, −OCH2CH3, and −OCH2CH2CH3 have successfully been synthesized and characterized. The chemical structures of the prepared compounds were confirmed by different spectroscopic techniques. Thermogravimetric analysis revealed that all the compounds exhibited excellent thermal stability and showed two-staged decomposition patterns. The optical microscopic study revealed that all compounds displayed only the nematic phase and lateral substituent played a crucial role in the formation of single mesophase. The broad X-ray scattering peaks for M1, M2, and M3 in the 2.5–5.5 nm−1 region was observed at temperatures of 154 °C, 85 °C, and 129 °C, respectively, upon cooling from the isotropic liquid, confirming the existence of nematic mesophase. The electronic spectra of M1-M3 showed two main absorption bands with λmax ranges of 263–266 and 369–377 nm. The E-Z photoisomerization study of M1-M3 showcased that the processes followed the first-order kinetic, and the isomerization rate decreased as the alkoxy chain length increased. On the contrary, the Z-E thermal isomerization rates for M1-M3 showed insignificant changes as the alkoxy chain length increased.

On the Simulation of Thermal Isomerization of Molecular Photoswitches in Biological Systems.

Molecular photoswitches offer precise, reversible photocontrol over biomolecular functions and are promising light-regulated drug candidates with minimal side effects. Quantifying thermal isomerization rates of photoswitches in their target biomolecules is essential for fine-tuning their light-controlled drug activity. However, the effects of protein binding on isomerization kinetics remain poorly understood, and simulations are crucial for filling this gap. Challenges in the simulation include describing multireference electronic structures near transition states, disentangling competing reaction pathways, and sampling protein-ligand interactions. To overcome these challenges, we used multiscale simulations to characterize the thermal isomerization of photostatins (PSTs), which are light-regulated microtubule inhibitors for potential cancer phototherapy. We employed a new ab initio multireference electronic structure method in a quantum mechanics/molecular mechanics setting and combined it with enhanced sampling techniques to characterize the cis to trans free-energy profiles of three PSTs in a vacuum, aqueous solution, and tubulin dimer. The significant advantage of our novel approach is the efficient treatment of the multireference character in PSTs' electronic wavefunction throughout the conformational sampling of protein-ligand interactions along their isomerization pathways. We also benchmarked our calculations using high-level ab initio multireference electronic structure methods and explored the competing isomerization pathways. Notably, calculations in a vacuum and implicit solvent models cannot predict the order of the PSTs' thermal half-lives in the aqueous solution observed in the experiment. Only by explicitly treating the solvent molecules can the correct order of isomerization kinetics be reproduced. Protein binding perturbs free-energy barriers due to hydrogen bonding between PSTs and nearby polar residues. Our work generates comprehensive, high-quality benchmark data and offers guidance for selecting computational methods to study the thermal isomerization of photoswitches. Ab initio multireference free-energy calculations in explicit molecular environments are crucial for predicting the effects of substituents on the thermal half-lives of photoswitches in biological systems.

Combined calorimetric, spectroscopic and microscopic investigation on the inclusion complex from cyclocurcumin and sulfobutylether-β-cyclodextrin in aqueous solution and Kinetics of thermal cis-trans isomerization

The complexation reaction between cyclocurcumin (CyCur), a natural curcuminoid with bioactive effects, and sulfobutylether-β-cyclodextrin (SBE-βCD), one of the more versatile and tolerate β-cyclodextrin derivates, was investigated in aqueous solution at 298 K. The UV–vis spectral changes of CyCur in the presence of SBE-βCD indicate the formation of the host-guest inclusion complex according to a 1:1 stoichiometry. The binding constant (Kb) determined by applying the Benesi-Hildebrand model was comparable to the value obtained by Isothermal Titration Calorimetry (ITC) measurements. Moreover, the thermodynamic parameters of the SBE-βCD/CyCur interactions demonstrate that the complexation process is enthalpically driven. Interestingly, microscopy analysis highlights the tendency of cyclocurcumin to aggregate into spherical fluorescent structures able to change their aspect and morphology in the presence of SBE-βCD. Finally, the thermal cis-trans isomerization rates of CyCur in the temperature range 294–314 K and the energetic parameters calculated by Arrhenius and Eyring plots were spectroscopically determined in SBE-βCD aqueous solution.

