Rate Of Isomerization Research Articles

Determination of photoisomerization parameters for a PMMA thin film doped with disperse orange 3

An analytic absorption function was derived to investigate the dynamics of photoisomerization in a poly(methyl methacrylate) thin film doped with disperse orange 3 (DO3). The temporal absorption measured using the pump-probe method was well-behaved, following an analytic function with a single exponential term. The isomerization and thermal-relaxation rates were evaluated by curve-fitting. The analytic absorption function was validated by measuring the thermal-relaxation rates with the pump separately on and off. Using this function, an analytic method for determining the photoisomerization parameters was demonstrated: for DO3 in poly(methyl methacrylate), the photoisomerization quantum yields for trans-cis and cis-trans processes were determined to be ϕTC=0.12±0.01 and ϕCT=0.77±0.06, respectively. The absorption cross section for the cis isomer was measured to be σC=(0.92±0.03)×10−16cm2. This analytic method can thus be used to characterize the dynamics of photoisomerization in dye doped thin films.

Synthesis, photochemical and luminescent properties of ortho-hydroxystyrylquinazolinone-linked benzocrown ethers

Abstract Photoinduced transformations of (E)-2-(2-hydroxystyryl)quinazolinone-linked benzo[15(18)]crown-5(6) ethers in solutions have been studied by using UV–vis absorption and NMR spectroscopy. These crown ethers were found to have dual emission at 520 and 650 nm, associated with proton-transfer tautomer emission (ESIPT-luminescence) as a rare case of excited-state proton-transfer reaction in the non-pseudocyclic chromophoric systems. It was established also, that the organic bases affect the luminescence intensity of solutions of these compounds in the 550–650-nm wavelength range. An X-ray crystallography analysis of molecular structures of crown ethers and their complexes in crystals has been carried out. The fact of reversible photo/thermal E-Z isomerization in DMF and Et3N for these macroheterocyclic compounds has been confirmed. An opportunity to control the photochemical isomerization rate of quinazolinone 2-(hydroxyphenyl)ethenyl derivatives by changing pH of the medium has been demonstrated.

Spin Changes Accompany Ultrafast Structural Interconversion in the Ground State of a Cobalt Nitrosyl Complex

AbstractUltrafast, reversible intersystem crossing (ISC) is reported under ambient conditions for the electronic ground state of the pentacoordinate cobalt nitrosyl complexes, [CoX2(NO)(PMePh2)2] (X=Cl, Br), in solution. ISCs on such short timescales are more typically observed in electronically excited states reached by absorption of ultraviolet or visible light. Singlet and triplet electron spin states of the complex, corresponding to two different isomers, are populated at room temperature, and the two isomers exchange on a timescale of a few picoseconds. Ultrafast two‐dimensional infrared spectroscopy observes the change in wavenumber of the NO ligand band accompanying the isomerization and associated ISC on the (spin) adiabatic ground potential energy surface. Comparison of the dynamics of the chloro‐ and bromo‐complexes shows that inertial effects of the ligand motion have a greater effect than spin–orbit coupling on determining the forward and reverse isomerization and ISC rates.

Spin Changes Accompany Ultrafast Structural Interconversion in the Ground State of a Cobalt Nitrosyl Complex

Ultrafast, reversible intersystem crossing (ISC) is reported under ambient conditions for the electronic ground state of the pentacoordinate cobalt nitrosyl complexes, [CoX2 (NO)(PMePh2 )2 ] (X=Cl, Br), in solution. ISCs on such short timescales are more typically observed in electronically excited states reached by absorption of ultraviolet or visible light. Singlet and triplet electron spin states of the complex, corresponding to two different isomers, are populated at room temperature, and the two isomers exchange on a timescale of a few picoseconds. Ultrafast two-dimensional infrared spectroscopy observes the change in wavenumber of the NO ligand band accompanying the isomerization and associated ISC on the (spin) adiabatic ground potential energy surface. Comparison of the dynamics of the chloro- and bromo-complexes shows that inertial effects of the ligand motion have a greater effect than spin-orbit coupling on determining the forward and reverse isomerization and ISC rates.

