Three-step Mechanism Research Articles

The coumarin synthesis: a combined experimental and theoretical study

Coumarin, which is an important material class of substrate in agricultural and pharmaceutical industries, can be obtained by the Pechmann condensation reaction. In this work, coumarin was synthesized from ethyl acetoacetate and resorcinol with sulfuric acid as the catalyst with 86% yield under a mild condition. The product was confirmed by IR, 1H NMR, and 13C NMR spectroscopy. Reaction rates at difference temperatures between 273 and 313 K were used to determine the apparent activation energy of the reaction to be 34.7 kJ/mol. Molecular-level understanding about the mechanism of Pechmann condensation reaction was revealed by the complimentary M06-2X density functional theory. The reaction proceeded via a three-step mechanism; transesterification, intramolecular hydroxylalkylation, and dehydration. The intrinsic activation energies of these three steps were calculated to be 136.7, 76.5, and 134.0 kJ/mol, respectively. The calculated apparent activation energy of 40.0 kJ/mol was in agreement with the experimental data. The transesterification was considered as the rate-determining step of the reaction.

Studies of Carbon Monoxide Release from Ruthenium(II) Bipyridine Carbonyl Complexes upon UV-Light Exposure.

The UV-light-induced CO release characteristics of a series of ruthenium(II) carbonyl complexes of the form trans-Cl[RuLCl2(CO)2] (L = 4,4'-dimethyl-2,2'-bipyridine, 4'-methyl-2,2'-bipyridine-4-carboxylic acid, or 2,2'-bipyridine-4,4'-dicarboxylic acid) have been elucidated using a combination of UV-vis absorbance and Fourier transform infrared spectroscopies, multivariate curve resolution alternating least-squares analysis, and density functional theory calculations. In acetonitrile, photolysis appears to proceed via a serial three-step mechanism involving the sequential formation of [RuL(CO)(CH3CN)Cl2], [RuL(CH3CN)2Cl2], and [RuL(CH3CN)3Cl]+. Release of the first CO molecule occurs quickly (k1 ≫ 3 min-1), while release of the second CO molecule proceeds at a much more modest rate (k2 = 0.099-0.17 min-1) and is slowed by the presence of electron-withdrawing carboxyl substituents on the bipyridine ligand. In aqueous media (1% dimethyl sulfoxide in H2O), the two photodecarbonylation steps proceed much more slowly (k1 = 0.46-1.3 min-1 and k2 = 0.026-0.035 min-1, respectively) and the influence of the carboxyl groups is less pronounced. These results have implications for the design of new light-responsive CO-releasing molecules ("photoCORMs") intended for future medical use.

Urate hydroperoxide oxidizes human peroxiredoxin 1 and peroxiredoxin 2

Urate hydroperoxide is a product of the oxidation of uric acid by inflammatory heme peroxidases. The formation of urate hydroperoxide might be a key event in vascular inflammation, where there is large amount of uric acid and inflammatory peroxidases. Urate hydroperoxide oxidizes glutathione and sulfur-containing amino acids and is expected to react fast toward reactive thiols from peroxiredoxins (Prxs). The kinetics for the oxidation of the cytosolic 2-Cys Prx1 and Prx2 revealed that urate hydroperoxide oxidizes these enzymes at rates comparable with hydrogen peroxide. The second-order rate constants of these reactions were 4.9 × 105 and 2.3 × 106 m-1 s-1 for Prx1 and Prx2, respectively. Kinetic and simulation data suggest that the oxidation of Prx2 by urate hydroperoxide occurs by a three-step mechanism, where the peroxide reversibly associates with the enzyme; then it oxidizes the peroxidatic cysteine, and finally, the rate-limiting disulfide bond is formed. Of relevance, the disulfide bond formation was much slower in Prx2 (k3 = 0.31 s-1) than Prx1 (k3 = 14.9 s-1). In addition, Prx2 was more sensitive than Prx1 to hyperoxidation caused by both urate hydroperoxide and hydrogen peroxide. Urate hydroperoxide oxidized Prx2 from intact erythrocytes to the same extent as hydrogen peroxide. Therefore, Prx1 and Prx2 are likely targets of urate hydroperoxide in cells. Oxidation of Prxs by urate hydroperoxide might affect cell function and be partially responsible for the pro-oxidant and pro-inflammatory effects of uric acid.

