Mechanism Of Isomerization Research Articles

Influence of delta-hexachlorocyclohexane (δ-HCH) to Phytophthora ×alni resistant Alnus glutinosa genotypes − Evaluation of physiological parameters and remediation potential

Hexachlorocyclohexanes (HCHs) are persistent organochlorine pesticides with the adverse effects on human health and the environment. The effect of delta-isomer of hexachlorocyclohexane (δ-HCH) on germination, growth parameters and physiological parameters was studied in different Alnus glutinosa (L.) Gaertn. progeny of resistant genotypes to pathogen Phytophthora ×alni. Two experiments were performed: a short-term experiment to determine the effect of δ-HCH on total germination (GT), germination energy (GE), speed of germination (SG), shoot length and biomass of seedlings, and a long-term experiment devoted to remediation aspects. In addition, changes in the hormonal system of alders were monitored in both cases. Significant differences were found between the treated and control group in most of the evaluated characteristics. Also, the content of studied phytohormones differs between groups. Furthermore, the obtained results indicate genetically determined variability in response to δ-HCH. Of the six tested, the Březové and Tuřany progeny seem to be suitable candidates for phytoremediation because of the adaptation to stress conditions or high remediation efficiency. The rest of tested progeny seems to be unsuitable due to higher mortality, lower remediation efficiency and higher levels of stress hormones resulting in significant decrease in biomass and plant height. Moreover, results indicate the role of the plant as a remediation accelerator, probably through released exudates, and a positive effect on the soil microbiome as the presence of plants increased the remediation efficiency by 20.85 – 35.89%. The obtained research findings may be helpful in better understanding the processes involved in removing these pesticides from the soil. Further research should be focused on rhizosphere microbiome, mechanism of in-plant isomerization and metabolites identification.

Theoretical study of the cis–trans isomerization mechanism of azobenzene containing carboxy groups

DFT calculations were used to study the cis → trans isomerization mechanism of 4,4′-DCA and 3,3′-DCA. We have detected two inversion transition states TSInv1 and TSInv2 for 4,4′-DCA and 3,3′-DCA, respectively. Calculation results show that substituents of carboxy groups have no obvious effect on the coplanarity of benzene rings and NN bond for trans isomers. Potential energy surfaces were calculated for 4,4′-DCA and 3,3′-DCA. In the ground state, the rotation-assisted inversion pathway was found to be preferred. A conical intersection was found between the ground and first excited states along the rotation pathway, indicating that the rotation mechanism is favored in the first excited state. We also analyzed two possible isomerization routes through the inversion and rotation pathways of 4,4′-DCA and 3,3′-DCA of S2 states.

Mechanistic insight into the tautomerization of histidine initiated by water-catalyzed N–H and C–H cleavages

The N-H and C-H activation is of great significance in organic chemistry and chemical industry fields, especially, in the utilization of petroleum raw materials. High NδH (tautomer of natural histidine) content would increase Alzheimer's disease risk. To inhibit this and improve the activation of N-H and C-H bonds, the isomerization mechanism from NδH to NεH of histidine-containing dipeptide catalyzed by water cluster was explored. The results discovered that water cluster assists this reaction by reducing the activation energies from 68.20 to 9.60kcalmol-1, and its size not only affects the reaction rate but also determines the reaction pathway in a degree. Moreover, water cluster, taken as a potential green catalyst, is more effective on the reactions involving N-H and C-H bond cleavages than reported common toxic organometallic compounds and has different catalytic mechanisms. This work also provides some theoretical guidance for the modulation of Alzheimer's disease induced by histidine isomerization.

Enhanced Photoelectrochemical Water Splitting of Black Silicon Photoanode with pH‐Dependent Copper‐Bipyridine Catalysts

Since the water oxidation half-reaction requires the transfer of multi-electrons and the formation of O-O bond, it's crucial to investigate the catalytic behaviours of semiconductor photoanodes. In this work, a bio-inspired copper-bipyridine catalyst of Cu(dcbpy) is decorated on the nanoporous Si photoanode (black Si, b-Si). Under AM1.5G illumination, the b-Si/Cu(dcbpy) photoanode exhibits a high photocurrent density of 6.31 mA cm-2 at 1.5 VRHE at pH 11.0, which is dramatically improved from the b-Si photoanode (1.03 mA cm-2 ) and f-Si photoanode (0.0087 mA cm-2 ). Mechanism studies demonstrate that b-Si/Cu(dcbpy) has improved light-harvesting, interfacial charge-transfer, and surface area for water splitting. More interestingly, b-Si/Cu(dcbpy) exhibits a pH-dependent water oxidation behaviour with a minimum Tafel slope of 241 mV/dec and the lowest overpotential of 0.19 V at pH 11.0, which is due to the monomer/dimer equilibrium of copper catalyst. At pH ∼11, the formation of dimeric hydroxyl-complex could form O-O bond through a redox isomerization (RI) mechanism, which decreases the required potential for water oxidation. This in-depth understanding of pH-dependent water oxidation catalyst brings insights into the design of dimer water oxidation catalysts and efficient photoanodes for solar energy conversion.

