Cis-trans Isomerization Reaction Research Articles

Twist and Shout: Single-Molecule Mechanochemistry

Chemical reactions can be accelerated by various means, including applied mechanical forces. If the direction of the force does not project well onto the desired reaction coordinate, then only poor acceleration is achieved. Recent developments in single polymer mechanics illustrate how to overcome this limitation, in a simple cis-trans isomerization reaction. Generalizing the approach, synthetic chemistry can be used to attach tethers to different parts of reacting molecular fragments to direct the force usefully. This Perspective explores the prospects for using applied mechanical forces to create exciting new chemistries. For example, it is possible to imagine making polymers that sense mechanical forces within hard-to-reach places, like biological cells, or using mechanical forces to make nanoscale electrical devices using conjugated polymers.

Theoretical insight into the excited-state intramolecular proton transfer mechanisms of three amino-type hydrogen-bonding molecules

Excited-state intramolecular proton transfer (ESIPT) dynamics of the amino-type hydrogen-bonding compound 2-(2′-aminophenyl)benzothiazole (PBT-NH2) as well as its two derivatives 2-(5′-cyano-2′-aminophenyl)benzothiazole (CN-PBT-NH2) and 2-(5′-cyano-2′-tosylaminophenyl)benzothiazole (CN-PBT-NHTs) were studied by the time-dependent density functional theory (TD-DFT) approach with the B3LYP density functional, and their absorption and emission spectra were also explored at the same level of theory. A good agreement is observed between the theoretical simulations and experimental spectra, indicating that the present calculations are reasonably reliable. In addition, it is also found that the energy barriers of the first excited singlet state of the three targeted molecules along the ESIPT reaction are computed to be 0.38, 0.34 and 0.12eV, respectively, showing the trend of gradual decrease, which implies that the introduction of the electron-withdrawing cyano or tosyl group can facilitate the occurrence of the ESIPT reaction of these amino-type H-bonding systems. Following the ESIPT, both CN-PBT-NH2 and CN-PBT-NHTs dye molecules can undergo the cis-trans isomerization reactions in the ground-state and excited-state potential energy curves along the C2-C3 bond between benzothiazole and phenyl moieties, where the energy barriers of the trans-tautomer→cis-tautomer isomerizations in the ground states are calculated to be 0.83 and 0.34eV, respectively. According to our calculations, it is plausible that there may exist the long-lived trans-tautomer species in the ground states of CN-PBT-NH2 and CN-PBT-NHTs.

Conformational Substrate Selection Contributes to the Enzymatic Catalytic Reaction Mechanism of Pin1.

Conformational changes in enzymes and their role in their catalytic activity have been thoroughly addressed experimentally and theoretically. There is a vivid discussion in the field of enzyme catalysis on whether conformational changes of the enzyme are coupled to catalysis, or whether transition state stabilization through the preorganized protein and its electrostatic properties govern the catalysis. In this study, an additional contribution to the catalysis of one specific enzyme, Pin1, is proposed, which arises from its conformational selection of the peptide substrate from aqueous solution with the lowest activation barrier. The most stable conformers of the reactant (cis) and product (trans) peptide were identified through molecular dynamics simulations in combination with metadynamics. The cis-trans isomerization reaction was studied with quantum mechanical/molecular mechanical molecular dynamics simulations and density functional theory together with the mean reaction force, which allows us to separate structural and electronic contributions to the activation barrier. Our results show that enzyme Pin1 binds the trans isomer in the conformation of the peptide with the smallest activation barrier and reduces the barrier further through specific substrate-enzyme interactions, as we have shown previously. The activation barrier of the cis peptide is independent of the conformer and remains unchanged in the enzyme.

Supercritical transesterification of beef tallow for biodiesel production in a batch reactor

Supercritical transesterification experiments of beef tallow with ethanol were carried out in a batch reactor in order to assess the effect of temperature (350 - 400°C), reactant molar ratio (9:1 - 15:1) and reaction time (8 - 40 min). Composition of the produced biofuel was assessed in terms of the percentage of peak area of the long chain Fatty Acid Ethyl Esters (FAEEs) identified, including also the decomposition products generated as a result of thermal cracking or cis-trans isomerization reactions. Thermal decomposition of FAEEs produced from beef tallow included short chain ethyl esters (C8 - C13), ethyl pentadecanoate (C15:0), heptadecanoate (C17:0), not initially present or prevalent in triglycerides sources, as well as ethyl stearate (C18:0) and n-alkanes. Glycerol decomposition reactions were also verified by the presence of glycerol ethers and water content in the produced biodiesel. The highest conversion of triglycerides was verified at 400°C, 15:1 triglycerides to ethanol molar ratio and 40-minute reaction time. At these conditions, ethyl oleate (C18:1) decomposed completely to form cis-trans isomers as well as ethyl octadecanoate (C18:0), which was attributed to double bond hydrogenation reactions. Short chain ethyl esters and glycerol decomposition products have the potential to benefit certain properties of the fuel such as viscosity and cold flow.

