Mechanism Of Isomerization Research Articles

Application of Ce modified zeolite to improve the performance of cresol isomerization

This study clarifies the mechanism behind the isomerization of cresol, focusing on a shaped cerium-modified Beta zeolite. The catalysts were characterized using a series of characterization techniques, including XRD, Py-IR, XPS, and TGA. The results emphasize the pivotal role of cerium, particularly at a 5 % modification concentration, in improving catalyst acidity. The mechanism of isomerization is revealed through kinetic calculation of reversible monomolecular systems, emphasizing the significance of acid sites. TGA analysis of catalyst deactivation reveals distinctive carbon deposition patterns, with the cerium-modified zeolite displaying enhanced resistance to pore blockage through Type II carbon deposition. XPS analysis post-deactivation indicates an increased proportion of Ce3+, suggesting elevated oxygen vacancies and unsaturated chemical bonds, influencing the catalytic activity negatively. In summary, an appropriate cerium modification, especially at the 5 % concentration, strikes a balance between enhanced acidity and resistance to carbon deposition, providing valuable insights for tailoring zeolite catalysts in cresol isomerization.

Photo/Mechanical/Acidic Multi-Stimuli Responses and Information Encryption Design of Acylhydrazone Derivative.

Stimuli-responsive crystalline materials have received much attention for being potential candidates of smart materials. However, the occurrence of polymorphism-driven stimuli responses in crystalline materials remains interesting but rare. Herein, three polymorphs of an acylhydrazone derivative, N'-[(E)-(1-benzofuran-2-yl) methylidene] pyridine -4-carbohydrazide (BFMP) were prepared. Form-1 undergoes a photomechanical response via E→Z photoisomerization under UV irradiation, accompanied by a decrease in fluorescence intensity and a change from colorless to yellow. Two types of Z→E thermal isomerization mechanisms with significant differences in conversion rate were observed at different temperatures in form-1. The solid-melt-solid transition has a faster conversion rate compared to the solid-solid transition due to freedom from lattice confinement. The transition from form-2 to form-3 can be achieved under grinding, coupled with a significant decrease in fluorescence intensity. The similar molecular stacking pattern of form-2 and form-3 provides a structural basis for the grinding-induced crystalline transition behavior. In addition, the presence of the pyridine moiety imparts an acidochromic property. The combination of photochromism and acidochromism explores the possible applications of acylhydrazone derivatives in information encryption.

Hydrosulfonylation of Alkynes for Stereodivergent Synthesis of Vinyl Sulfones: Synthetic Strategy and Mechanistic Insights.

Direct synthesis of thermodynamically less favorable (Z)-vinyl sulfones presents a notable challenge in organic synthesis. In addition, the development of a stereodivergent synthesis for (E)- and (Z)-vinyl sulfones is crucial but remains elusive. In this study, we present a hydrosulfonylation of aryl-substituted alkynes, achieving a stereodivergent synthesis of (E)- and (Z)-vinyl sulfones by leveraging both thermodynamic and kinetic controls. Notably, the synthesis of challenging (Z)-vinyl sulfones was achieved through a kinetically controlled process without the need for a catalyst. To synthesize (E)-vinyl sulfones, unconventional visible light-mediated isomerization was employed as a means of facilitating the transition to the thermodynamically favored form. The present study encompasses a comprehensive experimental and computational investigation, which provides valuable insights into the reaction mechanism. This investigation reveals two plausible isomerization pathways: a novel double spin-flip mechanism and a hydrogen atom transfer process in the presence of eosin Y. This study not only advances our understanding of isomerization mechanisms beyond conventional energy-transfer routes but also offers a robust and switchable strategy for synthesizing (E)- and (Z)-vinyl sulfones, thereby providing a versatile avenue for the creation of valuable compounds in the fields of organic synthesis and medicinal chemistry.

Ultrafast Primary Dynamics and Isomerization Mechanism of a Far-Red Sensing Cyanobacteriochrome.

