Kinetics Of Isomerization Research Articles

The unexpected and important role of alcohol stabilizer in thermal cis-trans isomerization of push-pull dyes in chloroform solution

The study demonstrates the influence of ethanol as a stabilizer in chloroform on the thermal cis-trans isomerization kinetics of photochromic compounds based on azobenzene and azopyridine derivatives. The significance of the addition of ethanol as a stabilizer in chloroform-based solutions on the isomerization reaction of the hydroxy- and the 6-hydroxylalkoxy-substituted azo compounds was investigated. The results have revealed that the presence of a polar stabilizer in a solvent can significantly reduce the reaction rate constant of the dark cis-trans isomerization due to the formation of hydrogen bonds at both ends of the azo-chromophore, thereby inhibiting the isomerization. Furthermore, a stabilizer can facilitate the reversion of azo-hydrazone tautomers of azophenols to their azobenzene form, resulting in a decrease in the reaction rate constant. The research presented in this paper can be essential for scientists who study the kinetics of the trans-cis and the cis-trans isomerization reactions of azo-chromophores. The results show that the use of solvents with polar stabilizers should be rather avoided, as their usage without information about stabilizers can lead to different experimental data. The authors should ensure that detailed information about stabilizers used in unstable solvents is included in the experimental section of their works (a detail currently often omitted in the literature).

Application of C–H Functionalization in the Construction of Pyrene-Azobenzene Dyads

AbstractHerein we report synthesis of pyrene-azobenzene dyads using the Pd(II)-catalyzed directing-group-assisted arylation of the ortho C(sp2)–H bond of pyrenecarboxamides as a key transformation. Many examples of directly connected pyrene-azobenzene dyads (without any linker) and glycine-based azobenzene-pyrene dyads have been synthesized. Initial incorporation of an acetanilide unit in the pyrene skeleton through Pd(II)-catalyzed directing-group-assisted ortho C(sp2)–H arylation by using iodoacetanilide was followed by the transformation of the acetanilide into an azobenzene unit to give the pyrene-azobenzene dyad. UV-Vis spectroscopic studies were performed to get the absorption properties (λmax (nm)) of all the compounds. Preliminary photoswitching studies in both forward and reverse directions and their related thermal reverse Z→E isomerization kinetics measurements were ascertained for representative compounds. Considering the importance of pyrene and azobenzene linked motifs as important chromophore-based photoswitchable molecules in chemical, materials, and supramolecular sciences research fields, this work enriches the library of pyrene-azobenzene dyads.

Strategies to control humidity sensitivity of azobenzene isomerisation kinetics in polymer thin films

Azobenzenes are versatile photoswitches that garner interest in applications ranging from photobiology to energy storage. Despite their great potential, transforming azobenzene-based discoveries and proof-of-concept demonstrations from the lab to the market is highly challenging. Herein we give an overview of a journey that started from a discovery of hydroxyazobenzene’s humidity sensitive isomerisation kinetics, developed into commercialization efforts of azobenzene-containing thin film sensors for optical monitoring of the relative humidity of air, and arrives to the present work aiming for better design of such sensors by understanding the different factors affecting the humidity sensitivity. Our concept is based on thermal isomerisation kinetics of tautomerizable azobenzenes in polymer matrices which, using pre-defined calibration curves, can be converted to relative humidity at known temperature. We present a small library of tautomerizable azobenzenes exhibiting humidity sensitive isomerisation kinetics in hygroscopic polymer films. We also investigate how water absorption properties of the polymer used, and the isomerisation kinetics are linked and how the azobenzene content in the thin film affects both properties. Based on our findings we propose simple strategies for further development of azobenzene-based optical humidity sensors.

Theoretical and modeling studies on the kinetics of diethylamine dehydrogenation and subsequent isomerization and decomposition reactions

Small-molecule nitrogen-containing contaminants can be produced by the pyrolysis of diethylamine (DEA) alone or in conjunction with other molecules. To investigate the theoretical chemistry of the combustion of DEA, the CBS method determines the potential energy surface and the rate constants are calculated based on a combination of RRKM and TST theories. The H-abstraction reactions by H radicals are more kinetically advantageous. Site α has the most difficult H-abstraction procedure, but site γ has the competitive capacity to form subsequent products. The H-abstraction by NO2 radical produces trans-HONO, cis-HONO, and HNO2. For the reaction channels of DEA radicals, decomposition reactions have more kinetic advantages than isomerization. Kinetic parameters were obtained and the model was modified based on the fitted rate constants. The modified model has better predictive ability at low temperatures. This work provides extensive data to improve the modeling of DEA combustion at low and medium temperatures.

