Reaction Mechanism Research Articles

A complete and sustained organic/inorganic reaction mechanism of Baeyer’s test

The Baeyer’s test for unsaturation has been used in Qualitative Organic Analysis for a long time. However, if an alkaline reagent is used, compounds having an active hydrogen (carbon acids) also give a positive test with potassium permanganate, detracting the test for unsaturation. The first steps of the reaction sequence have been described but the next stages are missing. These are very important because they involve the formation mode of the observed end product, brown manganese dioxide. In this communication, a complete and sustained reaction mechanism is provided for both reaction mediums, neutral and alkaline. It is in accordance with observed experimental facts. The missing steps are a redox reaction between hypomanganate and permanganate ions, and a second cyclic intermediate now formed with manganate ion. The instability of this intermediate leads directly to manganese dioxide and alkalinization of the neutral medium, as observed experimentally.

A mini-review on influence of physical exercise in remodeling the immune mechanism

Exercising on a regular basis has been associated with delay in onset of many lifestyle disorders and chronic conditions. Different types of exercise have varied effects on our innate immune cells, both positively and negatively. Low-intensity exercises like yoga or brisk walking, medium-intensity exercises like swimming or cycling, and long-term high-intensity exercises like playing sports like volleyball or working out in the gym are some examples. The immune system's function is impacted differently by exercise training depending on the type, duration, intensity, and other factors. Exercise training is a double-edged sword that helps the body's immune system by changing the immune cells' post-exercise reaction mechanisms. Regular physical exercise is one of the lifestyle adjustments aimed at minimizing morbidity and mortality associated with contemporary illnesses such as obesity, diabetes, cardiovascular disease, and cancer. Regular leisure exercise training is regarded to be beneficial, but extreme exercise, such as that performed by professional athletes, is thought to have possibly detrimental consequences. This review summarizes current information in the field of exercise-associated alterations of infection susceptibility and indicates knowledge gaps for further investigation. It highlights that long term effects of physical activity shows a positive association with longevity and exercise.

Theoretical study of the hydrolysis mechanism of β-lactam antibiotics catalysed by a Zn(II) dinuclear biomimetic organometallic complex

The degradation and metabolism of antibiotics have attracted the scientific community's attention due to the environmental problems caused by the inappropriate use and disposal of these drugs. Therefore, it is crucial to understand the reaction mechanism involved in the degradation of these compounds. We studied the hydrolysis of nitrocefin and benzylpenicillin, two β-lactam ring antibiotics, mediated by an enzymatic mimetic Zn organometallic compound, using DFT methods. The electronic effects of functional groups adjacent to the β-lactam ring were analysed and good agreement between experimental and theoretical results was found. The reaction involves the nucleophilic attack of the bridging hydroxide group on the Zn atoms towards the β-lactam ring. A stepwise mechanism was found to agree with the experimental results. Chemical hardness profiles were affected by the solvent and reaction synchronicity. Geometric rearrangements dominated the activation barrier, and both antibiotics exhibited late transition states.

Molecular Insights into Converting Hydroxide Adenosyltransferase into Halogenase.

Halogenation plays a unique role in the design of agrochemicals. Enzymatic halogenation reactions have attracted great attention due to their excellent specificity and mild reaction conditions. S-adenosyl-l-methionine (SAM)-dependent halogenases mediate the nucleophilic attack of halide ions (X-) to SAM to produce 5'-XDA. However, only 11 SAM-dependent fluorinases and 3 chlorinases have been reported, highlighting the desire for additional halogenases. SAM-dependent hydroxide adenosyltransferase (HATase) has a similar reaction mechanism as halogenases but uses water as a substrate instead of halide ions. Here, we explored a HATase from the thermophile Thermotoga maritima MSB8 and transformed it into a halogenase. We identified a key dyad W8L/V71T for the halogenation reaction. We also obtained the best performing mutants for each halogenation reaction: M1, M2 and M4 for Cl-, Br- and I-, respectively. The M4 mutant retained the thermostability of HATase in the iodination reaction at 80 °C, which surpasses the natural halogenase SalL. QM/MM revealed that these mutants bind halide ions with more suitable angles for nucleophilic attack of C5' of SAM, thus conferring halogenation capabilities. Our work achieved the halide ion specificity of halogenases and generated thermostable halogenases for the first time, which provides new opportunities to expand the halogenase repertoire from hydroxylase.