Development of Novel Chemical Probes for Examining Triplet Natural Organic Matter under Solar Illumination.

Excited triplet states of chromophoric dissolved organic matter (3CDOM*) are critical transient species in environmental photochemistry. In the present study, sorbic amine (2,4-hexadien-1-amine) and sorbic alcohol were employed as new probe molecules for triplet measurements and compared to the results measured from sorbic acid under identical conditions. Unlike sorbic acid, sorbic amine and sorbic alcohol were not directly photolyzed under solar irradiation. Photosensitized isomerization of the probes with the conjugated diene structure could yield four geometrical isomers. The separation and quantitative determination of the geometrical isomers were accomplished using HPLC and high-resolution NMR analyses. When photoirradiated Suwannee River natural organic matter (SRNOM) was employed as a source of 3CDOM*, significantly different photosensitized isomerization rates were observed for the diverse charged probes. The bimolecular reaction rate constants between 3SRNOM* and the probes were calculated as (0.42 ± 0.1) × 109 M-1 s-1 for sorbic acid, (1.1 ± 0.1) × 109 M-1 s-1 for sorbic alcohol, and (5.2 ± 0.4) × 109 M-1 s-1 for sorbic amine, respectively. The average apparent Φtriplet was (0.96 ± 0.03)% based on an irradiation range of 290 to 400 nm. We developed highly selective and efficient probes for triplet determination and elucidated the different reaction behaviors of these conjugated dienes containing different charged substituents within the photochemical energy transfer process.

Ancillary Ligand Effects upon the Photochemistry of Mn(bpy)(CO)3X Complexes (X = Br-, PhCC-).

The photochemistry of two Mn(bpy)(CO)3X complexes (X = PhCC-, Br-) has been studied in the coordinating solvents THF (terahydrofuran) and MeCN (acetonitrile) employing time-resolved infrared spectroscopy. The two complexes are found to exhibit strikingly different photoreactivities and solvent dependencies. In MeCN, photolysis of 1-(CO)(Br) [1 = Mn(bpy)(CO)2] affords the ionic complex [1-(MeCN)2]Br as a final product. In contrast, photolysis of 1-(CO)(CCPh) in MeCN results in facial to meridional isomerization of the parent complex. When THF is used as solvent, photolysis results in facial to meridional isomerization in both complexes, though the isomerization rate is larger for X = Br-. Pronounced differences are also observed in the photosubstitution chemistry of the two complexes where both the rate of MeCN exchange from 1-(MeCN)(X) by THFA (tetrahydrofurfurylamine) and the nature of the intermediates generated in the reaction are dependent upon X. DFT calculations are used to support analysis of some of the experiments.

Redox Control over Acyl Hydrazone Photoswitches.

Photoisomerization provides a clean and efficient way of reversibly altering physical properties of chemical systems and injecting energy into them. These effects have been applied in development of systems such as photoresponsive materials, molecular motors, and photoactivated drugs. Typically, switching from more to less stable isomer(s) is performed by irradiation with UV or visible light, while the reverse process proceeds thermally or by irradiation using another wavelength. In this work we developed a method of rapid and tunable Z→E isomerization of C=N bond in acyl hydrazones, using aromatic thiols as nucleophilic catalysts. As thiols can be oxidized into catalytically inactive disulfides, the isomerization rates can be controlled via the oxidation state of the catalyst, which, together with the UV irradiation, provides orthogonal means to control the E/Z state of the system. As a proof of this concept, we have applied this method to control the diversity of acyl hydrazone based dynamic combinatorial libraries.