Photodissociation of quinoline cation: Mapping the potential energy surface.

A detailed exploration of the potential energy surface of quinoline cation (C9H7N·+) is carried out to extend the present understanding of its fragmentation mechanisms. Density functional theory calculations have been performed to explore new fragmentation schemes, giving special attention to previously unexplored pathways, such as isomerization and elimination of HNC. The isomerization mechanisms producing five- to seven-membered ring intermediates are described and are found to be a dominant channel both energetically and kinetically. Energetically competing pathways are established for the astrochemically important HNC-loss channel, which has hitherto never been considered in the context of the loss of a 27amu fragment from the parent ions. Elimination of acetylene was also studied in great detail. Overall, the computational results are found to complement the experimental observations from the concurrently conducted PEPICO investigation. These could potentially open the doors for rich and interesting vacuum ultraviolet radiation-driven chemistry on planetary atmospheres, meteorites, and comets.

Crystallographic studies of fac- and mer-isomers of Cu[1,4,7,10,13,16-hexaazacyclooctadecane]2+. Influence of counterion and crystallization solvent on crystal structure and dynamic Jahn-Teller effects. Computational studies of structures, energetics, and mechanism of mer-fac isomerization

The syntheses and crystal structures of mer- and fac-isomers of [Cu(18N6)]2+(X−)2 are reported (18 N6 = 1,4,7,10,13,16-hexaazacyclooctadecane; X− = BF4−, ClO4−, NO3−) and compared to a previously reported example (X− = Cl−). Solution structures of the [Cu(18N6)]2+ dication in MeNO2 or MeOH are shown by FT-IR to be almost exclusively mer, and simple evaporation of these solutions or crystallization using Et2O co-solvent also afford the solid mer-salts. However, using C6H6 or CCl4 as crystallization co-solvents afforded the corresponding fac-isomers of the BF4− and ClO4− salts, in which the anions and the symmetrical solvent occupy locations on the crystallographic 3-fold axis. Similar treatment of the less symmetrical NO3− salts affords the mer-isomer without inclusion of C6H6. The solid-state structures of the mer-isomers each exhibit the anticipated tetragonal Jahn-Teller distortions, with two longer Cu-N bonds. In contrast the fac-isomers all show internally identical Cu-N distances, due to a dynamic exchange between Jahn-Teller distorted structures in the crystal. Density Functional Theory (DFT) is used to provide rationalizations of these observations and to elucidate an energetically feasible mechanistic pathway for the facile interconversion of mer and fac isomers in solution.

A lead selective dimeric quinoline based fluorescent chemosensor and its applications in milk and honey samples, smartphone and bio-imaging

Dimeric quinoline-based Schiff base was developed (DQS) for the specific detection of Pb2+ ion via fluorimetry. DQS coordinates with Pb2+, a variation in fluorescence intensity with enhanced radical blue shift was observed due to the restriction of CN rotation, CN isomerization, and photoinduced electron transfer (PET) mechanisms. In addition, the intramolecular charge transfer (ICT) from electron-donating morpholine to phenylene diamine acceptor linked quinoline bridge is responsible for the blue-shifted fluorescence enhancement in the DQS-Pb2+ complex. The binding stoichiometry of DQS: Pb2+ (1:2) was confirmed by host–guest titration and mass spectrometry. The limit of detection (LOD) of the DQS was found to be 1.3 × 10-7 M for Pb2+ ion. The DQS sensing ability of Pb2+ was further applied into milk and honey samples, smartphone, bio-imaging and to construct of an INHIBIT molecular logic gate.