Photoresponsive conductive polymer network based on azobenzene bridging crosslinked polycarbazole for boosting solar thermal storage

Azobenzene is one of the most extensively researched multifunctional chromophores and azobenzene including materials has a wide variety of applications due to their photoisomerization behavior. In this study, electroactive and light-harvesting carbazole and photoresponsive azobenzene units have been combined with a special macromolecular design. In this design the azo groups can be effectively isomerized in solid state, and free-standing films can be obtained by the electrochemical method. Thermal characterizations of both monomer and polymer have been performed and isomerization kinetics and solar-thermal properties have been investigated. The half-life at 60 °C and the gravimetric energy storage density of polymer was calculated as 103 min and 179.9 j g−1, respectively. Cross-linked polycarbazole structure causes dramatically increased solar thermal storage and half-life compared to respective monomer and brought unexpected mechanical and solvatochromic properties.

Dynamic visualization level 3 details of latent fingerprints by fluorescence imaging and photoluminescent macromolecules functionalized with spiropyran photoswitch

Detecting latent fingerprints (LFPs) poses a considerable challenge for individual identification in the case of the criminal scene because detecting more details about three levels of identification patterns at a fast rate and by conventional instruments is very important for investigators. This research involved creating nanoparticles made of a copolymer containing tertiary amine-functionalized methacrylate through emulsion copolymerization, and then modifying them with a spiropyran derivative. The concentration of tertiary amine groups significantly influenced the optical properties, with samples containing more than 10 wt% exhibiting negative photochromism, leading to the absence of dynamic emission and reversible photochromism. The study of the kinetics of isomerization from spiropyran to merocyanine using solid-state fluorescence spectroscopy highlighted the important role of negative photochromism in the photoswitching of spiropyran. The resulting dynamic photoluminescent polymer powders were effectively utilized for LFP visualization through powder dusting, fluorescence imaging, optical security tag production, and the development of innovative OLEDs. The study confirmed the efficiency of these polymer powders in visualizing LFPs, enabling the identification of intricate details and patterns at three distinct levels. The observed LFPs emitted fluorescence in a range of colors, displaying high contrast, resolution, maximum intensity, and brightness. Three levels of identification details were detected for an unknown LFP that remained on the surface of the glass bottle as a real sample in the criminal scene. Successful identification of the unknown offender indicates the potential application of samples for time-dependent visualization of LFPs in criminal scenes.

Insight into the Kinetics of Isomerization and β-Scission Reactions Following H-Abstraction in 2-Pentanone Combustion.

2-Pentanone is a significant carbon-neutral fuel. To better understand 2-pentanone combustion, the CCSD(T)/CBS method was used to calculate the potential energy surfaces (PES) for H-abstraction, isomerization, and β-scission reactions of 2-pentanone. Rate constants for the above reactions were calculated by the MESS employing conventional transition state theory (CTST) at 300-2000 K. The findings reveal adherence to the Evans-Polanyi principle in the H-abstraction reactions of 2-pentanone by H atoms. Specifically, the 2-site shows more competitive kinetics due to having the lowest energy barrier of 7.8 kcal/mol. The 4-position has the highest energy barrier, making the reaction difficult to occur. In the subsequent reactions, the breaking of C-H bonds is most competitive at low temperatures. In particular, the H transfer from INT1 to INT3 has a potential well height of 24.8 kcal/mol. The β-scission reactions become the main pathway for the depletion of pentanone radicals with increasing temperature. This study significantly extends the kinetic parameters of 2-pentanone combustion over a wide range of temperatures and pressures, which is expected to contribute to the development of 2-pentanone combustion models.

Solvent and Temperature Dependencies of the Rates of Thermal Cis-to-Trans Isomerization of Tetra-(ortho)substituted 4-Aminoazobenzenes Containing 2,6-Dimethoxy Groups.

The kinetics of thermal cis-to-trans isomerization of two tetra-(ortho)substituted 4-aminoazobenzene derivatives containing 2,6-dimethoxy groups in the 4-aminobenzene ring and either 2',6'-dimethyl (1) or 2',6'-dichloro groups in another ring was studied in 16 and 9 solvents, respectively, at room temperature. In addition, the kinetics of isomerization of 1 was studied at variable temperatures in 6 solvents. The solvent effects were analyzed in terms of multiparameter correlations using the Kamlet-Taft, Catalan, and Laurence scales. The temperature dependencies were analyzed in terms of the isokinetic relationship by using Exner's method. The correlation analysis was also extended to several previously reported systems, including isomerization of unsubstituted 4-aminoazobenzene and push-pull 4-NR2-4'-NO2 azobenzenes. It was established that for all 4-aminoazobenzenes in contrast to push-pull azobenzenes, the increase in solvent dipolarity does not affect or even inhibit isomerization rates; however, the increase in solvent acidity induces large rate accelerations. The isokinetic relationship holds only in aprotic solvents, while in alcohols and water, the temperature dependencies do not pass through the common point at T = Tiso, indicating different mechanisms operating in protic and aprotic solvents. The acceleration effect by protic solvents does not represent a type of general acid catalysis as follows from the small solvent isotope effect kH/kD = 1.26 in water. It is suggested that protic solvents induce a change in the reaction mechanism supposedly from inversion to rotation by hydrogen bonding stabilization of the negative charge developed on the azo group in a resonance structure involving a 4-amino group.

