Detailed mechanistic modeling of high-density polyethylene pyrolysis: Low molecular weight product evolution

A detailed, mechanistic model for high-density polyethylene pyrolysis was created based on the modeling framework developed in our previous work and was used to study the time evolution of low molecular weight products formed. Specifically, the role that unzipping, backbiting, and random scission reaction pathways play in the evolution of low molecular weight species was probed. The model tracked 151 species and included over 11,000 reactions. Rate parameters were adapted from our previous work, literature values, and regression against experimental data. The model results were found to be in excellent agreement with experimental data for the evolution of condensable low molecular weight products. The time evolution curves of specific low molecular weight products indicated that the random scission pathway was important for all species, while the backbiting pathway played a complementary role. Net rate analysis was used to further elucidate the competition between the pathways. Net rate analysis of end-chain radicals showed that the unzipping pathway was not competitive with the other pathways, as expected based on experimental yields of ethylene. The random scission pathway was found to be controlling, with the backbiting pathway playing a more minor role for product formation. By comparing the net rates for formation of specific mid-chain radicals via intramolecular hydrogen shift reactions, the contribution of the backbiting pathway was shown to vary, with radicals formed via the most facile x,x + 4-intramolecular hydrogen transfer reactions being favored.     

The formation mechanism of poly(vinyl acetate)/poly(butyl acrylate) core/shell latex in two-stage seeded semi-continuous starved emulsion polymerization process

In this paper, the morphological evolution of latex particles on poly(vinyl acetate) (PVAc)/poly(butyl acrylate) (PBA) in two-stage seeded semi-continuous starved emulsion polymerization is studied, and the thermodynamic analysis and a mathematic model are derived to describe the interfacial free energy changes corresponding to various possible thermodynamically unstable morphologies during the polymerization process. The comparisons between the morphological evolution and the related thermodynamic analysis show that the morphological evolution of latex particles is oriented to the thermodynamic preferred morphology which is an inverted core/shell structure with PBA as core and PVAc as shell. Based on the comparisons, the possible morphological developmental pathway of PVAc/PBA core/shell latex is described. The possible morphological developmental pathway suggests that the observed multi-particle morphology in the polymerization process is due to restricted chain mobility related to high internal viscosity. The formation mechanism of PVAc/PBA core/shell latex, based on the experiments as well as the thermodynamic and dynamic analyses, is proposed, which signifies that PBA is first formed outside the PVAc seed and then migrate to the inside of the PVAc seed.     

Continuous in vitro evolution of a ribozyme that catalyzes three successive nucleotidyl addition reactions

Variants of the class I ligase ribozyme, which catalyzes joining of the 3' end of a template bound oligonucleotide to its own 5' end, have been made to evolve in a continuous manner by a simple serial transfer procedure that can be carried out indefinitely. This process was expanded to allow the evolution of ribozymes that catalyze three successive nucleotidyl addition reactions, two template-directed mononucleotide additions followed by RNA ligation. During the development of this behavior, a population of ribozymes was maintained against an overall dilution of more than 10(406). The resulting ribozymes were capable of catalyzing the three-step reaction pathway, with nucleotide addition occurring in either a 5'-->3' or a 3'-->5' direction. This purely chemical system provides a functional model of a multi-step reaction pathway that is undergoing Darwinian evolution.     

Unlocking the Transition of Electrochemical Water Oxidation Mechanism Induced by Heteroatom Doping

Heteroatom doping has emerged as a highly effective strategy to enhance the activity of metal-based electrocatalysts toward the oxygen evolution reaction (OER). It is widely accepted that the doping does not switch the OER mechanism from the adsorbate evolution mechanism (AEM) to the lattice-oxygen-mediated mechanism (LOM), and the enhanced activity is attributed to the optimized binding energies toward oxygen intermediates. However, this seems inconsistent with the fact that the overpotential of doped OER electrocatalysts (<300 mV) is considerably smaller than the limit of AEM (>370 mV). To determine the origin of this inconsistency, we select phosphorus (P)-doped nickel-iron mixed oxides as the model electrocatalysts and observe that the doping enhances the covalency of the metal-oxygen bonds to drive the OER pathway transition from the AEM to the LOM, thereby breaking the adsorption linear relation between *OH and *OOH in the AEM. Consequently, the obtained P-doped oxides display a small overpotential of 237 mV at 10 mA cm⁻². Beyond P, the similar pathway transition is also observed on the sulfur doping. These findings offer new insights into the substantially enhanced OER activity originating from heteroatom doping.     