Geometric and electronic structure analyses on three Au42(SR)26 isomers

In this paper, we present the geometric and electronic structure analyses of three Au42(SR)26 isomers based on a combination of grand unified model (GUM), ring model, superatom network model, and density functional theory calculations. Structural decompositions, Au–Au and Au–S distances, Wiberg bond orders, density of states, composition of the frontier orbitals, and origin of the optical absorption spectra are presented and discussed in detail. The structural decomposition of the Au cores of the three isomers into eight tetrahedral Au4 elementary blocks based on GUM shows that the isomeric mechanism of the three isomers can be ascribed to core and complex isomerism. Inspection of Au–Au and Au–S distances reveals the key role of the aurophilic interactions in the stability of the three Au42(SR)26 isomers. Furthermore, by analyzing the composition of the frontier orbitals, the origin of the optical absorption spectra of the three isomers is attributed to the sp → sp transition. Overall, the geometric and electronic structure analyses of the three Au42(SR)26 isomers illustrate the inherent structure–property correlations among these isomers.

E-Z ИЗОМЕРИЗАЦИЯ ХЛОРПРОПЕНИЛЬНОГО ФРАГМЕНТА ПРИ СИНТЕЗЕ БИС(1-ХЛОР-1-ПРОПЕН-3-ИЛ)СЕЛЕНИДА

In the synthesis of bis(1-chloropropenyl)selenide from the E-isomer of 1,3-dichloropropene and selenium in the hydrazine hydrate-KOH system was obtained a mixture of isomers E,Z-; E,E- and Z,Z- in a ratio of 1:1,2:0,7. A possible mechanism of isomerization is discussed

The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization.

Photoactivation of bacteriophytochrome involves a cis–trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail. In our simulations the photoisomerization of the D ring occurs in the counterclockwise direction. On a subpicosecond time scale, the photoexcited chromophore adopts a short-lived intermediate with a highly twisted configuration stabilized by an extended hydrogen-bonding network. Within tens of picoseconds, these hydrogen bonds break, allowing the chromophore to adopt a more planar configuration, which we assign to the early Lumi-R state. The isomerization process is completed via helix inversion of the biliverdin chromophore to form the late Lumi-R state. The mechanistic insights into the photoisomerization process are essential to understand how bacteriophytochrome has evolved to mediate photoactivation and to engineer this protein for new applications.

Theoretical study on the structure and the isomerization mechanism of N‐nitropyrazole

AbstractN‐nitropyrazole, as a kind of important intermediate, is used to synthesize the novel energetic material. Therefore, it is necessary to get an insight into the isomerization mechanism. Herein, we propose three reaction pathways. Quantum chemistry theory was used to calculate the structure, energy, and thermal parameter. Pathway A is the main path with the lowest energy barrier. The theoretical rate constant is 0.022 min−1 which has a good agreement with the experimental result of 0.021 min−1. The proton shift was also studied to confirm that 2H‐3‐nitropyrazole is the final production.

Regiodivergent Synthesis of Methylene and Methyl Ring-Fused Isoquinolinones: Base-Promoted Isomerization of N-Allyl Amides.

Methylene and methyl tricyclic isoquinolinones were selectively prepared using a palladium(II)-catalyzed aerobic aza-Wacker reaction, followed by a base- and temperature-controlled Heck reaction catalyzed by palladium(0). Exo- to endo-double-bond migration in isoquinolinones was achieved with 93-99% yields by treatment of the Heck products with Cs2CO3 in dimethyl sulfoxide (DMSO) at 150 °C. A probable mechanism for Cs2CO3-promoted olefin isomerization was proposed and examined using D-isotope labeling experiments. Finally, yuanamide, a 13-methyl-8-oxoprotoberberine alkaloid, was synthesized using the palladium-catalyzed aza-Wacker/Heck/migration sequence.

Mechanochromophore-Linked Polymeric Materials with Visible Color Changes.

Mechanical force as a type of stimuli for smart materials has obtained much attention in the past decade. Color-changing materials in response to mechanical stimuli have shown great potential in the applications such as sensors and displays. Mechanochromophore-linked polymeric materials, which are a growing sub-class of these materials, are discussed in detail in this review. Two main types of mechanochromophores which exhibit visible color change, summarized herein, involve either isomerization or radical generation mechanisms. This review focuses on their synthesis and incorporation into polymer matrices, the type of mechanical force used, factors affecting the mechanochromic properties, and their applications.