Far-red cyanobacteriochromes (CBCRs) are bilin-based photosensory proteins that promise to be novel optical agents in optogenetics and deep tissue imaging. Recent structural studies of a far-red CBCR 2551g3 have revealed a unique all-Z,syn chromophore conformation in the far-red-absorbing Pfr state. Understanding the photoswitching mechanism through bilin photoisomerization is important for developing novel biomedical applications. Here, we employ femtosecond spectroscopy and site-directed mutagenesis to systematically characterize the dynamics of wild-type 2551g3 and four critical mutants in the 15Z Pfr state. We captured local relaxations in several picoseconds and isomerization dynamics in hundreds of picoseconds. Most mutants exhibited faster local relaxation, while their twisting dynamics and photoproducts depend on specific protein-chromophore interactions around the D-ring and C-ring. These results collectively reveal a unique dynamic pattern of excited-state evolution arising from a relatively rigid protein environment, thereby elucidating the molecular mechanism of Pfr-state photoisomerization in far-red CBCRs.

Biomolecular investigations into BBI reveal an enzymatic mechanism for PUFA isomerisation in bifidobacterium CFA bioconversion strains

Multiple species of Bifidobacterium exhibit the ability to bioconvert conjugated fatty acids (CFAs), which is considered an important pathway for these strains to promote host health. However, there has been limited progress in understanding the enzymatic mechanism of CFA bioconversion by bifidobacteria, despite the increasing number of studies identifying CFA-producing strains. The protein responsible for polyunsaturated fatty acid (PUFA) isomerization in B. breve CCFM683 has recently been discovered and named BBI, providing a starting point for exploring Bifidobacterium isomerases (BIs). This study presents the sequence classification of membrane-bound isomerases from four common Bifidobacterium species that produce CFA. Heterologous expression, purification, and enzymatic studies of the typical sequences revealed that all possess a single c9, t11 isomer as the product and share common features in terms of enzymatic properties and catalytic kinetics. Using molecular docking and alanine scanning, Lys84, Tyr198, Asn202, and Leu245 located in the binding pocket were identified as critical to the catalytic activity, a finding further confirmed by site-directed mutagenesis-based screening assays. Overall, these findings provide insightful knowledge concerning the molecular mechanisms of BIs. This will open up additional opportunities for the use of bifidobacteria and CFAs in probiotic foods and precision nutrition.

Isomerization performance of n-hexane in hydrogen atmosphere over the multistage porous composite NixPy-MCM-41/MOR catalyst

With the increasingly strict environmental protection requirements and the continuous improvement for the performance of clean fuel, it is imperative to develop technology for producing high octane gasoline blending components. Alkane isomerization was one of the important ways due to it contain little olefin and aromatic components which are harmful to the environment. In this study, the multistage porous composite NixPy-MCM-41/MOR catalysts were synthesized in the hydrogen atmosphere, the conversion rate and selectivity of n-hexane hydrogen isomerization with different conditions was tested in a fixed bed reactor. The results shown that the loading volume of active components is 4.0 wt%, nickel-phosphorus ratio of 0.5, reaction temperature of 250 °C, reaction pressure 3.0 MPa and volume space velocity is 2.0 h−1 with the hydrogen condition showed good catalytic activity for the n-hexane isomerization. The conversion rate of n-hexane is 73.0 % and the selectivity of 84.0 %, respectively. The isomerization stability of the Ni2P-MCM-41/MOR catalyst was investigated. After the long period test, the catalytic activity of the catalyst could keep good. Based on the study of reaction effect with different test conditions in hydrogen atmosphere, the mechanism of alkane isomerization for Ni2P-MCM-41/MOR catalyst was proposed.