Cavity-altered thermal isomerization rates and dynamical resonant localization in vibro-polaritonic chemistry

It has been experimentally demonstrated that reaction rates for molecules embedded in microfluidic optical cavities are altered when compared to rates observed under "ordinary" reaction conditions. However, precise mechanisms of how strong coupling of an optical cavity mode to molecular vibrations affects the reactivity and how resonance behavior emerges are still under dispute. In the present work, we approach these mechanistic issues from the perspective of a thermal model reaction, the inversion of ammonia along the umbrella mode, in the presence of a single-cavity mode of varying frequency and coupling strength. A topological analysis of the related cavity Born-Oppenheimer potential energy surface in combination with quantum mechanical and transition state theory rate calculations reveals two quantum effects, leading to decelerated reaction rates in qualitative agreement with experiments: the stiffening of quantized modes perpendicular to the reaction path at the transition state, which reduces the number of thermally accessible reaction channels, and the broadening of the barrier region, which attenuates tunneling. We find these two effects to be very robust in a fluctuating environment, causing statistical variations of potential parameters, such as the barrier height. Furthermore, by solving the time-dependent Schrödinger equation in the vibrational strong coupling regime, we identify a resonance behavior, in qualitative agreement with experimental and earlier theoretical work. The latter manifests as reduced reaction probability when the cavity frequency ωc is tuned resonant to a molecular reactant frequency. We find this effect to be based on the dynamical localization of the vibro-polaritonic wavepacket in the reactant well.

Fast relaxing red and near-IR switchable azobenzenes with chalcogen and halogen substituents: periodic trends, tuneable thermal half-lives and chalcogen bonding.

Molecular photoswitches operating in the red to near-IR region with controllable thermal relaxation rates are attractive components for photo-regulating biological processes. Herein, we report the synthesis of red-shifted azobenzenes functionalised with the heavier chalcogens and halogens that meet these requirements for biological application; namely fatigue-resistant photo-switching with red and near IR light and functional handles for further functionalisation for application. We report robust periodic trends for the chalcogen and halogen azobenzene series, and exploit intramolecular chalcogen bonding to tune and redshift the absorption maxima, supported by photo-physical measurements and solid-state structural analysis. Remarkably, the rate of the Z → E thermal isomerisation can be tuned over timescales spanning 107 s by judicious choice of chalcogen and halogen substituents.

Azobenzene/Tetraethyl Ammonium Photochromic Potassium Channel Blockers: Scope and Limitations for Design of Para-Substituted Derivatives with Specific Absorption Band Maxima and Thermal Isomerization Rate

Azobenzene/tetraethyl ammonium photochromic ligands (ATPLs) are photoactive compounds with a large variety of photopharmacological applications such as nociception control or vision restoration. Absorption band maximum and lifetime of the less stable isomer are important characteristics that determine the applicability of ATPLs. Substituents allow to adjust these characteristics in a range limited by the azobenzene/tetraethyl ammonium scaffold. The aim of the current study is to find the scope and limitations for the design of ATPLs with specific spectral and kinetic properties by introducing para substituents with different electronic effects. To perform this task we synthesized ATPLs with various electron acceptor and electron donor functional groups and studied their spectral and kinetic properties using flash photolysis and conventional spectroscopy techniques as well as quantum chemical modeling. As a result, we obtained diagrams that describe correlations between spectral and kinetic properties of ATPLs (absorption maxima of E and Z isomers of ATPLs, the thermal lifetime of their Z form) and both the electronic effect of substituents described by Hammett constants and structural parameters obtained from quantum chemical calculations. The provided results can be used for the design of ATPLs with properties that are optimal for photopharmacological applications.

Sensitivity of Isomerization Kinetics of 1,3,5-Triphenylformazan on Cosolvents Added to Toluene.