Biochemical Evolution of a Potent Target of Mosquito Larvicide, 3-Hydroxykynurenine Transaminase

A specific mosquito enzyme, 3-hydroxykynurenine transaminase (HKT), is involved in the processing of toxic metabolic intermediates of the tryptophan metabolic pathway. The HKT enzymatic product, xanthurenic acid, is required for Plasmodium spp. development in the mosquito vectors. Therefore, an inhibitor of HKT may not only be a mosquitocide but also a malaria-transmission blocker. In this work, we present a study investigating the evolution of HKT, which is a lineage-specific duplication of an alanine glyoxylate aminotransferases (AGT) in mosquitoes. Synteny analyses, together with the phylogenetic history of the AGT family, suggests that HKT and the mosquito AGTs are paralogous that were formed via a duplication event in their common ancestor. Furthermore, 41 amino acid sites with significant evidence of positive selection were identified, which could be responsible for biochemical and functional evolution and the stability of conformational stabilization. To get a deeper understanding of the evolution of ligands’ capacity and the ligand-binding mechanism of HKT, the sequence and the 3D homology model of the common ancestor of HKT and AGT in mosquitoes, ancestral mosquito AGT (AncMosqAGT), were inferred and built. The homology model along with 3-hydroxykynurenine, kynurenine, and alanine were used in docking experiments to predict the binding capacity and ligand-binding mode of the new substrates related to toxic metabolites detoxification. Our study provides evidence for the dramatic biochemical evolution of the key detoxifying enzyme and provides potential sites that could hinder the detoxification function, which may be used in mosquito larvicide and design.     

Surface organization and cooperativity during nonspecific protein adsorption events

Despite many experimental studies on cooperative effects during protein adsorption events, this phenomenon is still poorly characterized and subject of much controversy. In this study, we address the topic of cooperativity using two distinct experimental approaches, namely, kinetic analysis and surface imaging, both based on supercritical angle fluorescence (SAF) microscopy. Several model systems comprising the two proteins BSA and fibrinogen, two different ionic strength conditions and varying pH environments were investigated. The combination of the experimental information obtained from kinetic analysis and from real-time in situ scan images unravel a clear correlation between cooperative adsorption and a heterogeneous protein layer build-up. We propose a mechanistic model of protein adsorption based on an overlap of classical Langmuir-type adsorption on unoccupied surface areas and an additional cooperative adsorption pathway near preadsorbed proteins which is consistent with the experimental observations. Moreover, the growth of two-dimensional surface clusters as an often assumed element of cooperativity could be excluded for the studied systems. The model includes the often observed phenomenon that the adsorption rate decelerates abruptly above a certain coverage limit. Furthermore, the observed evolution of the heterogeneous protein distribution on the surface is in good agreement with the proposed model.     

Self-assembly Mechanism and Chiral Transfer in CuO Superstructures

Chiral inorganic superstructures have received considerable interest due to the chiral communication between inorganic compounds and chiral organic additives. However, the demanding fabrication and complex multilevel structure seriously hinder the understanding of chiral transfer and self-assembly mechanisms. Herein, we use chiral CuO superstructures as a model system to study the formation process of hierarchical chiral structures. Based on a simple and mild synthesis route, the time-resolved morphology and the in situ chirality evolution could be easily followed. The morphology evolution of the chiral superstructure involves hierarchical assembly, including primary nanoparticles, intermediate bundles, and superstructure at different growth stages. Successive redshifts and enhancements of the CD signal support chiral transfer from the surface penicillamine to the inorganic superstructure. Full-field electro-dynamical simulations reproduced the structural chirality and allowed us to predict its modulation. This work opens the door to a large family of chiral inorganic materials where chiral molecule-guided self-assembly can be specifically designed to follow a bottom-up chiral transfer pathway.     

Novel thieno[2,3-b]quinoline-procaine hybrid molecules: A new class of allosteric SHP-1 activators evolved from PTP1B inhibitors

Small molecule activators could equally provide powerful tools as inhibitors do for interrogating cellular signal transduction. However, targeted protein activation is chemically challenging. Developing activators against Src homology region 2 domain-containing phosphatase-1 (SHP-1) to block STAT3 pathway represents a promising strategy for DLBCL therapy. Here we reported a new class of thieno[2,3-b]quinoline-procaine hybrid molecules as SHP-1 allosteric activators. The representative hybrid compound 3b displayed SHP-1 activating effect with EC₅₀ of 5.48 ± 0.28 µmol/L. Further investigations confirmed that 3b allosterically interacted with SHP-1, switched it from close to open conformation, blocked SHP-1/p-STAT3 pathway, induced apoptosis and inhibited ABC-DLBCL cell proliferation in vitro, and delayed tumor growth in the xenograft model of SU-DHL-2. Overall, this work offered a novel paradigm to develop SHP-1 allosteric activators through chemical space evolution of PTPs inhibitors, and firstly validated the therapeutic strategy that directly activating SHP-1 alone could be a potential therapy against ABC-DLBCL via blocking STAT3 pathway.     