The role of memory-dependent friction and solvent viscosity in isomerization kinetics in viscogenic media

Molecular isomerization kinetics in liquid solvent depends on a complex interplay between the solvent friction acting on the molecule, internal dissipation effects (also known as internal friction), the viscosity of the solvent, and the dihedral free energy profile. Due to the absence of accurate techniques to directly evaluate isomerization friction, it has not been possible to explore these relationships in full. By combining extensive molecular dynamics simulations with friction memory-kernel extraction techniques we consider a variety of small, isomerising molecules under a range of different viscogenic conditions and directly evaluate the viscosity dependence of the friction acting on a rotating dihedral. We reveal that the influence of different viscogenic media on isomerization kinetics can be dramatically different, even when measured at the same viscosity. This is due to the dynamic solute-solvent coupling, mediated by time-dependent friction memory kernels. We also show that deviations from the linear dependence of isomerization rates on solvent viscosity, which are often simply attributed to internal friction effects, are due to the simultaneous violation of two fundamental relationships: the Stokes-Einstein relation and the overdamped Kramers prediction for the barrier-crossing rate, both of which require explicit knowledge of friction.

Theoretical study on iso‐pentanol oxidation chemistry: Fuel radical isomerization and decomposition kinetics and mechanism development

AbstractThis study undertakes a detailed theoretical investigation into the iso‐pentanol radical isomerization and decomposition kinetics and the mechanism development of the iso‐pentanol oxidation. The CCSD(T)/CBS//M08‐HX/6‐311+G(2df,2p) method was adopted to calculate the reaction potential energy surface. The reaction rate coefficients were calculated by variational transition state theory (VTST) with multistructural torsional (MS‐T) partition function and small curvature tunneling (SCT) correction. Moreover, the pressure‐dependent rate coefficients were determined using the system‐specific quantum Rice‐Ramsperger‐Kassel theory (SS‐QRRK). The variational and tunneling effects were discussed, and the dominant reaction channels were identified. It reveals that the isomerization reactions play a significant role at low temperatures, while the decomposition reactions dominate the high‐temperature regime. Notably, the quantitative rate expressions for iso‐pentanol radical decomposition reactions were also obtained. Furthermore, a new kinetic model incorporating the calculated rate coefficients was constructed, exhibiting satisfactory prediction performance on ignition delay times and improved predictive accuracy of species mole fractions. This work provides accurate rate data of isomerization and decomposition kinetics and contributes to a more comprehensive understanding of the iso‐pentanol oxidation mechanism.

Theoretical Studies on the Isomerization Kinetics of Low-Lying Isomers of the SiC4H2 System.

The low-lying isomers of SiC4H2 are investigated to understand the kinetics of isomerization pathways using density functional theory. In our earlier work, we studied the various possible isomers (J. Phys. Chem. A, 2020, 124, 987-1002) and the chemical bonding of low-lying isomers of SiC4H2 (J. Phys. Chem. A, 2022, 126, 9366-9374). Among them, four isomers, 1-ethynyl-3-silacycloprop-1-en-3-ylidene (1), 3-silapent-1,4-diyn-3-ylidene (2), 1-silapent-1,2,3,4-tetraen-1-ylidene (4), and 1-silapent-2,4-diyn-1-ylidene (5) have already been identified in the laboratory. The previously known theoretical isomer 2-methylene-1-silabicyclo[1.1.0]but-1(3)-en-4-ylidene (3) and the newly identified unknown isomer through the present kinetic studies 5-silabicyclo[2.1.0]pent-1(4),2-dien-5-ylidene (N6) remain elusive in the laboratory to date. The isomerization pathways of the low-lying isomers of SiC4H2 are predicted through the transition state structures. Intrinsic reaction coordinate analysis identifies the minimum energy reaction pathways connecting the transition state from one isomer to another of the investigated system. The present kinetic data reveal the isomerization of global minimum energy isomer 1 to thermodynamically stable low-lying isomers, 2 and 5. Interestingly, isomer 3 interconverts to the experimentally known low-energy isomer 4, the second most thermodynamically stable isomer among them. The thermodynamic and kinetic parameters of the low-lying isomers of SiC4H2 are also documented in this work. The rate coefficient and equilibrium constant for isomerization reactions are calculated using the Rice-Ramsperger-Kassel-Marcus theory. The equilibrium constant delineates the difficulties in forming N6 and 3 through the isomerization pathways. Furthermore, ab initio molecular dynamics studies dictate the stability of low-lying isomers of SiC4H2 within the time scale of the simulation.