Formazan molecules exhibit photochromism because isomerization processes following excitation may occur in both the azo group and the hydrazone group; thus, each formazan may be present in various forms with different colors. The ratio of these forms depends on the illumination conditions and the environment of the formazan with a most incisive sensibility of the thermal anti-syn relaxation of the C═N toward slight traces of impurities in toluene solutions, as reported most prominently for 1,3,5-triphenylformazan. Here, we study the latter compound with transient absorption spectroscopy to investigate the role of these traces by adding small amounts of both protic and aprotic cosolvents. Whereas the activation barrier decreases if the binary solvent mixture has a higher polarity, the role of hydrogen bonding can have a reverse impact on the thermal isomerization rate. Both the addition of an aprotic cosolvent and the addition of a protic cosolvent can slow the reaction due to their hydrogen-bond accepting and hydrogen-bond donating properties, respectively. In the case of methanol as a cosolvent, this effect outweighed that of the polarity increase for small concentrations, which was not observed for the fluorinated alcohol hexafluoroisopropanol. The results are explained in the context of a competition between solute-cosolvent and cosolvent-cosolvent hydrogen bonding.

A comprehensive spectroscopic, solvatochromic and photochemical analysis of 5-hydroxyquinoline and 8-hydroxyquinoline mono-azo dyes

A series of novel substituted-azo dyes 8-(aryldiazenyl)quinolin-5-ol (5a-i) were synthesized by the coupling reaction of 5-hydroxyquinoline with diazotized aniline derivatives in the presence of NaNO2 in HCl/H2O mixture. The study of the spectroscopic and solvatochromic properties were performed by FT-IR, 1H and 13C-NMR and UV-Visible spectroscopies. The tautomerism of these dyes was studied using the deuteration technique and solvatochromic measurements. Photochromic properties of these 5-hydroxyquinoline azo dyes were also examined via E/Z and Z/E photochemical isomerization reactions and compared with the existing 8-hydroxyquinoline analogous. The novel substituted-azo dyes exhibited higher Z/E thermal isomerization rates and have larger absorbance wavelength range than their 8-hydroxyquinoline analogous, making them potential molecular switches.

Disruption of Hydrogen-Bond Network in Rhodopsin Mutations Cause Night Blindness

Rhodopsin is the photosensitive protein, which binds to 11-cis-retinal as its chromophore. In the dark, rhodopsin exists as a stable complex between the opsin moiety and 11-cis-retinal. The absorption of a light photon converts 11-cis-retinal to all-trans-retinal and initiates our vision. As a result, the increase in the rate of dark activation of rhodopsin reduces its photosensitivity resulting in night blindness. The mutations, G90D and T94I are night blindness-causing mutations that exhibit completely different physicochemical characteristics associated with the dark activation of rhodopsin, such as a high rate of thermal isomerization of 11-cis-retinal and a slow pigment regeneration. To elucidate the molecular mechanism by which G90D and T94I mutations affect rhodopsin dark activation and regeneration, we performed light-induced difference FTIR spectroscopy on dark and primary photo-intermediate states of G90D and T94I mutants. The FTIR spectra clearly show that both charged G90D and hydrophobic T94I mutants alter the H-bond network at the Schiff base region of the chromophore, which weakens the electrostatic interaction with Glu113 counterion. Our results further show an altered water-mediated H-bond network around the central transmembrane region of mutant rhodopsin, which is reminiscent of the active Meta-II state. This altered water-mediated H-bond network may cause thermal isomerization of the chromophore and facilitate rhodopsin dark activation.

Effect of Oriented External Electric Fields on the Photo and Thermal Isomerization of Azobenzene.

Azobenzene is a prototype molecule with potential applications in molecular switches, solar thermal batteries, sensors, photoresponsive membranes, molecular electronics, data storage, and nonlinear optics. Photo and thermal isomerization pathways exhibit different charge-transfer character and dipole moments, implying that the use of electric fields can be used to modulate the reactivity of azobenzene. This article examines the differential effect of orientated electric fields on the rotation and inversion thermal and photoisomerization pathways of azobenzene to explore the feasibility of using electric fields in the design of azobenzene-based molecular devices. Our findings demonstrate that the application of orientated electric fields modifies the accessibility of the S0/S1 seam of electronic degeneracy, as well as changes the energetically favored relaxation pathway in the branching space to yield different photoproducts. In addition, we observed strong-field dipole-inversion effects that cause a topographical change in the response of the potential energy surface to the applied field and can result in geometric minima that do not exist under field-free conditions. On the S0 surface, transition barriers can be modified on the order of ±10 kcal mol-1, enabling control of thermal isomerization rates.