Effect of cucurbituril on the primary photoprocesses in indocarbocyanine dyes in water

The effect of cucurbit[7,8]urils (CB7, CB8) on photoprocesses in indocarbocyanine dyes has been studied. Complexation with CB7 and CB8 reveals bathochromic shifts of the maxima in the absorption and fluorescence spectra. Fluorescence enhancement and decreasing have been observed for the complexes with CB7 and CB8, respectively. The dyes and their complexes are capable of trans–cis photoisomerization and hardly undergo intersystem crossing to the triplet state. The rate of the thermal cis–trans isomerization reaction is decreased due to complexation.

Reversible photochemical isomerization of N,N'-di(t-butoxycarbonyl)indigos.

We report on the photophysics of N,N'-di(t-butoxycarbonyl)indigos (tBOC indigos), finding that reversible photochemical trans-cis and cis-trans isomerization reactions proceed with high quantum yields (0.10-0.46). Absorption of wavelengths in the 500-600 nm region induces trans-cis isomerism, while blue light leads to the reverse cis-trans process. Like their parent indigos, trans-BOC indigos have low fluorescence yields (∼1 × 10(-3)), while the cis isomers have no measurable emission. These compounds are the first examples of photoisomerizable indigoid dyes in which photochemical isomerism effectively outcompetes radiative decay processes. Though indigo dyes typically have poor solubility in organic solvents, tBOC indigos can be dissolved at concentrations up to 8 w% in common organic solvents like acetone. Furthermore, unlike other photoisomerizable indigoids, tBOC indigos are not sensitive to quenching by proton and electron donors. These features, combined with high quantum yields of reversible photoisomerism induced by relatively low-energy photons (∼2 eV), make tBOC indigo derivatives potentially interesting for photochromic applications, such as photomechanically actuated materials.

Effect of thermal decomposition on biodiesel viscosity and cold flow property

Thermal stressing experiments were performed in batch reactors at 250–425°C for 3–63min to evaluate the influence of thermal decomposition on biodiesel viscosity and cold flow properties. Dynamic viscosity was measured by a micro viscometer, and cold flow properties were characterized by differential scanning calorimetry (DSC). The crystallization onset temperature determined by DSC correlates with cold flow properties. Results showed that the cis–trans isomerization reactions had a minimal effect on both viscosity and cold flow properties of biodiesel, but polymerization and pyrolysis reactions had significant influence on both properties. Polymerization reactions resulted in increases in both viscosity and the crystallization onset temperature, while pyrolysis reactions showed the opposite effect. The current study suggests that polymerization reactions should be avoided or minimized during high-temperature non-catalytic homogeneous transesterification reactions for biodiesel production.

Cis–trans isomerization of omega dihedrals in proteins

Peptide bonds in protein structures are mainly found in trans conformation with a torsion angle ω close to 180°. Only a very low proportion is observed in cis conformation with ω angle around 0°. Cis-trans isomerization leads to local conformation changes which play an important role in many biological processes. In this paper, we reviewed the recent discoveries and research achievements in this field. First, we presented some interesting cases of biological processes in which cis-trans isomerization is directly implicated. It is involved in protein folding and various aspect of protein function like dimerization interfaces, autoinhibition control, channel gating, membrane binding. Then we reviewed conservation studies of cis peptide bonds which emphasized evolution constraints in term of sequence and local conformation. Finally we made an overview of the numerous molecular dynamics studies and prediction methodologies already developed to take into account this structural feature in the research area of protein modeling. Many cis peptide bonds have not been recognized as such due to the limited resolution of the data and to the refinement protocol used. Cis-trans proline isomerization reactions represents a vast and promising research area that still needs to be further explored for a better understanding of isomerization mechanism and improvement of cis peptide bond predictions.