A combined theoretical and thermal analysis study on the solid state linkage isomerization of Ni(II)-nitrite complexes with ethylenediamine derivatives

Solid state stepwise nitro–nitrito linkage isomerization of trans-[dinitrobis(ethylenediamine)nickel(II)], [Ni(en)2(NO2)2] (N,N-en), trans-[dinitrobis(N,N′-dimethylethylenediamine)nickel(II)], [Ni(N,N′-dmen)2(NO2)2] (N,N-dmen), and trans-[dinitritobis(N,N-dimethylethylenediamine)nickel(II)], [Ni(N,N-dmen)2(ONO)2] (O,O-udmen) were investigated by performing non-isothermal differential scanning calorimetry (DSC) analyses and the thermodynamic and thermokinetic parameters of isomerization were determined using DSC curves. Both N,N-en and N,N-dmen DSC curves show an endothermic peak at elevated temperatures, attributed to dinitro-to-dinitrito linkage isomerization. Similar exothermic peaks were observed in the cooling cycle, assigned to the reverse dinitrito-to-dinitro isomerization. The O,O-udmen isomer is more stable than the corresponding dinitro one at ambient temperatures, but an exothermic dinitrito-to-dinitro isomerization occurs upon cooling down to −70 °C and reverts endothermically to dinitrito isomer upon heating up to ambient temperature. The overlapping DSC peaks associated with stepwise linkage isomerization were resolved using nonlinear fitting method. The peak temperature and the enthalpy changes of linkage isomerization are inversely dependent on the steric hindrance provided by diamine ligands, which increases in the order udmen > dmen > en. The results showed that the steric factor of the co-ligands also influences the kinetic parameters of isomerization, so that more bulky ligand substituent leads to higher isomerization rate constants. A DFT and TD-DFT calculations have been carrid out on both dinitro complexes of this investigation .

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.

Dynamic Allostery Modulates Catalytic Activity by Modifying the Hydrogen Bonding Network in the Catalytic Site of Human Pin1.

Allosteric communication among domains in modular proteins consisting of flexibly linked domains with complimentary roles remains poorly understood. To understand how complementary domains communicate, we have studied human Pin1, a representative modular protein with two domains mutually tethered by a flexible linker: a WW domain for substrate recognition and a peptidyl-prolyl isomerase (PPIase) domain. Previous studies of Pin1 showed that physical contact between the domains causes dynamic allostery by reducing conformation dynamics in the catalytic domain, which compensates for the entropy costs of substrate binding to the catalytic site and thus increases catalytic activity. In this study, the S138A mutant PPIase domain, a mutation that mimics the structural impact of the interdomain contact, was demonstrated to display dynamic allostery by rigidification of the α2-α3 loop that harbors the key catalytic residue C113. The reduced dynamics of the α2-α3 loop stabilizes the C113–H59 hydrogen bond in the hydrogen-bonding network of the catalytic site. The stabilized hydrogen bond between C113 and H59 retards initiation of isomerization, which explains the reduced isomerization rate by ~20% caused by the S138A mutation. These results provide new insight into the interdomain allosteric communication of Pin1.

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.

Visible-light fluorescence photomodulation in azo-BF2 switches

Azo-BF2 switches 1 and 2 with their extended phenanthridinyl π-system exhibit red-light fluorescence whose intensity can be photomodulated using visible-light. The para-methoxy group in 2 leads to a bathochromic shift in the emission band, pushing its tail further to the near infrared region. This group also changes the isomerization properties in 2, as it does not display the concentration-dependent isomerization rate change observed in 1, most likely because of a change in mechanism from rotation to inversion, and weaker π−π interaction in the system.

Kinetics of n-hexane isomerization over supported palladium catalysts

The steady- and unsteady-state kinetics of n-hexane isomerization over Ni- or Co-promoted Pd/HZSM-5 catalysts in the presence of hydrogen has been investigated. The kinetics of the reaction is described by similar fractional rational rate equations differing in the values of their constants. Hydrogen exerts a favorable effect on the isomerization rate. The catalysts have been characterized by the BET-N2 method, X-ray diffraction, transmission electron microscopy, H2-TPR, and NH3-TPD. The introduction of a promoter (Ni or Со) strengthens the adsorption of the reactants and increases the amount of reactants adsorbed.