Reactive direct simulation Monte Carlo modeling of gas reactive transport in three dimensional porous fibrous media across rarefied to continuum regimes

Gas flow in complex porous media can vary across rarefied to continuum regimes depending on the characteristic size of porous media. To study the gas reactive transport process in three dimensional porous fibrous media across rarefied to continuum regimes, a comprehensive reactive direct simulation Monte Carlo model coupling with heat conduction and radiation model as well as reaction process is proposed. The results calculated by the proposed model are verified to fit well with those obtained using analytical model and experimental data. The “inlet” effect promoting the skeleton temperature is found. There are existing competitions between the heat conduction, reaction rate and convection, radiation process. The temperature of porous fibrous media skeleton increases with the catalyst coverage, and decreases with increase of Knudsen number. When the proportion of hydrogen increases, the increase in the temperature of the porous fibrous media skeleton is initially rapid and then gradual. These studies help to deeply understand the chemical reaction mechanism in porous media across rarefied to continuum regimes.

Electron Donor‐Acceptor (EDA) Complex Enabled C−C Cross‐Coupling Reactions of α‐Amino Radicals

AbstractElectron‐donor acceptor (EDA) complex has been an integral part of visible‐light photocatalysis and is different from the traditional photoredox catalysis, which requires an exogenous photocatalyst, typically a colored compound to initiate the photocatalytic cycle. Interestingly, the EDA‐complex photochemistry has found profound use in activating the inert α‐C−H bonds of amines. The strategy relied upon the formation of colored EDA‐complex between the donor (amine) and acceptor (Lewis acid), which upon harvesting light energy perform a SET process to generate radical cation and anion intermediates. The radical cation then loses the activated acidic proton (because of the SET, the acidity of α‐proton increases by lowering the BDE) to form α‐amino radical, which then participates in various C−C coupling cascades. In this review, different conceptual approaches for the generation of α‐amino radicals and their coupling for the C−C bond‐forming reaction under EDA‐complex triggered photocatalysis will be discussed with particular emphasis on the reaction mechanism from 2018 onwards.

Functionalization of 1,3‐Butadiene Derivatives under Photo/Electrocatalysis

In recent years, the functionalization of 1,3‐butadiene has become an attractive strategy for constructing allyl compounds with molecular and structural complexity, and the current research focuses on synthetic chemistry and organic synthesis. Compared with the traditional synthesis method, the synthesis methods promoted by visible light or electrochemistry represent an environmentally friendly and mild strategy. In this review, the functionalization reactions of 1,3‐butadiene under photochemical/electrochemical in recent years are reviewed according to the classification of functionalization systems, with particular emphasis on the corresponding reaction mechanism, which lays a foundation for further exploration of new catalytic methods.

Target-Oriented Synthesis of Triphenylphosphine Functionalized Carbon Dots with Negative Charge for ROS Scavenging and Mitochondrial Targeting.

Triphenylphosphine functionalized carbon dots (TPP-CDs) showcase robust mitochondria targeting capacity owing to their positive electrical properties. However, TPP-CDs typically involve complicated synthesis steps and time-consuming postmodification procedures. Especially, the one-step target-oriented synthesis of TPP-CDs and the regulation of TPP linkage modes remain challenges. Herein, we propose a free-radical-initiated random copolymerization in combination with hydrothermal carbonation to regulate the TPP backbone linkage for target-oriented synthesis of triphenylphosphine copolymerization carbon dots (TPPcopoly-CDs). The linkage mechanism of random copolymerization reactions is directional, straightforward, and controllable. The TPP content and IC50 of hydroxyl radicals scavenging ability of TPPcopoly-CDs are 53 wt % and 0.52 mg/mL, respectively. TPP serves as a charge control agent to elevate the negatively charged CDs by 20 mV. TPPcopoly-CDs with negative charge can target mitochondria, and in the corresponding mechanism the TPP moiety plays a crucial role in targeting mitochondria. This discovery provides a new perspective on the controlled synthesis, TPP linkage modes, and mitochondrial targeting design of TPP-CDs.

Zn2+-storage mechanism in V6O13 with nanosheets for high-capacity and long-life aqueous zinc-metal batteries.

V6O13 with a nanosheet structure was employed as a cathode material for aqueous zinc metal batteries. V6O13 delivered a high specific capacity of 425 mA h g-1, outstanding rate performance and durable cycling with high capacity retention of 86% after 3000 cycles. Moreover, in situ X-ray diffractometer (XRD), ex situ X-ray photoelectron spectroscopy (XPS) and X-ray absorption near-edge structure (XANES) were employed to ascertain the reaction mechanism of Zn2+ storage.