A Polyoxoniobate-Polyoxovanadate Double-Anion Catalyst for Simultaneous Oxidative and Hydrolytic Decontamination of Chemical Warfare Agent Simulants.

A novel double-anion complex, H13 [(CH3 )4 N]12 [PNb12 O40 (VV O)2 ⋅(VIV4 O12 )2 ]⋅22 H2 O (1), based on bicapped polyoxoniobate and tetranuclear polyoxovanadate was synthesized, characterized by routine techniques and used in the catalytic decontamination of chemical warfare agents. Under mild conditions, 1 catalyzes both hydrolysis of the nerve agent simulant, diethyl cyanophosphonate (DECP) and selective oxidation of the sulfur mustard simulant, 2-chloroethyl ethyl sulfide (CEES). In the oxidative decontamination system 100 % CEES was transformed selectively to nontoxic 2-chloroethyl ethyl sulfoxide and vinyl ethyl sulfoxide using nearly stoichiometric 3 % aqueous H2 O2 with a turnover frequency (TOF) of 16 000 h-1 . Importantly, the catalytic activity is maintained even after ten recycles and CEES is completely decontaminated in 3 mins without formation of the highly toxic sulfone by-product. A three-step oxidative mechanism is proposed.

Zinc Electrodeposition on Polycrystalline Copper: Electrochemical Study of Early-Stage Growth Mechanism

The early stage growth mechanism of zinc clusters electrodeposited on polycrystalline copper is studied by electrochemical methods. By analyzing the chronoamperometric and chronocoulometric data, nucleation and growth of the Zn layer as a function of time are investigated, and a growth model is proposed and discussed. Experimental and theoretical details about chronocoulometric data reveal a three-step growth mechanism. The results provide insights into the mechanism of electrodeposition of metallic particles. The same analysis process can also be described as the stripping mechanism. The formation and stripping mechanisms of a zinc adlayer can be predicted considering the contribution of four-different processes: a Langmuir-type adsorption/desorption process, the two-dimensional nucleation and growth in instantaneous and progressive cases, and a three-dimensional nucleation and growth process under diffusion-limited condition.

Computational study of backdraft dynamics and the effects of initial conditions in a compartment

Backdraft dynamics and effects of initial fuel mass fraction on backdraft behavior were studied computationally using fire dynamics simulator with a Model-free simulation (MFS). The effects of one- and three-step reaction mechanisms on backdraft development and temporal pressure variation were examined. Thermal radiation effects were studied by considering the gray-gas-radiation (GRAY) and adiabatic model (ADIA). The gravity current and backdraft development were reasonably reproduced by the MFS. The temporal pressure rise inside the compartment showed a similar trend to previous experiments. ADIA did not predict the local ignition near the bottom wall, while GRAY did predict. The critical fuel mass fraction (Yf) for backdraft occurrence was determined from the two-peak characteristic in the pressure, and the predicted Yf was reasonable, compared with the experiments. Complex mixed combustion modes were found locally during backdraft development. MFS with finite chemistry was found to be a potentially good computational tool for backdraft dynamics.

Investigating the mechanism of ADP-forming acetyl-CoA synthetase from the protozoan parasite Entamoeba histolytica.