Solution Phase and Surface Photoisomerization of a Hydrazone Switch with a Long Thermal Half-Life.

Photoswitches can be employed for various purposes, with the half-life being a crucial parameter to optimize for the desired application. The switching of a photochromic hydrazone functionalized with a C6 alkyl thiolate spacer (C6 HAT) was characterized on a number of metal surfaces. C6 HAT exhibits a half-life of 789 years in solution. Tip-enhanced Raman spectroscopy (TERS) was used to study the photoisomerization of the C6 HAT self-assembled monolayers (SAMs) on Au, Ag, and Cu surfaces. The unique spectroscopic signature of the E isomer at 1580 and 1730 cm-1 in TER spectra allowed for its discrimination from the Z isomer. It was found that C6 HAT switches on Au and Cu surfaces when irradiated with 415 nm; however, it cannot isomerize on Ag surfaces, unless higher energy light is used. Based on this finding, and supported by density functional theory calculations, we propose a substrate-mediated photoisomerization mechanism to explain the behavior of C6 HAT on these different metal surfaces. This insight into the hydrazone's switching mechanism on metal surfaces will contribute to the further exploitation of this new family photochromic compounds on metal surfaces. Finally, although we found that the thermal isomerization rate of C6 HAT drastically increases on metal surfaces, the thermal half-life is still 6.9 days on gold, which is longer than that of the majority of azobenzene-based systems.

Synthesis of Bis-β-Diketonate Lanthanide Complexes with an Azobenzene Bridge and Studies of Their Reversible Photo/Thermal Isomerization Properties.

The ligand, bis-β-diketone with an azobenzene bridge (4,4′-(4,4,4-trifluoro-1,3-butanedione)azobenzene, H2L), was prepared for the synthesis of a series of dinuclear lanthanide complexes with the formula [Ln2L3(DMSO)4] (Ln = Eu3+, Gd3+, Tb3+, and DMSO = dimethyl sulfoxide). X-ray crystallographic analysis reveals that the three complexes are triple-stranded dinuclear structures formed by three bis-β-diketonate ligands with two lanthanide ions (Ln3+). The trans-to-cis photoisomerization rates of the azobenzene group of the three [Ln2L3(DMSO)4] complexes in ethanol and acetonitrile solutions are similar to those of the pure H2L ligand and other azobenzene-containing mononuclear lanthanide complexes, but the trans-to-cis quantum yields (Φt→c = 10–3) are 1 order of magnitude smaller. The first-order rate constant for the cis-to-trans thermal isomerization at 50 °C of the H2L ligand is similar to those of azobenzene derivatives, while those for the [Ln2L3(DMSO)4] complexes (kiso = 10–4 s–1) are higher than those of the mononuclear azobenzene-containing lanthanide complexes. Furthermore, as the lanthanide ionic radius becomes smaller from Eu3+ to Gd3+ to Tb3+, the thermal isomerization rate constant decreases and the half-life increases. All these results are proposed to arise from the rigidity at both ends of the azo group by coordination to the dinuclear lanthanide ions and the different isomerization mechanisms. These are the first examples of bis-β-diketonate dinuclear lanthanide complexes with an azobenzene bridge and help illustrate the mechanism of azobenzene isomerization.

Tuning a timing device that regulates lateral root development in rice.