Reactivity of Thiyl Radicals Generated from Thiomethoxide and Dimethyldisulfide in Microheterogeneous Media

Abstract: Sodium thiomethoxide and dimethyldisulfide will be shown to be convenient sources of methyl thiyl radicals for effecting the cis-trans double bond isomerization of oleic acid to elaidic acid residues arranged in phospholipid bilayers of the microheterogeneous aqueous environment of liposomes. The methods used for methyl thiyl radical generation encompass radiolytic and photochemical meth-ods. The convenience of these methyl thiyl radical sources will be interpreted in terms of the turn-over numbers in the radical chain cis-trans isomerization reaction of unsaturated lipids. Keywords: Methyl thiyl radicals, Sodium thiomethoxide, Dimethyldisulfide, cis-trans isomerization. INTRODUCTION Thiyl radicals have been extensively studied in the context of free radical double bond isomerization. Fig. ( 1 ) shows the reaction mechanism of free thiyl radical RS• double bond isomerization that consists of a reversible addition of radical RS• to the double bond. The regeneration of the double bond is obtained by
-elimination of RS• and the result is in favor of the

Cis-Dichlorido[2,3-dimethyl-3-(4,4,5,5-tetra-methyl-1,3,2λ(5)-dioxaphospho-lan-2-yl-oxy)butan-2-olato-κ(2)O,P]oxido(triphenyl-phosphane-κP)rhenium(V).

The title compound, cis-[Re(C12H24O4P)Cl2O(C18H15P)], was prepared from the analogous trans isomer [Głowiak et al. (2000 ▶). Polyhedron, 19, 2667–2672] by a trans–cis isomerization reaction. The ReV atom adopts a distorted octa­hedral coordination geometry. Besides being coordinated by the oxide and the butano­late O atoms, the ReV atom is coordinated by a pair of chloride ligands and two P atoms in cis positions with respect to each other. In the crystal, adjacent mol­ecules are linked by weak C—H⋯Cl inter­actions, forming a three-dimensional network.

Ultrafast Photodynamics of Drugs in Nanocavities: Cyclodextrins and Human Serum Albumin Protein

In this feature article, we discuss recent advances in studying ultrafast dynamic and structural aspects of host-guest interactions. Steady-state and time-resolved techniques exploring events from the femto- to nanosecond regime were used to examine the ultrafast photodynamics and subsequent events in selected nanostructures of the formed complexes. These consist of aromatic systems, biologically relevant molecules, and drugs trapped within cyclodextrins (CD) and human serum albumin (HSA) protein pockets. We examine the effects exerted by these chemical and biological cavitands on internal twisting motions, proton transfer and charge transfer, and cis-trans isomerization reactions that may occur in the confined molecular systems. In addition, the influence of a restricting environment on the interaction of guest molecules with biological water is considered. The dynamic details of the complexes (diffusion, early interactions, formation, stability, internal guest diffusion, and conformational changes) and the excited-state relaxation pathways, rate constants of the involved processes, and changes in the electronic distribution within encapsulated guests gave clues to elucidate their photobehavior and are relevant to the photostability and delivery of drugs when using nanocarriers.

Photoinduced vitrification near the surfaces of single crystals of azobenzene-based molecular materials with glass-forming ability

Photoinduced vitrification was observed to take place near the surfaces of the single crystals of azobenzene-based molecular materials with glass-forming ability. The phenomenon was caused by repetition of the trans-cis and cis-trans isomerization reactions and hence can be regarded as a kind of photomechanical effect.

Determining symmetry changes during a chemical reaction: the case of diazene isomerization

Analysis of reaction paths in terms of the Continuous Symmetry Measure (CSM) provides an alternative way to analyze the geometrical changes that take place during a reaction. Unique symmetry-profiles, describing the symmetry changes along the internal reaction coordinate were calculated for the cis-trans isomerization reaction of N2H2 and for its halogeno derivatives. A “symmetry transition point” is identified at the extremum point along the symmetry-profiles. At this point, the deviation of the molecule from the rotational symmetry of the reactant is the same as its deviation from the rotational symmetry of the product. In a second application we show that the CSM can be used as an alternative reaction coordinate. Calculations at the MP2 and DFT levels result in similar symmetry profiles.