Ultrafast and nanomolar detection of Al3+: Furazan based fluorescent chemosensor and its practices in Smartphone, test kit, water samples and living–cell

A new fluorescent chemoprobe (SDAF) was successfully synthesized and utilized as a sensor for the recognition of Al3+ in EtOH:HEPES (3:2, v:v, pH: 7.0) media. The SDAF depicted a selective “turn–on” response at λem = 467 nm to Al3+ over competitive cations, and the SDAF–Al3+ complex had a reversible response with F−. The limit of detection (LOD) was found about at nano–molar level (28.0 nM), demonstrating the sensitivity of the chemoprobe toward Al3+. The binding stoichiometry of SDAF–Al3+ was investigated by TOF–MS, Job's plot, 1H NMR and 13C NMR methods and found as 1:1. The recognition mechanisms of SDAF for the detection of Al3+ were the –C = N isomerization and photoinduced electron transfer (PET) mechanisms, and they were confirmed by density functional theory (DFT) computation. Furthermore, the SDAF was successfully employed in living–cell bioimaging and cytotoxicity, it was also utilized in Smartphone, test–kit and natural spring water (recovery values; 89.01 %– 96.33 %)applications.

Detection of Zn2+ and its imaging in plant roots by a bisphenol A-Based fluorescent chemosensor

Application of a chemosensor for imaging Zn2+ in plant’s root has rarely been reported. We report here synthesis and characterization of 4,4′-(propane-2,2-diyl)bis(2-(((2morpholinoethyl)imino)methyl)phenol) (H2L) as a Zn2+ sensor and its application in plant root imaging. It has been synthesized by a reaction between bisphenol A dialdehyde and 2-morpholinoethanamine (1:2 ratio) in methanol under mild condition. It shows significant enhancement (76-fold) in its fluorescence intensity at 473 nm in the presence of Zn2+ ions. Quantum yield of H2L increases from 0.004 to 0.635 upon interaction with the cation. It forms a 1:2 complex (ligand/metal) with Zn2+ with an association constant of 2.89 × 105 M−2. The limit of detection has been determined as 7.05 × 10-8 M signifying high sensitivity. Fluorescence increment of the probe has been attributed to chelation enhanced fluorescence (CHEFF) mechanism and restriction of CN isomerization. H2L has been successfully utilized to image Zn2+ in rice plant’s root.

Follow-Up Study of Trans-C to Cis-C Thermally or Photochemically Induced Isomerization of Terpyridine Adducts of Cycloruthenated 2-Aryl-2'-pyridine Compounds.

The mechanism of isomerization of the known 2-phenyl,pyridine (phpy) derivatives [Ru(phpy-κC,N) (MeCN-trans-N)(terpy)]PF6, 2, to [Ru(phpy-κC,N)(MeCN-trans-C)(terpy)]PF6 (terpy = 2,2';6',2″-terpyridine), 3, at temperatures >50 °C has been investigated both by 1H NMR spectroscopy and by DFT calculations. The photoisomerization of 2 to 3 by UV light occurred also quantitatively in MeCN after 20 h at room temperature. A similar behavior to that of 2 could be established for the related compound [Ru(3-acridine-2'-C5H4N-κC,N)(MeCN-trans-N)(2,2';6',2″-terpyridine)]PF6, 6 (acridine = dibenzo[b,e]pyridine or 2,3-benzoquinoline), that was obtained from the reaction between [Ru(3-acridine-2'-C5H4N-κC,N) (MeCN)4]PF6, 4, and terpy in MeOH/MeCN at 60 °C for 24 h. Similar to 2, the isomerization of 6 to [Ru(3-acridine-2'-C5H4N-κC,N)(MeCN-trans-C) (terpy)]PF6, 7, could be induced thermally (48 h at 60 °C in pure MeOH) or photochemically under UV radiation in MeCN at room temperature. A compound closely related to 7 but in which MeCN was replaced by H2O was described earlier (Tanaka et al. Inorg. Chem. 2012, 51, 5386-539). The presence of water on this compound had a dramatic effect as far as the coordination of terpy was concerned as its isomerization to a compound related to 6 (in which H2O instead of MeCN is coordinated to Ru) occurred indeed photochemically via irradiation with visible light.

Computational studies of the isomerization mechanism of azobenzene and its derivatives

Computational studies of the isomerization mechanism of azobenzene and its derivatives

Iron Heme Enzyme-Catalyzed Cyclopropanations with Diazirines as Carbene Precursors: Computational Explorations of Diazirine Activation and Cyclopropanation Mechanism.