ADP-forming acetyl-CoA synthetase (ACD) catalyzes the interconversion of acetyl-CoA and acetate. The related succinyl-CoA synthetase follows a three-step mechanism involving a single phosphoenzyme, but a novel four-step mechanism with two phosphoenzyme intermediates was proposed for Pyrococcus ACD. Characterization of enzyme variants of Entamoeba ACD in which the two proposed phosphorylated His residues were individually altered revealed that only His252 is essential for enzymatic activity. Analysis of variants altered at two residues proposed to interact with the phosphohistidine loop that swings between distinct parts of the active site are consistent with a mechanism involving a single phosphoenzyme intermediate. Our results suggest ACDs with different subunit structures may employ slightly different mechanisms to bridge the span between active sites I and II.

Aggregation Kinetics and Self-Assembly Mechanisms of Graphene Quantum Dots in Aqueous Solutions: Cooperative Effects of pH and Electrolytes.

The cooperative effects of pH and electrolytes on the aggregation of GQDs and the aggregate morphologies are characterized. Because GQDs have an average size of 9 nm with abundant O-functionalized edges, their suspension was very stable even in a high electrolyte concentration and low pH solution. Divalent cations (Mg2+ and Ca2+) excelled at aggregating the GQD nanoplates, while monovalent cations (Na+ and K+) did not disturb the stability. For Na+ and K+, positive linear correlations were observed between the critical coagulation concentration (CCC) and pH levels. For Mg2+ and Ca2+, negative, but nonlinear, correlations between CCC and pH values could not be explained and predicted by the traditional DLVO theory. Three-step mechanisms are proposed for the first time to elucidate the complex aggregation of GQDs. The first step is the protonation/deprotonation of GQDs under different pH values and the self-assembly of GQDs into GQD-water-GQD. The second step is the self-assembly of small GQD pieces into large plates (graphene oxide-like) induced by the coexisting Ca2+ and then conversion into 3D structures via π-π stacking. The third step is the aggregation of the 3D-assembled GQDs into precipitates via the suppression of the electric double layer. The self-assembly of GQDs prior to aggregation was supported by SEM and HRTEM imaging. Understanding of the colloidal behavior of ultrasmall nanoparticles like GQDs is significantly important for the precise prediction of their environmental fate and risk.

A Quasi-chemical Model for Bacterial Spore Germination Kinetics by High Pressure

High pressure processing (HPP) is an emerging non-thermal technology that is growing exponentially in use worldwide for the pasteurization of commercial foodstuffs. At combinations of elevated pressures and temperatures, HPP inactivates bacterial spores, but HPP has not yet been implemented commercially for food sterilization. Studies of the mechanisms of bacterial spore inactivation by HPP using primarily spores of Bacillus species have shown that spore germination precedes inactivation, with the release of dipicolinic acid from the spore core as the rate-determining step. Investigations probing spore resistance to and germination by HPP using Bacillus subtilis, a number of selected B. subtilis mutants, Bacillus amyloliquefaciens, and Clostridium difficile spores have compiled a wealth of detailed mechanistic information, while also accumulating abundant germination kinetics data that has not previously been analyzed by predictive models. Presently, we devise a “quasi-chemical” model for bacterial spore germination dynamics by HPP. This quasi-chemical germination model (QCGM) hypothesizes a three-step mechanism and derives a set of ordinary differential equations to model the observed germination dynamics. The results with this model are viewed in the context of historical studies of spore activation, germination, and inactivation, with an eye toward potentially integrating differential equation models for germination and inactivation into a single, comprehensive model for spore dynamics by HPP. With the increasing use of high hydrostatic pressure to investigate mechanisms of bacterial spore resistance and physiology, the QCGM results help promote the efficient control of bacterial spores, whether for the inactivation of Clostridium botulinum spores in low-acid foods or aerosolized Bacillus anthracis spores on textiles used in protective clothing, tents, or shelters.