Diphosphene and Diphosphinylidene

The equilibrium structures of P(2)H(2) isomers and the associated isomerization transition states have been investigated systematically starting from self-consistent-field theory and proceeding to coupled cluster methods using a wide range of basis sets. For each structure, the geometry, energy, dipole moment, harmonic vibrational frequencies, and infrared intensities have been predicted. The global minimum has been confirmed to be planar trans-HPPH diphosphene, lying 3.2 kcal mol(-1) below cis-HPPH with the aug-cc-pVQZ CCSD(T) method upon inclusion of zero-point vibrational energy corrections. Diphosphinylidene, which has the connectivity PPH(2) and C(2v) symmetry, lies 25.2 kcal mol(-1) above the global minimum. The trans-cis isomerization reaction occurs via internal rotation with a barrier of 35.2 kcal mol(-1) using the cc-pVQZ Mk-MRCCSD (2e/2MO) method. This transition state exhibits multireference character and consequently properties were evaluated using CASSCF, MRCI, CASPT2, and Mk-MRCCSD methods with various basis sets. At the aug-cc-pVQZ CCSD(T) level, the transition state for the isomerization reaction between trans-HPPH and diphosphinylidene (planar PPH(2)) is predicted to be nonplanar with a torsional angle of 101.1 degrees . The corresponding barrier is estimated to be 48.2 kcal mol(-1).

Cis–trans isomerization of methyl cis-9-octadecenoate in the presence of cobalt tin catalysts

The isomerization of methyl cis-9-octadecenoate (cis isomer) to methyl trans-9-octadecenoate (trans isomer) was studied in the presence of CoSn/ZnO catalysts under hydrogen pressure. The cis–trans isomerization of methyl cis-9-octadecenoate over a CoSn/ZnO catalysts prepared by co-impregnation, was strongly influenced by the nature of the catalytic sites. The support ZnO did not favour this reaction but the hydrogen played an important role since it influenced the relative amount of different cobalt species. In fact cobalt-containing sites (zerovalent species as well as cobalt oxides) predominated over these reactions. The tin species, which acted as a cobalt modifier for the preferential adsorption of the carbonyl group, inhibited the isomerization of the olefinic bond. Such changes could have also been due to a significant diminution of the cobalt content at the catalyst surface especially for a bulk Sn/Co>1. Consequently, the active sites for the cis–trans isomerization reaction should be cobalt species.

A Self-Starting Method for Obtaining Analytic Potential-Energy Surfaces from ab Initio Electronic Structure Calculations

Previous methods proposed for obtaining analytic potential-energy surfaces (PES) from ab initio electronic structure calculations are not self-starting. They generally require that the sampling of configuration space important in the reaction dynamics of the process being investigated be initiated by using chemical intuition or a previously developed semiempirical potential-energy surface. When the system under investigation contains four or more atoms undergoing three- and four-center reactions in addition to bond scission processes, obtaining a sufficiently converged initial sampling can be very difficult due to the extremely large volume of configuration space that is important in the reaction dynamics. It is shown that by combining direct dynamics (DD) with previously reported molecular dynamics (MD), novelty sampling (NS), and neural network (NN) methods, an analytical surface suitable for MD computations for large systems may be obtained. Application of the method to the investigation of N-O bond scission and cis-trans isomerization reactions of HONO followed by comparison of the resulting neural network potential-energy surface to one obtained by using a semiempirical potential to initiate the sampling shows that the two potential surfaces are the same within the fitting accuracy of the surfaces. It is concluded that the combination of direct dynamics, molecular dynamics, novelty sampling, and neural network fitting provides a self-starting, robust, and accurate DD/MD/NS/NN method for the execution of first-principles, ab initio, molecular dynamics studies in systems containing four or more atoms which are undergoing simultaneous two-, three-, and four-center reactions.

Trans-cis photoisomerization and photoinduced electron transfer as competitive reactions of 9-etylthiacarbocyanine in binary mixtures