Acetal‐thiol Click‐like Reaction: Facile and Efficient Synthesis of Dynamic Dithioacetals and Recyclable Polydithioacetals

Dithioacetals are heavily used in organic, material and medical chemistries, and exhibit huge potential to synthesize degradable or recyclable polymers. However, the current synthetic approaches of dithioacetals and polydithioacetals are overwhelmingly dependent on external catalysts and organic solvents. Herein, we disclose a catalyst‐ and solvent‐free acetal‐thiol click‐like reaction for synthesizing dithioacetals and polydithioacetals. High conversion, higher than acid catalytic acetal‐thiol reaction, can be achieved. High universality was confirmed by monitoring the reactions of linear and cyclic acetals (including renewable bio‐sourced furan‐acetal) with aliphatic and aromatic thiols, and the reaction mechanism of monomolecular nucleophilic substitution (SN1) and auto‐protonation (activation) by thiol was clarified by combining experiments and density functional theory computation. Subsequently, we utilize this reaction to synthesize readily recyclable polydithioacetals. By simple heating and stirring, linear polydithioacetals with w of ~110 kDa were synthesized from acetal and dithiol, and depolymerization into macrocyclic dithioacetal and repolymerization into polydithioacetal can be achieved; through reactive extrusion, a semi‐interpenetrating polymer dynamic network with excellent mechanical properties and continuous reprocessability was prepared from poly(vinyl butyral) and pentaerythritol tetrakis(3‐mercaptopropionate). This green and high‐efficient synthesis method for dithioacetals and polydithioacetals is beneficial to the sustainable development of chemistry.

Acetal-thiol Click-like Reaction: Facile and Efficient Synthesis of Dynamic Dithioacetals and Recyclable Polydithioacetals.

Dithioacetals are heavily used in organic, material and medical chemistries, and exhibit huge potential to synthesize degradable or recyclable polymers. However, the current synthetic approaches of dithioacetals and polydithioacetals are overwhelmingly dependent on external catalysts and organic solvents. Herein, we disclose a catalyst- and solvent-free acetal-thiol click-like reaction for synthesizing dithioacetals and polydithioacetals. High conversion, higher than acid catalytic acetal-thiol reaction, can be achieved. High universality was confirmed by monitoring the reactions of linear and cyclic acetals (including renewable bio-sourced furan-acetal) with aliphatic and aromatic thiols, and the reaction mechanism of monomolecular nucleophilic substitution (SN1) and auto-protonation (activation) by thiol was clarified by combining experiments and density functional theory computation. Subsequently, we utilize this reaction to synthesize readily recyclable polydithioacetals. By simple heating and stirring, linear polydithioacetals with w of ~110 kDa were synthesized from acetal and dithiol, and depolymerization into macrocyclic dithioacetal and repolymerization into polydithioacetal can be achieved; through reactive extrusion, a semi-interpenetrating polymer dynamic network with excellent mechanical properties and continuous reprocessability was prepared from poly(vinyl butyral) and pentaerythritol tetrakis(3-mercaptopropionate). This green and high-efficient synthesis method for dithioacetals and polydithioacetals is beneficial to the sustainable development of chemistry.

Atomic Design of Copper Active Sites in Pristine Metal-Organic Coordination Compounds for Electrocatalytic Carbon Dioxide Reduction.

Electrocatalytic carbon dioxide reduction reaction (CO2RR) has emerged as a promising and sustainable approach to cut carbon emissions by converting greenhouse gas CO2 to value-added chemicals and fuels. Metal-organic coordination compounds, especially the copper (Cu)-based coordination compounds, which feature well-defined crystalline structures and designable metal active sites, have attracted much research attention in electrocatalytic CO2RR. Herein, the recent advances of electrochemical CO2RR on pristine Cu-based coordination compounds with different types of Cu active sites are reviewed. First, the general reaction pathways of electrocatalytic CO2RR on Cu-based coordination compounds are briefly introduced. Then the highly efficient conversion of CO2 on various kinds of Cu active sites (e.g., single-Cu site, dimeric-Cu site, multi-Cu site, and heterometallic site) is systematically discussed, along with the corresponding catalytic reaction mechanisms. Finally, some existing challenges and potential opportunities for this research direction are provided to guide the rational design of metal-organic coordination compounds for their practical application in electrochemical CO2RR.