3D hierarchical golden wattle-like TiO2 microspheres: polar acetone-based solvothermal synthesis and enhanced water purification performance

3D hierarchical TiO2 microsphere structures self-assembled from 1D nanostructures have attracted considerable research attention due to their unique microstructures and properties, and non-polar solvent-based solvothermal methods have been proved to be effective techniques to synthesize such structures. However, to the best of our knowledge, no successful products have been reported based on polar solvents in the available literature. Herein, for the first time, uniform and sophisticated golden wattle (Acacia pycnantha)-like TiO2 microsphere structures, self-assembled from highly crystallized and radially grown 1D rutile nanorods, were successfully synthesized via a template-free solvothermal reaction using only polar acetone as the solvent in the presence of hydrochloric acid (HCl). The obtained samples showed good water purification performance, even superior to Degussa P25, owing to their unique 1D nanorod building block structure, fast electron transfer rate, excellent light harvesting capability and good crystallinity. In addition, a three-step growth mechanism of the golden wattle-like TiO2 microspheres was proposed based on a time-dependent morphology and crystal form evolution process. The synthetic strategy for the golden wattle-like TiO2 microspheres employed in this study provides new insights into the design of 3D hierarchical TiO2 structures for practical environmental purification applications.

Pure copper phosphate nanostructures with controlled growth: a versatile support for enzyme immobilization

In the present work, we report a simple method to develop pure copper phosphate nanoflowers without any assistance of additives. The blooming state of these nanoflowers can be controlled precisely by the growth time, pH value, temperature, and component of the precursor solution. A three-step growth mechanism is proposed, and the roles of the different factors are discussed for the formation of the nanoflowers. Relying on the hierarchical porous structure, the nanoflowers exert effective immobilization of enzymes. Compared with the free enzyme, the immobilized one maintains significantly enhanced catalytic activity against extreme pH and temperature variations as well as the presence of a denaturant. Such results can push the development of more hierarchical porous materials which hold promising applications for enzyme immobilization and biotechnology.

Phaselocked Solutions Of The Finite Size Kuramoto Coupled Oscillator Model

We investigate properties of phaselocked solutions of the finite size Kuramoto coupled oscillator model. There are minimal assumptions on the frequencies $\omega_{1},\ldots,\omega_{N}$ in the model. The coupling constant is denoted by $\alpha,$ and a key parameter $\gamma$ is introduced which is proportional to ${\frac {1}{\alpha}}.$ Theorem 1.1(III) gives new predictions for the location of $\gamma^{*},$ the “phaselocking threshold.” When $N$ is large these predictions show that the size of the $\gamma$ interval $[\gamma_{*},\gamma^{*})$ where two phaselocked solutions coexist (one stable and the other unstable) is uniformly bounded away from zero. To demonstrate the utility of this result we give an application which is motivated by recent reports of an increasing number of cyber-attacks on electric power grids. In this application, which is related to a large scale electric grid model, we identify a three-step mechanism which shows how a subtle change in frequencies $\omega_{1},\ldots,\omega_{N}$ causes phaselocked synchronization collapse as the system undergoes a transition from stable synchronization to decoherence. In an electric grid such synchronization collapse may potentially cause electricity blackouts.

Nonclassical Crystal Growth as Explanation for the Riddle of Polarity in Centrosymmetric Glycine Crystals

The riddle of anomalous polar behavior of the centrosymmetric crystal of α-glycine is resolved by the discovery of a polar, several hundred nanometer thick hydrated layer, created at the {010} faces during crystal growth. This layer was detected by two independent pyroelectric analytical methods: (i) periodic temperature change technique (Chynoweth) at ambient conditions and (ii) contactless X-ray photoelectron spectroscopy under ultrahigh vacuum. The total polarization of the surface layer is extremely large, yielding ≈1 μC·cm-2, and is preserved in ultrahigh vacuum, but disappears upon heating to 100 °C. Molecular dynamics simulations corroborate the formation of polar hydrated layers at the sub-microsecond time scale, however with a thickness of only several nanometers, not several hundred. This inconsistency might be reconciled by invoking a three-step nonclassical crystal growth mechanism comprising (i) docking of clusters from the supersaturated solution onto the evolving crystal, (ii) surface recognition and polar induction, and (iii) annealing and dehydration, followed by site-selective recrystallization.