Peptidyl Prolyl Isomerases (PPIases) accelerate cis-trans isomerization of prolyl peptide bonds. In rice, the PPIase LRT2 is essential for lateral root initiation. LRT2 displays in vitro isomerization of a highly conserved W-P peptide bond (104W-P105) in the natural substrate OsIAA11. OsIAA11 is a transcription repressor that, in response to the plant hormone auxin, is targeted to ubiquitin-mediated proteasomal degradation via specific recognition of the cis isomer of its 104W-P105 peptide bond. OsIAA11 controls transcription of specific genes, including its own, that are required for lateral root development. This auxin-responsive negative feedback circuit governs patterning and development of lateral roots along the primary root. The ability to tune LRT2 activity via mutagenesis is crucial for understanding and modeling the role of this bimodal switch in the auxin circuit and lateral root development. We present characterization of the thermal stability and isomerization rates of several LRT2 mutants acting on the OsIAA11 substrate. The thermally stable mutants display activities lower than that of wild-type (WT) LRT2. These include binding diminished but catalytically active P125K, binding incompetent W128A, and binding capable but catalytically incompetent H133Q mutations. Additionally, LRT2 homologs hCypA from human, TaCypA from Triticum aestivum (wheat) and PPIB from E. coli were shown to have 110, 50 and 60% of WT LRT2 activity on the OsIAA11 substrate. These studies identify several thermally stable LRT2 mutants with altered activities that will be useful for establishing relationships between cis-trans isomerization, auxin circuit dynamics, and lateral root development in rice.

Pinopsin evolved as the ancestral dim-light visual opsin in vertebrates

Pinopsin is the opsin most closely related to vertebrate visual pigments on the phylogenetic tree. This opsin has been discovered among many vertebrates, except mammals and teleosts, and was thought to exclusively function in their brain for extraocular photoreception. Here, we show the possibility that pinopsin also contributes to scotopic vision in some vertebrate species. Pinopsin is distributed in the retina of non-teleost fishes and frogs, especially in their rod photoreceptor cells, in addition to their brain. Moreover, the retinal chromophore of pinopsin exhibits a thermal isomerization rate considerably lower than those of cone visual pigments, but comparable to that of rhodopsin. Therefore, pinopsin can function as a rhodopsin-like visual pigment in the retinas of these lower vertebrates. Since pinopsin diversified before the branching of rhodopsin on the phylogenetic tree, two-step adaptation to scotopic vision would have occurred through the independent acquisition of pinopsin and rhodopsin by the vertebrate lineage.

Building Strain with Large Macrocycles and Using It To Tune the Thermal Half-Lives of Hydrazone Photochromes.

Strain has been used as a tool to modulate the reactivity (e.g., mechanochemistry) and thermal isomerization kinetics of photochromic compounds. Macrocyclization is used to build-up strain in such systems, and in general the reactivity and rates increase with the decrease in macrocycle size. To ascertain the effect of strain on recently reported bistable hydrazone photoswitches, we incorporated them into macrocycles having varying aliphatic linker lengths (C3-C7), and studied their switching behavior, and effect of macrocycle size on the thermal isomerization rate. Surprisingly, while the systems with C3-C5 linkers behave as expected (i.e., the rate is faster with smaller linkers), the isomerization rate in the systems with larger aliphatic linkers (C6-C8) is enhanced up to 4 orders of magnitude. NMR spectroscopy, X-ray crystallography and DFT calculations were used to elucidate this unexpected behavior, which on the basis of our analyses results from the buildup of Pitzer (torsional), Prelog (transannular) and Baeyer (large angle) strain in the longer linkers.

Comparative characterization of thermal isomerization rates of 6‐phenyl‐1,5‐diazabicyclo[3.1.0]hexane at convection and microwave heating

AbstractRate constants of thermal isomerization of 6‐phenyl‐1,5‐diazabicyclo[3.1.0]hexane into 1‐(benzyl)‐4,5‐dihydro‐1H‐pyrazole at convection and microwave heating in toluene and chlorobenzene (solvents) were determined within the temperature range 90°C to 120°С. These data were used for the calculation of activation parameters of isomerization. It is shown that microwave heating increases the rate constants at the same temperature by a factor of 2 to 2.5 as compared with those using convection heating. The reason is that the effective temperature of microwave heating exceeds that of convection heating by 6°C to 9°С in toluene and by 12°C to 20°С in chlorobenzene as solvent.

Tuning the Thermal Isomerization of Phenylazoindole Photoswitches from Days to Nanoseconds.