The mechanism of cyclopropanations with diazirines as air-stable and user-friendly alternatives to commonly employed diazo compounds within iron heme enzyme-catalyzed carbene transfer reactions has been studied by means of density functional theory (DFT) calculations of model systems, quantum mechanics/molecular mechanics (QM/MM) calculations, and molecular dynamics (MD) simulations of the iron carbene and the cyclopropanation transition state in the enzyme active site. The reaction is initiated by a direct diazirine-diazo isomerization occurring in the active site of the enzyme. In contrast, an isomerization mechanism proceeding via the formation of a free carbene intermediate in lieu of a direct, one-step isomerization process was observed for model systems. Subsequent reaction with benzyl acrylate takes place through stepwise C-C bond formation via a diradical intermediate, delivering the cyclopropane product. The origin of the observed diastereo- and enantioselectivity in the enzyme was investigated through MD simulations, which indicate a preferred formation of the cis-cyclopropane by steric control.

Azo dye polyelectrolyte multilayer films reversibly re-soluble with visible light

Polymeric multilayer films were prepared using a layer-by-layer (LBL) technique on glass surfaces, by repeated and sequential dipping into dilute aqueous solutions of various combinations of water-soluble polyanions (polyacrylic acid (PAA)), polycations (polyallylamine hydrochloride (PAH) or chitosan (CS)), with bi-functional water-soluble cationic azo dyes bismark brown R bismarck brown red or bismark brown Y (BBY), or anionic azo dyes allura red (ALR) or amaranth (AMA), as ionic cross-linkers. The electrostatically-assembled ionically-paired films showed good long-term stability to dissolution, with no re-solubility in water. However, upon exposure to low power visible light under running water, the films photo-disassembled back to their water-soluble constituent components, via structural photo-isomerization of the azo ionic crosslinkers. The relative rate of the disassembly (RRD) of the films was established using UV-Vis spectroscopy, demonstrating that these assemblies can in principle represent fully recyclable, environmentally structurally degradable materials triggered by exposure to sunlight, with full recovery of starting components. A density functional theory treatment of the allura red azo dye rationalizes the geometrical isomerization mechanism of the photo-disassembly and provides insight into the energetics of the optically-induced structural changes that trigger the disassembly and recovery.

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.

Photoinduced isomerization mechanism of isatin N<sup>2</sup>-diphenylhydrazones molecular switch

Hydrazone molecular switches have significant application value in supramolecular chemistry. A new type of hydrazone molecular switch, named isatin N<sup>2</sup>-diphenylhydrazone, has been synthesized. Owing to its cis-trans isomerization characteristics under visible light excitation, ease of synthesizing of derivatives, and sensitivity to external stimuli, it has important application value in the field of biochemistry. Because of its forward and backward visible light excitation characteristics, it is considered a class of compound that is very suitable for molecular switches, and it has a wide application value in fields such as biotechnology. In addition, the derivatives compound exhibits strong interactions with negative ions, which enhances its function as a molecular switch, making it a four-state molecular switch that can be achieved by a single molecule. However, the photo-induced isomerization mechanism of these new molecular switches is not yet clear, and whether there are novel phenomena in the isomerization process is also unknown. In this work, a semi empirical OM2/MRCI based trajectory surface hopping dynamics method is adopted to systematically study a photo induced isomerization mechanism based on the E-Z isomerization process of the isatin N<sup>2</sup>-diphenylhydrazones molecular switch. Optimization configuration and the average lifetime of the first excited S<sub>1</sub> state are obtained by using the semi-empirical OM2/MRCI method of molecular switch. It is found that the average lifetime of the S<sub>1</sub> excited state of the E-configuration molecular switch is about 107 fs, and the quantum yield of E-Z isomerization of the molecular switch is 16.01%. By calculating the photo induced isomerization process of the molecular switch, two different isomerization mechanisms of the molecular switch are identified. In addition to the traditional molecular switch isomerization mechanism revolving around the C=N bond, a new isomerization mechanism, i.e. the face-to-face twisting of the molecular switch rotor part is elucidated. By calculating the time-resolved fluorescence radiation spectrum, it is predicted that there may be a very fast fluorescence quenching phenomenon occurring in about 75 fs in the isomerization process, slightly faster than the S<sub>1</sub> average decay events (107 fs). The information about wavelength-resolved attenuation at different times is also calculated, which reflects the ultrafast fluorescence quenching process accompanied by fluorescence red shift, ranging from 2.1 × 10<sup>4</sup> cm<sup>–1</sup> to 3.4 × 10<sup>4</sup> cm<sup>–1</sup>. By comparing the calculated fluorescence spectra with the average lifetime of excited states, the existence of “dark states” is proposed, and possible explanations for the existence of “dark states” are provided, and those “dark states” may be related to lower quantum yields. The research results can provide theoretical guidance for the design and application of new molecular switches. The ease of synthesis and sensitivity to external stimuli of its derivatives make those compounds extremely valuable in molecular switching and light measurement applications.