Kinetic Study of the Thermochemical Degradation of Lignocellulosic Materials Based on TG-FTIR, Py-GC/MS and 13 C NMR Experiments

Pyrolysis of a hardwood representative, beech sawdust (Fagus sylvatica), was investigated by thermogravimetry, a thermal analysis technique. A suitable kinetic approach for the determination of kinetic parameters was proposed. The model fitting method was used to optimize the kinetic parameters of the reaction pathways of the selected reaction mechanisms. The experiments were conducted starting from ambient temperature up to 600 °C using the following five heating rates: 2, 5, 10, 15, and 20 °C min–1. FTIR, PyGC/MS, 13C NMR, and elemental analysis were also used to analyse the pyrolysis products. Differentiation among the reaction mechanisms of lignocellulosic material pyrolysis was performed. The three-step parallel mechanism containing an intermediate was the most suitable mechanism based on 13C NMR analysis of solid residues prepared at the selected temperatures from 230–500 °C. The NMR results showed that the inclusion of an intermediate into the reaction scheme was a reasonable step. It was concluded that the intermediate was connected with the lignin structure.

Tomographic docking suggests the mechanism of auxin receptor TIR1 selectivity.

We study the binding of plant hormone IAA on its receptor TIR1, introducing a novel computational method that we call tomographic docking and that accounts for interactions occurring along the depth of the binding pocket. Our results suggest that selectivity is related to constraints that potential ligands encounter on their way from the surface of the protein to their final position at the pocket bottom. Tomographic docking helps develop specific hypotheses about ligand binding, distinguishing binders from non-binders, and suggests that binding is a three-step mechanism, consisting of engagement with a niche in the back wall of the pocket, interaction with a molecular filter which allows or precludes further descent of ligands, and binding on the pocket base. Only molecules that are able to descend the pocket and bind at its base allow the co-receptor IAA7 to bind on the complex, thus behaving as active auxins. Analysing the interactions at different depths, our new method helps in identifying critical residues that constitute preferred future study targets and in the quest for safe and effective herbicides. Also, it has the potential to extend the utility of docking from ligand searches to the study of processes contributing to selectivity.

Investigation of the Li-S Battery Mechanism by Real-Time Monitoring of the Changes of Sulfur and Polysulfide Species during the Discharge and Charge.

The mechanism of the sulfur cathode in Li-S batteries has been proposed. It was revealed by the real-time quantitative determination of polysulfide species and elemental sulfur by means of high-performance liquid chromatography in the course of the discharge and recharge of a Li-S battery. A three-step reduction mechanism including two chemical equilibrium reactions was proposed for the sulfur cathode discharge. The typical two-plateau discharge curve for the sulfur cathode can be explained. A two-step oxidation mechanism for Li2S and Li2S2 with a single chemical equilibrium among soluble polysulfide ions was proposed. The chemical equilibrium among S52-, S62-, S72-, and S82- throughout the entire oxidation process resulted for a single flat recharge curve in Li-S batteries.

DFT modeling of the post-titanocene catalytic system LTiCl2-Bu2Mg-Et2AlCl for alkene polymerization: The role of alkyl bridge Mg–C–Ti and β-agostic C–H–Ti bonds in the formation of active centers

DFT modeling of the active centers formation in the catalytic system LTiCl2-Bu2Mg-Et2AlCl for alkene polymerization, where L is a bidentate ligand of saligenin type, suggests the three-step mechanism of this process. This mechanism includes the addition of the most probable alkylating agent, RMg(μ-Cl)2AlR2 or RMg(μ-Cl)2MgR (R=alkyl), to LTiCl2 with the formation of the trinuclear heterocomplex with the alkyl bridge bond Mg–C–Ti, followed by its two-step isomerization into the active center via the β-agostic intermediate. The free energy changes at the stages of the addition and isomerization are negative; the maximal energy barrier on the reaction pathway is small. In the Mg-free system LTiCl2-AlR3, the isomerization proceeds through the single energy barrier with a significantly higher amplitude. This could be the reason for a relatively high activity of the Mg-containing system and inactivity of the Mg-free system.