Synthesis of (S)- and (R)-β-Tyrosine by Redesigned Phenylalanine Aminomutase

Phenylalanine aminomutase from Taxus chinensis (TchPAM) is employed in the biosynthesis of the widely used antitumor drug paclitaxel. TchPAM has received substantial attention due to its strict enantioselectivity towards (R)-β-phenylalanine, in contrast to the bacterial enzymes classified as EC 5.4.3.11 which are (S)-selective for this substrate. However, the understanding of the isomerization mechanism of the reorientation and rearrangement reactions in TchPAM might support and promote further research on expanding the scope of the substrate and thus the establishment of large-scale production of potential synthesis for drug development. Upon conservation analysis, computational simulation, and mutagenesis experiments, we report a mutant from TchPAM, which can catalyze the amination reaction of trans-p-hydroxycinnamic acid to (R)- and (S)-β-tyrosine. We propose a mechanism for the function of the highly conserved residues L179, N458, and Q459 in the active site of TchPAM. This work highlights the importance of the hydrophobic residues in the active site, including the residues L104, L108, and I431, for maintaining the strict enantioselectivity of TchPAM, and the importance of these residues for substrate specificity and activation by altering the substrate binding position or varying the location of neighboring residues. Furthermore, an explanation of (R)-selectivity in TchPAM is proposed based on the mutagenesis study of these hydrophobic residues. In summary, these studies support the future exploitation of the rational engineering of corresponding enzymes with MIO moiety (3,5-dihydro-5-methylidene-4H-imidazole-4-one) such as ammonia lyases and aminomutases of aromatic amino acids.

Effect of the alkyl linker length on the photoisomerization of hydrazone switches on metal surfaces

A series of bistable hydrazone switches containing alkyl thiolate linkers of various lengths (Cn HAT, n = 3, 8, 10, and 11) were synthesized. We explore the length effect of the carbon chain on the photoisomerization of hydrazone switches using UV–vis spectroscopy and tip-enhanced Raman spectroscopy (TERS). The conversion efficiency (photostationary state, PSS, after irradiation at 415 or 340 nm) of the isomerization of Cn HAT monolayers on Au rises with the increasing length of the alkyl chain, with an optimum result for n-octyl (C8) thiolate or longer linkers. The low PSS415 of C3 HAT is attributed to strong quenching by the metal surface, as confirmed by density functional theory (DFT) calculations based on a one-dimensional double-well model. The partial trap of photo-induced hot carriers in the excited states of C3 HAT in the potential well of Au reduces the lifetime of its excited states. Such calculation results provide insight into the detailed mechanism of the surface quenching effect. Furthermore, UV–vis results suggest that after irradiation at 415 nm, Cn HATs cannot isomerize when bound to Ag; higher photon energies are necessary in this case. These results validate the previously proposed substrate-mediated isomerization mechanism.

A photochromic salicylaldehyde hydrazone derivative based on C[dbnd]N isomerization and ESIPT mechanisms and its detection of Al3+ in aqueous solution

A simple photochromic Schiff base was successfully prepared by the condensation of salicylaldehyde and benzoyl hydrazine. This compound has reversible photochromic properties based on isomerization and ESIPT mechanisms. In organic solvents, after irradiation with 365 nm UV light for 2 min, the absorption peak at 367 nm of the compound showed a significant decrease, while a double absorption peak appeared at 418 nm and 438 nm, accompanied by a significant change of the solution color from colorless to yellow. The compound can also complex with Al3+ at the molar ratio of 2:1 in the water solution (acetonitrile/water, v/v, 1:99), resulting in significantly enhanced fluorescence of the compound, so as to achieve fluorescence detection of Al3+ in living cells and water samples.

Highly efficient isomerization of glucose to fructose over a novel aluminum doped graphitic carbon nitride bifunctional catalyst

Glucose isomerization to fructose is a crucial step for the efficient production of fuel and valuable chemicals from renewable carbohydrates. Aluminum (Al) was introduced into the structure of a graphitic carbon nitride (g-C3N4) by a simple thermal polycondensation of urea and aluminum chloride, and thereby, provided a series of Al-doped g-C3N4 (xAl-UCN) catalysts for the isomerization reaction. A high fructose yield of 48.29%, comparable to the quantitative yields (ca. 50%) by enzymatic routes, was achieved with the 0.5Al–UCN catalyst. Detailed characterizations of a series of Al–UCN catalysts, with different Al loadings, showed that 1) the Al loading amount has a profound effect on the physical-chemical properties of Al–UCN catalysts; 2) excess Al loading can inhibit the formation of a crystalline g-C3N4 structure; and 3) at lower Al loadings, the Al appears to be doped into the g-C3N4 framework possibly via coordination bonds. The mechanism for glucose isomerization to fructose may involve both Lewis acid and base catalyzed routes, with the coordinated Al species (Al[6]) providing Lewis acidity, and N-containing groups on g-C3N4 providing basicity. The additive effect of this dual-functionality is likely responsible for the high catalytic activity. The 0.5Al–UCN catalyst was readily recycled, demonstrating near-constant activity after 5 cycles of use. Altogether, glucose isomerization to fructose over the readily synthesized and recyclable Al–UCN catalyst could provide a highly-efficient and cost-effective step in lignocellulosic biomass valorization.