Is this how bromine spiropyran salt is converted to merocyanine under UV irradiation? A look through the prism of quantum chemical calculations.

The stability of merocyanine forms formed under UV irradiation of a solution of a spiropyran salt, in which an organic part acts as a cation and a compact bromide ion as an anion, their photophysical properties, and the formation mechanism are studied in this work using time-dependent density functional theory. Theoretical calculations show that TTC and CTT are the most stable open forms (the difference in stability energies is 10.5 and 12.0 kcal mol-1 relative to the formation energy of spiropyran, respectively). The simulated absorption bands in the UV spectrum of the merocyanine forms are observed both in the UV region at 308-366 nm and in the visible region at 544-757 nm due to n → π* and π → π* type transitions. We found that the isomerisation mechanism of spiropyran into merocyanine forms includes two key stages: the ring opening to form cisoid merocyanine forms (except unstable TCC) through conical intersection and their subsequent isomerisation to form stable transoid isomers. The length of the Cspiro-O bond is 1.97 Å and the C1'-C2'-C3'-C4' angle is 70° in the structure close to conical intersection. The stage that determines the rate of this process is the isomerisation between transoid forms, as in the case of transformation of open merocyanine forms into spiropyran.

Designed synthesis N-doped sulfonated bifunctional catalyst for efficient 5-hydroxymethylfurfural production: A pyridinic N-triggered proton-shift mechanism at basic sites

Considering the essential role of acidic/basic sites in efficient 5-hydroxymentylfurfural (5-HMF) production from cellulose, the superiority of acid-base bifunctional catalysts was unfolded. However, the lack of in-depth research on catalytic mechanism of active sites, especially the basic sites, greatly hinders its chemical utilization. Herein, N-doped sulfonated bifunctional catalysts were rationally designed. The synthesized NCS-1H catalyst exhibited outstanding activity and recyclability. Favorable 5-HMF yield of 50.0 % with 62.9 % of selectivity was obtained. Spin polarized density function theory (DFT) analysis revealed a pyridinic N-triggered proton-shift mechanism of glucose isomerization. Catalyzed by pyridinic N, the proton of glucose on C2 was shifted to O5, leading to the cleavage of C1-O1 bond. As a result, an enol intermediate was formed and converted to fructose. Compared to pyrrolic N and graphitic N, pyridinic N significantly reduced the reaction energy barrier of rate-determining step to 0.79 eV, i.e., C1-O1 bond cleavage.

Construction and Application of Fluorescent Probes with Imine Protective Groups for Hypochlorite Detection.