Kinetic study of azobenzene photoisomerization under ambient lighting

Laboratory illumination is sufficiently intense to produce a photostationary state (PSS) of amphiphilic azobenzene compounds in water. We observed [cis]PSS/[trans]PSS ratios equal to 0.33–1.2 in D2O and 0.37 – 3.8 in dimethyl sulfoxide-d6. ortho-Fluoroazobenzene amphiphiles produced 2–3 times more cis-isomer at equilibrium compared to non-fluorinated compounds which is explained by the isomeric variation in optical absorption profiles. Isomerization kinetics were measured using UV–Vis spectroscopy and the ratio of trans-to-cis over cis-to-trans rates does not quantitatively correlate with the observed PSS. The kinetics define the timescale of ambient photoisomerization where the half-life for PSS formation is 40 min for the fluorinated compounds and 80 min for non-fluorinated compounds.

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.

Allosteric control of olefin isomerization kinetics via remote metal binding and its mechanochemical analysis

Allosteric control of reaction thermodynamics is well understood, but the mechanisms by which changes in local geometries of receptor sites lower activation reaction barriers in electronically uncoupled, remote reaction moieties remain relatively unexplored. Here we report a molecular scaffold in which the rate of thermal E-to-Z isomerization of an alkene increases by a factor of as much as 104 in response to fast binding of a metal ion to a remote receptor site. A mechanochemical model of the olefin coupled to a compressive harmonic spring reproduces the observed acceleration quantitatively, adding the studied isomerization to the very few reactions demonstrated to be sensitive to extrinsic compressive force. The work validates experimentally the generalization of mechanochemical kinetics to compressive loads and demonstrates that the formalism of force-coupled reactivity offers a productive framework for the quantitative analysis of the molecular basis of allosteric control of reaction kinetics. Important differences in the effects of compressive vs. tensile force on the kinetic stabilities of molecules are discussed.

Dynamic anticounterfeiting polymeric inks for multipurpose time-dependent encryption with a high level of security

Development of dynamic anticounterfeiting inks with time-dependent photochromism and photoluminescence characteristics has become highly interesting in advanced encryption systems. These inks are applicable in different fields, such as tracking UV rays and gas leakage and also quality monitoring. In this study, semi-continuous copolymerization of butyl acrylate and methyl methacrylate in the heterogeneous miniemulsion medium was used to synthesize colloidal nanoparticles with different flexibilities and polarities. Then, hydroxyl-functional spiropyran (SPOH) was physically incorporated into the nanoparticles to prepare photochromic and photoluminescent inks. The nanoparticles showed low light reflectance due to their small size, which makes them applicable in photoresponsive and sensing applications. In addition, the nanoparticles exhibited different glass transition temperature (Tg) that affects their photoresponsivity. Microscopic analysis revealed that all the latex samples have spherical nanoparticles with a mean size of about 70 nm and a low polydispersity index. UV–vis absorption and fluorescence emission spectra, isomerization kinetics, and photofatigue resistance of the photochromic latex nanoparticles were studied, which depend on chain polarity and flexibility of the latex nanoparticles. The optical properties of the photochromic materials are closely related to the structure and composition of the latex samples. Time-dependent features of the inks originate from their spiropyran molecules which gradually turns into the merocyanine form upon visible light induction. Photochromic inks with advanced encryption and dynamic characteristics were developed from the SPOH-doped colloidal latex nanoparticles. Different polarities and Tg of the inks result in their different dynamic chromism, which show their high level of information encryption technology. By virtue of these unique time-dependent properties, the encryption capabilities of these inks are significantly improved. These inks achieved unprecedented advances in the field of information security and encryption because of their innovative features.

Photoisomerization of 2-Arylazoimidazoles under Visible Light: Identifying a Predictive Tool to Anticipate and Tune Likely Photoswitching Performance and Cis Half-Life.