Binding of the five multistate species of the anthocyanin analog 7-β-D-glucopyranosyloxy-4′-hydroxyflavylium to the β-cyclodextrin derivative captisol

The host-guest chemistry of the anthocyanin analog 7-β-D-glucopyranosyloxy-4′-hydroxyflavylium (GHF) was studied in the presence of the β-cyclodextrin derivative captisol by stopped flow, UV–visible spectroscopy, flash photolysis, circular dichroism and isothermal titration calorimetry. The equilibrium and rate constants of the multistate of chemical species derived from the flavylium ion were calculated and compared with those in the absence of the host. A new procedure to obtain the host-guest association constants of the multistate (including the transient species) by superimposing the two energy level diagrams, in the presence and absence of the cyclodextrin, was developed. The results indicate that the magnitude of the association constants follows the order, trans-chalcone ≈ cis-chalcone ≈ hemiketal > quinoidal base > flavylium cation. The hydration equilibrium constant increases ca. 42 times in the presence of captisol as the hydration and dehydration rate constants respectively increases and decreases. The other equilibrium constants are modestly affected: the rate constants of ring closure and opening are significantly decreased in the complex and the isomerization rate constants increase in both directions. The quantum yield of the photochromic system in the presence of captisol is 0.3, i.e. 3 times higher than in the absence of the host.

Light penetration-coupled photoisomerization modeling for photodeformation of diarylethene single crystal: upscaling isomerization to macroscopic deformation

Diarylethene is one of the photo-responsive materials that show rapid and reversible changes in their color/electrochemical properties and macroscopic deformations in the crystalline phase by light irradiation. Photoisomerization is the main cause of the photo reactivity of diarylethene, and we established a statistical model based on the density matrix formalism, which predicts quantitative isomerization progress as a population term. The model reflects photo-switching properties of the target molecule, which were characterized by first principle calculations, and external stimulus factors (light irradiation conditions and temperature). By merging light penetration physics with the model, we derived light penetration depth dependent isomerization progress to theoretically investigate photodeformation of single crystal. The model well reproduced in-plane shear deformation under ultraviolet light irradiation which would provide guideline for photoactuator design. In addition, the statistical model addressed crucial findings (primary stimuli and molecular design parameter for increasing the isomerization rate, external stimuli enhancing fluorescence performance) itself.

Structural communication between the chromophore-binding pocket and the N-terminal extension in plant phytochrome phyB.

The N-terminal extension (NTE) of plant phytochromes has been suggested to play a functional role in signaling photoinduced structural changes. Here, we use resonance Raman spectroscopy to study the effect of the NTE on the chromophore structure of B-type phytochromes from two evolutionarily distant plants. NTE deletion seems to have no effect on the chromophore in the inactive Pr state, but alters the torsion of the C-D ring methine bridge and the surrounding hydrogen bonding network in the physiologically active Pfr state. These changes are accompanied by a shift of the conformational equilibrium between two Pfr substates, which might affect the thermal isomerization rate of the C-D double bond and, thus, account for the effect of the NTE on the dark reversion kinetics.

Mechanistic Studies on a Cu-Catalyzed Asymmetric Allylic Alkylation with Cyclic Racemic Starting Materials.

Mechanistic studies on Cu-catalyzed asymmetric additions of alkylzirconocene nucleophiles to racemic allylic halide electrophiles were conducted using a combination of isotopic labeling, NMR spectroscopy, kinetic modeling, structure-activity relationships, and new reaction development. Kinetic and dynamic NMR spectroscopic studies provided insight into the oligomeric Cu-ligand complexes, which evolve during the course of the reaction to become faster and more highly enantioselective. The Cu-counterions play a role in both selecting different pathways and in racemizing the starting material via formation of an allyl iodide intermediate. We quantify the rate of Cu-catalyzed allyl iodide isomerization and identify a series of conditions under which the formation and racemization of the allyl iodide occurs. We developed reaction conditions where racemic allylic phosphates are suitable substrates using new phosphoramidite ligand D. D also allows highly enantioselective addition to racemic seven-membered-ring allyl chlorides for the first time. 1H and 2H NMR spectroscopy experiments on reactions using allylic phosphates showed the importance of allyl chloride intermediates, which form either by the action of TMSCl or from an adventitious chloride source. Overall these studies support a mechanism where complex oligomeric catalysts both racemize the starting material and select one enantiomer for a highly enantioselective reaction. It is anticipated that this work will enable extension of copper-catalyzed asymmetric reactions and provide understanding on how to develop dynamic kinetic asymmetric transformations more broadly.