Several fluorescent probes have been designed to detect ClO- in biological systems based on the isomerization mechanism of C = N bonds. Particularly, fluorescein has emerged as an important fluorophore for detecting ClO- because of its unique properties. Previously, we introduced the fluorescein analog F-1 with an active aldehyde group. In this study, two ClO- fluorescent sensors (F-2 and F-3) with imine groups were designed and synthesized using diaminomaleonitrile and 2-hydrazylbenzothiazole as amines. The electron cloud distribution of F-2 and F-3 in ground and excited states was explored via Gaussian calculations, reasonably explaining their photophysical properties. The fluorescence detection of ClO- in solution using the two probes (F-2 and F-3) was realized based on the mechanism of imine deprotection with ClO-. NaClO concentration titration demonstrated that the colorimetric detection of ClO- with the naked eye could be achieved using both F-2 and F-3. However, after adding ClO-, the fluorescence intensity of probe F-2 increased, whereas that of probe F-3 first decreased and then increased. Probes F-2 and F-3 exhibited good selectivity, anti-interference capability, and sensitivity, with the detection limits of 169.95 and 37.30 µM, respectively. Owing to their low cell toxicity, probes F-2 and F-3 can be applied to detect ClO- in vivo. The design approach adopted in this study will further advance the future development of ClO- chemical probes through the removal of C = N bond isomerization.

Singlet and Triplet Pathways Determine the Thermal Z/E Isomerization of an Arylazopyrazole-Based Photoswitch.

Understanding the thermal isomerization mechanism of azobenzene derivatives is essential to designing photoswitches with tunable half-lives. Herein, we employ quantum chemical calculations, nonadiabatic transition state theory, and photosensitized experiments to unravel the thermal Z/E isomerization of a heteroaromatic azoswitch, the phenylazo-1,3,5-trimethylpyrazole. In contrast to the parent azobenzene, we predict two pathways to be operative at room temperature. One is a conventional ground-state reaction occurring via inversion of the aryl group, and the other is a nonadiabatic process involving intersystem crossing to the lowest-lying triplet state and back to the ground state, accompanied by a torsional motion around the azo bond. Our results illustrate that the fastest reaction rate is not controlled by the mechanism involving the lowest activation energy, but the size of the spin-orbit couplings at the crossing between the singlet and the triplet potential energy surfaces is also determinant. It is therefore mandatory to consider all of the multiple reaction pathways in azoswitches in order to predict experimental half-lives.

Nonadiabatic simulations of photoisomerization and dissociation in ethylene using abinitio classical trajectories.

We simulate the nonadiabatic dynamics of photo-induced isomerization and dissociation in ethylene using abinitio classical trajectories in an extended phase space of nuclear and electronic variables. This is achieved by employing the linearized semiclassical initial value representation method for nonadiabatic dynamics, where discrete electronic states are mapped to continuous classical variables using either the Meyer-Miller-Stock-Thoss representation or a more recently introduced spin mapping approach. Trajectory initial conditions are sampled by constraining electronic state variables to a single initial excited state and by drawing nuclear phase space configurations from a Wigner distribution at a finite temperature. An ensemble of classical abinitio trajectories is then generated to compute thermal population correlation functions and analyze the mechanisms of isomerization and dissociation. Our results serve as a demonstration that this parameter-free semiclassical approach is computationally efficient and accurate, identifying mechanistic pathways in agreement with previous theoretical studies and also uncovering dissociation pathways observed experimentally.

In search of universalities in the dissociative photoionization of PANHs via isomerizations.

In search of the cause behind the similarities often seen in the fragmentation of PANHs, vacuum ultraviolet (VUV) photodissociation of two pairs of isomers quinoline-isoquinoline and 2-naphthylamine-3-methyl-quinoline are studied using the velocity map imaging technique. The internal energy dependence of all primary fragmentation channels is obtained for all four target molecules. The decay dynamics of the four molecules is studied by comparing their various experimental signatures. The dominant channel for the first pair of isomers is found to be hydrogen cyanide (HCN) neutral loss, while the second pair of isomers lose HCNH neutral as its dominant channel. Despite this difference in their primary decay products and the differences in the structures of the four targets, various similarities in their experimental signatures are found, which could be explained by isomerization mechanisms to common structures. The fundamental role of these isomerization in controlling different dissociative channels is explored via a detailed analysis of the experimental photoelectron-photoion coincidences and the investigation of the theoretical potential energy surface. These results add to the notion of a universal PANH fragmentation mechanism and suggests the seven member isomerization as a key candidate for this universal mechanism. The balance between isomerization, dissociation, and other key mechanistic processes in the reaction pathways, such as hydrogen migrations, is also highlighted for the four molecules.