The growing interest in light-driven molecular switches and optical oscillators led to the development of molecules that are able to interconvert from a stable to a metastable configuration upon photochemical triggering and to return to the thermodynamically stable form as soon as the light stimulus is removed. Controlling a wide range of back-isomerization lifetimes in the dark is a crucial goal for potential application of these compounds such as molecular machines. We herein present a novel class of easily synthesizable azo photoswitches based on the arylazoindole core. Most notably, minimal modifications of the core, such as methylation, dramatically change the Z-to-E thermal isomerization rate from days (Me in position 1) to the nanosecond range (Me in position 2). Moreover, fine-tuning of the Z-to-E lifetimes can be achieved choosing a proper dimethyl sulfoxide-water (or buffered water) solvent mixture. The photochemical and thermal mechanisms have been elucidated by a thorough computational and spectroscopic analysis. This allowed to detect three different pathways of thermal isomerization and to identify the hydrazone tautomer of the phenylazoindole as the major actor in the fast Z-E thermal isomerization of the NH-substituted switch in protic media.

Control of Intramolecular Isomerization Reactivity of an Azobenzene Derivative Anchored to ZrO2 Nanoparticle Thin Films

Chemical adsorption of molecules to nanomaterials imparts thermodynamic and kinetic variations to molecular reactivity. However, these differences are challenging to measure or predict and thus are frequently overlooked in nanomaterial/molecular interfacial systems. In this study, interfacial attachment of an azobenzene derivative to ZrO2 nanoparticle thin films more than doubles the azobenzene thermal isomerization rate and decreases the extent of photoisomerization by up to a factor of 3 compared to that of fluid solution. The magnitude of these changes can be controlled by selectively anchoring either the cis or trans isomer of azobenzene to the ZrO2 film. Furthermore, the coadsorption of the sterically hindering molecule chenodeoxycholic acid to a ZrO2 thin film previously treated with cis-azobenzene results in a decreased extent of isomerization that mimics the trans-azobenzene anchored ZrO2 film. Accordingly, steric hindrance of the azobenzene isomerization at the interface is implicated as an expla...

Concentration dependence of thermal isomerization process of methyl orange in ethanol

Abstract The thermal isomerization (TI) rates of methyl orange (MO) and 4-dimethylaminoazobenzene (DMAAB) in ethanol (EtOH) are measured. Usually TI rates of azobenzene dyes are known to be concentration independent. However, the TI rate of MO showed a concentration dependence whereas that of DMAAB did not. The TI rate of DMAAB in EtOH became larger by the addition of alkali halide. This phenomenon is caused mainly by the interaction between DMAAB and cation. MO is a derivative of DMAAB in which one end of the azobenzene is substituted by a SO3−Na+ group. The interaction with the dissociated Na+ ion is considered to be an origin of the concentration dependence of the TI rate of MO.

Adaptation of cone pigments found in green rods for scotopic vision through a single amino acid mutation

Most vertebrate retinas contain a single type of rod for scotopic vision and multiple types of cones for photopic and color vision. The retinas of certain amphibian species uniquely contain two types of rods: red rods, which express rhodopsin, and green rods, which express a blue-sensitive cone pigment (M1/SWS2 group). Spontaneous activation of rhodopsin induced by thermal isomerization of the retinal chromophore has been suggested to contribute to the rod's background noise, which limits the visual threshold for scotopic vision. Therefore, rhodopsin must exhibit low thermal isomerization rate compared with cone visual pigments to adapt to scotopic condition. In this study, we determined whether amphibian blue-sensitive cone pigments in green rods exhibit low thermal isomerization rates to act as rhodopsin-like pigments for scotopic vision. Anura blue-sensitive cone pigments exhibit low thermal isomerization rates similar to rhodopsin, whereas Urodela pigments exhibit high rates like other vertebrate cone pigments present in cones. Furthermore, by mutational analysis, we identified a key amino acid residue, Thr47, that is responsible for the low thermal isomerization rates of Anura blue-sensitive cone pigments. These results strongly suggest that, through this mutation, anurans acquired special blue-sensitive cone pigments in their green rods, which could form the molecular basis for scotopic color vision with normal red rods containing green-sensitive rhodopsin.