Cyclometalated Platinum(II) Complexes in a Cis-N,N Configuration: Photophysical Properties and Isomerization to Trans Isomers.

Synthesis, isomerization, and photophysical properties of novel cis-N,N-cyclometalated complexes [Pt(C∧N)(l-Phe)] (C∧N = benzoquinolinate (1), phenylpyridinate (2), 2-(p-tolyl)pyridinate (3), and 1-phenylpyrazolate (4); l-Phe- = l-phenylalaninate) are reported herein. In solution, the cis forms of the complexes isomerize to their trans forms via an associative mechanism. This cis/trans isomerism barely influences the absorption and luminescence properties of the complexes in solution, except for a characteristic absorption at approximately 340 nm in the absorption spectra of the cis complexes that is not observed for the trans complexes. Interestingly, the cis complexes are spontaneously assembled in a crystalline phase and show bathochromic absorption and emission colors compared with those of the corresponding trans isomers, which are aggregated in an amorphous phase. cis-1 and cis-2 demonstrate hypsochromic luminescence mechanochromism. The influence of the geometrical isomerism on the photophysical properties and the isomerization mechanism are supported by density functional theory calculations.

Crystal structure and biochemical analysis of the specialized deoxynivalenol–detoxifying glyoxalase SPG from Gossypium hirsutum

Deoxynivalenol (DON) and its acetylated derivatives such as 3-acetyldeoxynivalenol (3A-DON) and 15-acetyldeoxynivalenol (15A-DON) are notorious mycotoxins in Fusarium contaminated cereals, which pose a great threat to human and livestock health. The specialized glyoxalase I from Gossypium hirsutum (SPG) can lower the toxicity of 3A-DON by conducting isomerization to transfer C8 carbonyl to C7 and double bond from C9-C10 to C8-C9. Here we report that the substrate–flexible SPG can also recognize 15A-DON and DON, probably following the same isomerization mechanism as that for 3A-DON. The crystallographic, mutagenesis, and biochemical analyses revealed that SPG provides a hydrophobic pocket to accommodate the substrate and residue E167 might serve as the catalytic base. A variant SPGY62A that was constructed based on structure–based protein engineering exhibited elevated catalytic activity towards DON, 3A-DON, and 15A-DON by >70%. Furthermore, variant SPGY62A was successfully expressed in Pichia pastoris, whose catalytic activity was also compared to that produced in Escherichia coli. These results provide a blueprint for further protein engineering of SPG and reveal the potential applications of the enzyme in detoxifying DON, 3A-DON and 15A-DON.

Combined in situ XAS and DFT studies on the role of Pt in zeolite-supported metal catalysts for selective n-hexane isomerization

In this study, we used several in situ, and spectroscopy analyses to investigate the roles of platinum (Pt) in zeolite-supported Pt catalysts for selective n-alkane isomerization. HY zeolites were synthesized using the rice husk silica and impregnated with Pt precursor by incipient wetness impregnation. Typically, HY zeolites have proved to be active hydrocarbon cracking catalysts. The particular challenge is to find an effective catalyst, which favors the isomerization of n-alkanes without too much cracking. In this work, adding Pt atoms to HY zeolite provides an enhanced multifunctional catalyst for converting n-alkanes to branched hydrocarbons. To understand the effect of Pt, we further investigated the reaction mechanism of n-hexane isomerization to 2–methylpentane (2MP) and 3-methylpentane (3MP) by DFT simulations, using a cluster of 30T HY zeolite modeled through B3LYP + 3D calculations. We found that, at 450 °C, the isomerization on Pt-HY gives higher cracking products. Decreasing temperature to 300 °C yielded greater selectivity of branched hydrocarbons. In addition, DFT calculations demonstrate that the 2MP production via route A1 (C3-C4 bond activation) and a rate-determining step of 0.97 eV proved more thermodynamically and kinetically favorable than the 3MP product. This agrees well with our experimental observations. Consequently, the presence of Pt on the HY zeolite plays an essential role in both CC forming and breaking. Finally, the Pt–HY zeolite is an efficient catalyst for petroleum production, improving the octane number for catalytic performance and product selectivity by isomerizing straight-chain alkanes to their branched chain isomers.