Preparation of MWCNT/CoMn2O4 nanocomposite for effectual degradation of picric acid via peroxymonosulfate activation

In recent years, using nanomaterials based on multi-wall carbon nanotubes (MWCNT) through the activation of peroxymonosulfate (PMS) has attracted more attention to the degradation of organic pollutants. This research presented a new route for the synthesis of MWCNT/CoMn2O4 nanocomposite for the degradation of picric acid using advanced oxidation processes (AOPs). Firstly, CoMn2O4 nanoparticles were prepared and then loaded on MWCNT using ultrasonic waves. The results of various analyzes confirmed the successful loading of nanoparticles on carbon nanotubes. As the degradation process proceeds through oxidation processes, the high electronic conductivity of MWCNT and the active sites of Mn and Co in the nanocomposite play an essential role in activating PMS to generate reactive oxygen species (ROS). An investigation of the reaction mechanism in different conditions showed that the highest speed of picric acid decomposition in the presence of nanocomposite (98%) was in 47 min. However, the scavenger test showed that HO· and SO4·− radicals are more important in the degradation process. Meanwhile, the results showed that removing picric acid using MWCNT/CoMn2O4 was more effective than CoMn2O4 alone and confirmed the interaction effect of MWCNT nanotubes with AB2O4 nanocatalyst.

Comparison of the Mechanisms of Hydrolysis of Organophosphates with Good and Poor Leaving Group by Phosphotriesterase from Pseudomonas diminuta

Abstract Combined quantum mechanics/molecular mechanics approaches are used to determine the mechanisms of organophosphate hydrolysis in an active site of Pseudomonas diminuta phosphotriesterase. For a substrate with a good leaving group, the reaction proceeds through two elementary stages with low energy barriers, and a gain in energy is observed. With a poor leaving group, only the formation of an unstable reaction intermediate is possible, and hydrolysis is incomplete. A comparison of the resulting reaction mechanisms explains the experimental kinetic data, according to which the enzyme hydrolyzes only substrates with good leaving groups.

Kinetic analysis for the interpretation of polychlorinated biphenyls removal mechanism

AbstractRemoving polychlorinated biphenyls (PCBs) from subsurface water, soils, and transformer oil is crucial to save the environment from these pollutant materials. Hydrodechlorination (HDC) of PCBs consists of numerous chemical reactions and the simple kinetic models may not provide details for the process. To gain more awareness of the reaction mechanism, in the proposed approach, the isoconversional methods of the Friedman were investigated paralleling other kinetic models of Langmuir‐Hinshelwood (L‐H), Eley‐Rideal (E‐R), pseudo‐first‐order, and pseudo‐second‐order methods. The analysis was validated by laboratory results of HDC of contaminated transformer oil in front of Pd/MWCNTs. The most reactivity was observed for biphenyls with a higher number of chlorines. Finding a suitable model, Akaike Information Criteria were applied. It was attained that Friedman model was the most suitable for monitoring of HDC of PCBs in front of catalyst. Besides, E‐R reaction was appropriate to elucidate the theoretical interpretations of the adsorption and desorption of reactants and chlorinated benzene.

Theoretical Insights into Enhancing Catalytic Performance of Al-Cu Alloy for CO2 Electroreduction toward Ethene Production.

The understanding of the reaction mechanism of CO2 electroreduction (CO2RR) is essential for the precise design of catalysts for specific products with high selectivity. In this work, combined with the computational hydrogen electrode model and kinetic energy barrier calculations, CO2RR pathways on Cu(100) and Al1Cu3(100) are intensively investigated. The free energy barrier of the rate-determining step of ethylene formation is reduced from 1.08 eV for *CCOH formation on Cu(100) to 0.51 eV for *CH2OCHOH formation on Al1Cu3(100) and enhances the catalytic activity. The reaction free energy of *CO-*CO coupling is remarkably reduced from 0.86 eV on Cu(100) to -0.43 eV on Al1Cu3(100) and the coupling barrier is reduced from 0.97 to 0.37 eV, suppressing the production of gas phase CO and enhancing the production of C2 products. Furthermore, the selectivity toward C-O breaking of *CH2CHOH on Cu(100) and *CH2CH2OH on Al1Cu3(100) ensures high selectivity toward ethene rather than ethanol.

Exploring the chemical dynamics of phenanthrene (C14H10) formation via the bimolecular gas-phase reaction of the phenylethynyl radical (C6H5CC) with benzene (C6H6).