Azopyrazoles are an emerging class of photoswitches, whereas analogous azoimidazole-based switches are unable to draw much attention because of their short cis half-lives, poor cis-trans photoreversion yields, and toxic ultraviolet (UV) light-assisted isomerization. A series of 24 various aryl-substituted N-methyl-2-arylazoimidazoles were synthesized, and their photoswitching performances and cis-trans isomerization kinetics were thoroughly investigated experimentally and theoretically. Para-π-donor-substituted azoimidazoles with highly twisted T-shaped cis conformations showed nearly complete bidirectional photoswitching, whereas di-o-substituted switches exhibited very long cis half-lives (days-years) with nearly ideal T-shaped conformations. This study demonstrates how the electron density in the aryl ring affects cis half-life and cis-trans photoreversion via twisting of the NNAr dihedral angle that can be used as a predictive metric for envisaging and tuning the likely switching performance and half-life of any given 2-arylazoimidazole. By applying this tool, two better-performing azoimidazole photoswitches were engineered. All switches permitted irradiation by violet (400-405 nm) and orange (>585 nm) light for forward and reverse isomerization, respectively, and displayed comparatively high quantum yields and impressive resistance to photobleaching.

Kinetics of the dark cis–trans isomerization of azobenzene and azo pyridine derivatives in ethanol and chloroform solutions

The paper presents a series of azobenzene and azo pyridine compounds containing hydroxyl or 6-hydroxyhexyloxyl substituents. The nitrogen atom is located at the ortho-, meta- or para-position in the structure of azo pyridine derivatives. The impact of the structural features of azo chromophores on their thermal (DSC, TGA) and optical (UV–Vis) properties was investigated. The dark cis–trans isomerization kinetics was studied in ethanol and chloroform at 298 K. The formation of noncovalent hydrogen bonds between azo molecules and/or chromophore-solvent was monitored using the 1H NMR spectroscopy and estimated by density functional theory (DFT) calculations. Based on experimental and computational studies we proposed the mechanism of the dark cis–trans isomerization for hydroxy-substituted azo compounds.

Effect of polymer host matrix on multi-stage isomerization kinetics of DASA photochromes

Molecular photoswitches provide a means for imparting synthetic structures with intrinsically logical and highly tunable photoresponsive properties. One variety of organic photoswitches known as Donor-Acceptor Stenhouse Adducts, or DASAs, are promising candidates for next generation light responsive materials because of their unique ability to stabilize three photochemically distinct isomeric states in solution, while their counterparts are strictly limited to binary state behavior. In this work, we show how polymethacrylate host matrices shift the energetic landscape of DASA relative to solution, prohibiting accumulation of an intermediate third isomeric state by decelerating critical steps in the photoswitching mechanism. Specifically, we employ a dual-wavelength, phase locked detection scheme to probe thermal isomerizations in the switching process that occur at fast (∼ms) time scales that are inaccessible by standard UV–Vis spectroscopic techniques. The results of this study provide valuable insight into the mechanism of multistate DASA reactivity and establish the foundation necessary to guide future efforts in offsetting kinetic matrix effects to enable dynamic, three state photoswitching in polymeric hosts.

Optically Controlled Construction of Three-Dimensional Protein Arrays.

Protein crystallization is an important tool for structural biology and nanostructure preparation. Here, we report on kinetic pathway-dependent protein crystals that are controlled by light. Photo-responsive crystallites are obtained by complexing the model proteins with cationic azobenzene dyes. The crystalline state is readily switched to a dispersed phase under ultraviolet light and restored by subsequent visible-light illumination. The switching can be reversibly repeated for multiple cycles without noticeable structure deterioration. Importantly, the photo-treatment not only significantly increases the crystallinity, but creates crystallites at conditions where no ordered lattices are observed upon directly mixing the components. Further control over the azobenzene isomerization kinetics produces protein single crystals of up to ≈50 μm. This approach offers an intriguing method to fabricate metamaterials and study optically controlled crystallization.

Optically Controlled Construction of Three‐Dimensional Protein Arrays

AbstractProtein crystallization is an important tool for structural biology and nanostructure preparation. Here, we report on kinetic pathway‐dependent protein crystals that are controlled by light. Photo‐responsive crystallites are obtained by complexing the model proteins with cationic azobenzene dyes. The crystalline state is readily switched to a dispersed phase under ultraviolet light and restored by subsequent visible‐light illumination. The switching can be reversibly repeated for multiple cycles without noticeable structure deterioration. Importantly, the photo‐treatment not only significantly increases the crystallinity, but creates crystallites at conditions where no ordered lattices are observed upon directly mixing the components. Further control over the azobenzene isomerization kinetics produces protein single crystals of up to ≈50 μm. This approach offers an intriguing method to fabricate metamaterials and study optically controlled crystallization.