Photoresponsive hollow molecularly imprinted polymer for trace triamterene in biological samples

This paper reports a photoresponsive hollow molecularly imprinted polymer for the determination of trace triamterene in biological sample. The photoresponsive hollow molecularly imprinted polymer was prepared on sacrificial silica microspheres via surface imprinting technique through atom transfer radical polymerization using a novel water-soluble azobenzene derivative, 4-[(4-methacryloyloxy)phenylazo]-3,5-dimethyl benzenesulfonic acid, as the functional monomer, and the sacrificial silica core was subsequently removed using HF etching method with 1.25vol.% HF ethanolic solution. The morphologies and properties of the photoresponsive hollow molecularly imprinted polymer were further characterized and compared systematically with the corresponding photoresponsive surface molecularly imprinted polymer. Compared with surface imprinted polymer, the hollow material displayed higher binding capacity, better recognition ability, faster mass-transfer rate, and larger isomerization rate constants toward triamterene. The static binding properties of the imprinted materials were investigated under three irradiation conditions. The photoresponsive hollow molecularly imprinted polymer showed better specificity toward triamterene than its structural analogues (folic acid and caffeine) as examined by UV–vis and HPLC. The photoresponsive hollow molecularly imprinted polymer was utilized for the determination of trace triamterene in biological samples (human urine and serum) with advantages of simple sample pre-treatment, good recovery and good sensitivity.

Ultrafast Excited State Dynamics in Molecular Motors: Coupling of Motor Length to Medium Viscosity

Photochemically driven molecular motors convert the energy of incident radiation to intramolecular rotational motion. The motor molecules considered here execute four step unidirectional rotational motion. This comprises a pair of successive light induced isomerizations to a metastable state followed by thermal helix inversions. The internal rotation of a large molecular unit required in these steps is expected to be sensitive to both the viscosity of the medium and the volume of the rotating unit. In this work, we describe a study of motor motion in both ground and excited states as a function of the size of the rotating units. The excited state decay is ultrafast, highly non-single exponential, and is best described by a sum of three exponential relaxation components. The average excited state decay time observed for a series of motors with substituents of increasing volume was determined. While substitution does affect the lifetime, the size of the substituent has only a minor effect. The solvent polarity dependence is also slight, but there is a significant solvent viscosity effect. Increasing the viscosity has no effect on the fastest of the three decay components, but it does lengthen the two slower decay times, consistent with them being associated with motion along an intramolecular coordinate displacing a large solvent volume. However, these slower relaxation times are again not a function of the size of the substituent. We conclude that excited state decay arises from motion along a coordinate which does not necessarily require complete rotation of the substituents through the solvent, but is instead more localized in the core structure of the motor. The decay of the metastable state to the ground state through a helix inversion occurs 14 orders of magnitude more slowly than the excited state decay, and was measured as a function of substituent size, solvent viscosity and temperature. In this case neither substituent size nor solvent viscosity influences the rate, which is entirely determined by the activation barrier. This result is different to similar studies of an earlier generation of molecular motors, which suggests different microscopic mechanisms are in operation in the different generations. Finally, the rate of photochemical isomerization was studied for the series of motors, and those with the largest volume substituents showed the highest photochemical cross section.

Influence of increasing steric demand on isomerization of terminal alkenes catalyzed by bifunctional ruthenium complexes

Preparation of a series of cyclopentadienyl- and imidazolyl-phosphine-containing Ru-based complexes bearing a different degree of the Cp-ring methylation has been attempted. According to experimental and structural data the steric factors prevented the formation of the last complex in the series that contains permethylated Cp ring. These complexes were then subjected to alkene isomerization using 1-hexene. The rate of isomerization decreased, in general, with the increase in the Cp-ring methylation suggesting that the initial alkene coordination and/or imidazolyl N decoordination steps are restricted in the overall mechanism.