The exploration of the fundamental formation mechanisms of polycyclic aromatic hydrocarbons (PAHs) is crucial for the understanding of molecular mass growth processes leading to two- and three-dimensional carbonaceous nanostructures (nanosheets, graphenes, nanotubes, buckyballs) in extraterrestrial environments (circumstellar envelopes, planetary nebulae, molecular clouds) and combustion systems. While key studies have been conducted exploiting traditional, high-temperature mechanisms such as the hydrogen abstraction-acetylene addition (HACA) and phenyl addition-dehydrocyclization (PAC) pathways, the complexity of extreme environments highlights the necessity of investigating chemically diverse mass growth reaction mechanisms leading to PAHs. Employing the crossed molecular beams technique coupled with electronic structure calculations, we report on the gas-phase synthesis of phenanthrene (C14H10)-a three-ring, 14π benzenoid PAH-via a phenylethynyl addition-cyclization-aromatization mechanism, featuring bimolecular reactions of the phenylethynyl radical (C6H5CC, X2A1) with benzene (C6H6) under single collision conditions. The dynamics involve a phenylethynyl radical addition to benzene without entrance barrier leading eventually to phenanthrene via indirect scattering dynamics through C14H11 intermediates. The barrierless nature of reaction allows rapid access to phenanthrene in low-temperature environments such as cold molecular clouds which can reach temperatures as low as 10 K. This mechanism constitutes a unique, low-temperature framework for the formation of PAHs as building blocks in molecular mass growth processes to carbonaceous nanostructures in extraterrestrial environments thus affording critical insight into the low-temperature hydrocarbon chemistry in our universe.

Effect of gas pre-decomposition device on the growth of GaN epitaxial layer

Abstract In previous studies, the influence of gas phase and surface reactions on the growth of GaN was mainly calculated through simulations. In this study, a novel gas pre-decomposition device (GPDD) was designed to experimentally investigate the effects of gas phase and surface reactions on GaN growth by changing the length and height of the isolation plates. By varying the structure of the GPDD, the effects on the growth rate and thickness uniformity of the GaN films were studied. The growth rate of the GaN sample slowed with the extension of the isolation plates because the longer partition plates led to insufficient gas mixing and premature consumption of the precursor trimethylgallium (TMG). The use of GPDD simultaneously achieves high crystal quality and smooth surface morphology of the GaN film. Owing to the use of GPDD, the decomposition of TMG in the pyrolysis pathway was promoted, which suppressed Ga vacancies and C impurities, resulting in weak yellow luminescence (YL) bands in the photoluminescence (PL). This study provides a comprehensive understanding of the chemical reaction mechanism of GaN and plays an important role in promoting the development of metal-organic chemical vapor deposition (MOCVD) equipment.

Synthesis of Dihydrobenzosiloles and Silacyclopentane via Double Hydroalumination of Terminal Alkynes

We developed an efficient method for the synthesis of dihydrobenzosiloles in 19% to 90% isolated yields from 1-hydrosilyl-2-ethynylbenzenes using two equivalents of diisobutylaluminum hydride. The reaction mechanism involves regioselective double hydroalumination of the alkyne moiety followed by cyclization to 2-alanyldihydrobenzosilole. A silacyclopentane was also synthesized in 97% isolated yield from the corresponding 4-silylbut-1-yne under the same reaction conditions. Although the substrate scope was conducted on a 0.5 mmol scale, a gram-scale reaction of 1-diphenylsilyl-2-ethynylbenzene under the optimized reaction conditions successfully afforded the desired product in 94% isolated yield without loss of reactivity.

Transcription factors ERα and Sox2 have differing multiphasic DNA and RNA binding mechanisms.

Many transcription factors (TFs) have been shown to bind RNA, leading to open questions regarding the mechanism(s) of this RNA binding and its role in regulating TF activities. Here we use biophysical assays to interrogate the kon, koff, and Kd for DNA and RNA binding of two model human transcription factors, ERα and Sox2. Unexpectedly, we found that both proteins exhibited multiphasic nucleic acid binding kinetics. We propose that Sox2 RNA and DNA multiphasic binding kinetics could be explained by a conventional model for sequential Sox2 monomer association and dissociation. In contrast, ERα nucleic acid binding exhibited biphasic dissociation paired with novel triphasic association behavior, where two apparent binding transitions are separated by a 10-20 min "lag" phase depending on protein concentration. We considered several conventional models for the observed kinetic behavior, none of which adequately explained all the ERα nucleic acid binding data. Instead, simulations with a model incorporating sequential ERα monomer association, ERα nucleic acid complex isomerization, and product "feedback" on isomerization rate recapitulated the general kinetic trends for both ERα DNA and RNA binding. Collectively, our findings reveal that Sox2 and ERα bind RNA and DNA with previously unappreciated multiphasic binding kinetics, and that their reaction mechanisms differ with ERα binding nucleic acids via a novel reaction mechanism.