The effect of the composition of the dioxane-water mixture on the ability of 9-ethylthiacarbocyanine to participate in competitive reactions of trans-cis photoisomerization and photoinduced electron transfer was studied. An increase in the dioxane content in the range 0–50 vol % leads to a shift of the equilibrium between the dye dimers and monomers toward the monomers (cis-monomers), which is accompanied by a drop in the yield of the triplet dimer molecules, which appear under the action of a laser flash, and electron-transfer products that are formed via the triplet state of dimers in the presence of methylviologen. With growing the dioxane content in the range 50–80 vol %, a shift of the equilibrium between the cis-and trans-monomers toward the trans-monomers occurs, which is accompanied by an increase in the fluorescence intensity. At the dioxane content above 80 vol %, a further shift of the equilibrium toward the trans-monomers occurs, which is accompanied by a substantial increase in the fluorescence intensity and an appearance under the action of a laser flash of the band of the triplet-triplet absorption of the trans-monomer and the absorption band of the cis-monomer as a result of trans-cis photoisomerization. The trans-monomers in the triplet state participate in the electron-transfer reaction with methylviologen. The intersystem crossing process competes with fluorescence and the trans-cis isomerization reaction, which occurs via the excited singlet state of the trans-monomers.

Stability and Unfolding of Reduced Escherichia coli Glutaredoxin 2: A Monomeric Structural Homologue of the Glutathione Transferase Family

Glutaredoxin 2 (Grx2) from Escherichia coli is monomeric and an atypical glutaredoxin that takes part in the monothiol deglutathionylation of proteins. Unlike its orthologs, Grx2 is a larger molecule with a canonical glutathione transferase (GST) fold that consists of two structurally distinct domains, an N-terminal glutaredoxin domain and a C-terminal alpha-helical domain. While GSTs are dimeric proteins, the conformational stability and unfolding kinetics of Grx2 were investigated to establish the contribution made by the domain interface to the stability of the tertiary structure of GST-like proteins without any influence from quaternary interactions. Equilibrium unfolding transitions for Grx2, using urea as a denaturant, are monophasic and exhibit coincidence of the fluorescence and CD data indicative of a concerted loss or formation of tertiary and secondary structure. The data fit well to a two-state N <--> U model with no evidence that an intermediate is being formed. The experimental m value [2.7 kcal mol (-1) (M urea) (-1)] is in excellent agreement with a predicted value of 2.5 kcal mol (-1) (M urea) (-1) based on the amount of surface area expected to become exposed during unfolding. These findings provide evidence that the two structurally distinct domains of Grx2 behave as a single cooperative folding unit. The unfolding kinetics are complex which, as a result of native-state heterogeneity, are characterized by two observable unfolding reactions that occur in parallel. A major population representing one distinct nativelike form unfolds on a fast track to denatured Grx2 with cis-Pro49. This is followed by a spectroscopically silent cis-trans proline isomerization reaction as determined by interrupted unfolding experiments. A minor population representing the other distinct nativelike form unfolds slowly with its rate being limited by an undetermined structural isomerization reaction. Further, there is no evidence indicating that unfolding proceeds via a high-energy intermediate that might suggest independent unfolding of the two nonidentical domains in Grx2. The kinetics data are, therefore, consistent with the existence of cooperativity between the domains, in agreement with the equilibrium data.

Protein Diffusion Probed by the Transient Grating Method with a New Type of Photochromic Molecule†

A new type of photochromic molecule that can be used for diffusion coefficient (D) measurements of various proteins in solution is described. The absorption spectrum of this molecule is changed upon photoexcitation by the trans-cis isomerization reaction. Target proteins were labeled by this photochromic molecule in the dark and the translational motion of the proteins was detected by the transient grating (TG) method. The TG signal was simple enough to determine D accurately and was stable even for long-time irradiation by the laser light. The TG method using this probe molecule improves many drawbacks of the other techniques.

Photochromic reaction-induced changes of ordering in liquid crystalline films

Kinetics of photochemically and thermally driven isomerization was studied in a photochromic azobenzene derivative dissolved in three liquid crystalline matrices. Deviations from the Arrhenius law, observed for the thermal cis-trans isomerization reaction in the vicinity of nematic–isotropic (N–I) phase transitions, have been explained by a reduction of the intensity of light measured in the experiments, due to scattering. The isotropic phase was found to appear in all studied systems upon UV irradiation, at temperatures substantially lower than the thermodynamic temperatures of the respective N–I phase transitions. The nematic phase reappears due to the cis-trans isomerization reaction that can be thermally driven or can occur upon irradiation with the visible light. The occurrence of ‘photo-induced phase transitions’ reported for photochromic dye-doped liquid crystals can be rationalised taking into account different compatibilities (and hence different solubilities) of both forms of photochromic systems. The effects observed should be common to many other photochromic systems dissolved in liquid crystals, in the vicinity of phase transitions of the matrices.