Embodied energy as key parameter for sustainable materials selection: The case of reusing coal fly ash for removing anionic surfactants

Coal fly ash (CFA) is an industrial by-product derived from coal combustion in thermal power plants. This abundant and low cost by-product is generally reemployed as an additive in the building industry. This work explores the possibility of recovering CFA as an adsorbing material for the removal of anionic surfactants dissolved in water, on the basis of data about concerning its embodied energy. Indeed, Although the CO2 footprint of CFA and activated carbon is comparable, CFA shows an extremely lower embodied energy with respect to activated carbon, the most used widely used material for surfactant removal. Surfactant are widely used in several detergents products, and enter into the environment through the discharge of sewage effluents. In this paper, Sodium Dodecyl Sulfate (SDS) is used as a model surfactant. Upon careful optimization of the CFA/SDS mass ratio, it was found that CFA is able to remove SDS from water with efficiency up to 96%. SDS adsorption onto the CFA surface was investigated and results point to a three-step mechanism, which stops with the final formation of a CFA supported SDS bilayer. There are two main results: first, the first one in the era of raw materials scarcity, the choice of to investigate the employ employment of a material in terms of its embodied energy must be considered; second, the second result this work opens new perspectives in the field of anionic surfactant removal.

The Mechanism of Hsp90 ATPase Stimulation by Aha1.

Hsp90 is a dimeric molecular chaperone responsible for the folding, maturation, and activation of hundreds of substrate proteins called ‘clients’. Numerous co-chaperone proteins regulate progression through the ATP-dependent client activation cycle. The most potent stimulator of the Hsp90 ATPase activity is the co-chaperone Aha1p. Only one molecule of Aha1p is required to fully stimulate the Hsp90 dimer despite the existence of two, presumably identical, binding sites for this regulator. Using ATPase assays with Hsp90 heterodimers, we find that Aha1p stimulates ATPase activity by a three-step mechanism via the catalytic loop in the middle domain of Hsp90. Binding of the Aha1p N domain to the Hsp90 middle domain exerts a small stimulatory effect but also drives a separate conformational rearrangement in the Hsp90 N domains. This second event drives a rearrangement in the N domain of the opposite subunit and is required for the stimulatory action of the Aha1p C domain. Furthermore, the second event can be blocked by a mutation in one subunit of the Hsp90 dimer but not the other. This work provides a foundation for understanding how post-translational modifications regulate co-chaperone engagement with the Hsp90 dimer.

Electrochemistry of Selenium with Sodium and Lithium: Kinetics and Reaction Mechanism.

There are economic and environmental advantages by replacing Li with Na in energy storage. However, sluggishness in the charge/discharge reaction and low capacity are among the major obstacles to development of high-power sodium-ion batteries. Among the electrode materials recently developed for sodium-ion batteries, selenium shows considerable promise because of its high capacity and good cycling ability. Herein, we have investigated the mechanism and kinetics of both sodiation and lithiation reactions with selenium nanotubes, using in situ transmission electron microscopy. Sodiation of a selenium nanotube exhibits a three-step reaction mechanism: (1) the selenium single crystal transforms into an amorphous phase Na0.5Se; (2) the Na0.5Se amorphous phase crystallizes to form a polycrystalline Na2Se2 phase; and (3) Na2Se2 transforms into the Na2Se phase. Under similar conditions, the lithiation of Se exhibits a one-step reaction mechanism, with phase transformation from single-crystalline Se to a Li2Se. Intriguingly, sodiation kinetics is generally about 4-5 times faster than that of lithiation, and the kinetics during the different stages of sodiation is different. Na-based intermediate phases are found to have improved electronic and ionic conductivity compared to those of Li compounds by first-principles density functional theory calculations.