木质素模化物紫丁香酚热解机理的量子化学研究

采用密度泛函理论方法B3LYP/6-31G++(d,p),对木质素模化物紫丁香酚的热解反应机理进行了量子化学理论研究。提出了三种可能的热解反应途径,对各种反应的反应物、产物、中间体和过渡态的结构进行了能量梯度全优化。计算了各热解反应途径的标准动力学参数,分析了各种主要热解产物的形成演化机理。键离解能计算结果表明,紫丁香酚中CH₃-O键的键离解能最小,各种键离解能的大小顺序为CH₃-O < O-H < CH₃O-C_aromatic < CH₂-H < HO-C_aromatic < C_aromatic-H。在反应路径(1)中,主要热解产物是3-甲氧基邻苯二酚,其形成反应的总能垒为366.6 kJ/mol;在反应路径(2)中主要热解产物是2-甲氧基-6-甲基苯酚,其形成反应的总能垒为474.8 kJ/mol;在反应路径(3)中形成邻甲氧基苯酚的总能垒很低,为21.4 kJ/mol,这表明,在连接甲氧基的碳原子上加氢后能够有效地降低木质素芳环模化物紫丁香酚去甲氧基反应的反应能垒。     

Mechanistic study on the palladium-catalyzed (3 + 2) intramolecular cycloaddition of alk-5-enylidenecyclopropanes

The intramolecular (3 + 2) cycloaddition of alkenylidenecyclopropanes to alkenes under palladium catalysis provides a practical and stereoselective entry into a variety of interesting bicycles. The reaction outcome and stereoselectivity of the process are somewhat dependent on the characteristics of the substrate and of the palladium ligand, which is not easy to justify on the basis of the current mechanistic understanding. We therefore decided to study the different mechanistic alternatives from a theoretical point of view. The energies of the reaction intermediates and transition states for different possible pathways have been explored at DFT level in a model system, and using PH(3) and P(OMe)(3) as ligands. The results obtained suggest that the most favourable reaction pathway involves an initial oxidative addition of Pd(0) at the distal position of the cyclopropane to afford a palladacyclobutane intermediate. The evolution of this intermediate into the final cycloadduct can occur following different paths, the most favorable depending on the configuration and substitution of the alkene cycloaddition partner, and the number of ancillary ligands coordinated to Pd. The computational results are consistent with the experimental observations and provide the basis for proposing which would be the operative mechanistic pathway in different cases. The results also allow us to explain the stereochemical divergences observed in some of the reactions.     

Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism

Methanol is a valuable raw material used in the manufacture of useful chemicals as well as a potential source of energy to replace coal and petroleum. Biotechnological interest in the microbial utilization of methanol has increased because it is an ideal carbon source and can be produced from renewable biomass. Formaldehyde, a cytotoxic compound, is a central metabolic intermediate in methanol metabolism. Therefore, microorganisms utilizing methanol have adopted several metabolic strategies to cope with the toxicity of formaldehyde. Formaldehyde is initially detoxified through trapping by some cofactors, such as glutathione, mycothiol, tetrahydrofolate, and tetrahydromethanopterin, before being oxidized to CO2. Alternatively, free formaldehyde can be trapped by sugar phosphates as the first reaction in the C1 assimilation pathways: the xylulose monophosphate pathway for yeasts and the ribulose monophosphate (RuMP) pathway for bacteria. In yeasts, although formaldehyde generation and consumption takes place in the peroxisome, the cytosolic formaldehyde oxidation pathway also plays a role in formaldehyde detoxification as well as energy formation. The key enzymes of the RuMP pathway are found in a variety of microorganisms including bacteria and archaea. Regulation of the genes encoding these enzymes and their catalytic mechanisms depend on the physiological traits of these organisms during evolution.     

A Cocatalyst that Stabilizes a Hydride Intermediate during Photocatalytic Hydrogen Evolution over a Rhodium‐Doped TiO2 Nanosheet

The hydrogen evolution reaction using semiconductor photocatalysts has been significantly improved by cocatalyst loading. However, there are still many speculations regarding the actual role of the cocatalyst. Now a photocatalytic hydrogen evolution reaction pathway is reported on a cocatalyst site using TiO₂ nanosheets doped with Rh at Ti sites as one‐atom cocatalysts. A hydride species adsorbed on the one‐atom Rh dopant cocatalyst site was confirmed experimentally as the intermediate state for hydrogen evolution, which was consistent with the results of density functional theory (DFT) calculations. In this system, the role of the cocatalyst in photocatalytic hydrogen evolution is related to the withdrawal of photo‐excited electrons and stabilization of the hydride intermediate species; the presence of oxygen vacancies induced by Rh facilitate the withdrawal of electrons and stabilization of the hydride.     

Comparative study of pyrolytic decomposition of polymers alone or in EVA/PS,EVA/PVC and EVA/cellulose mixtures

The behavior of mixtures of EVA–PS, EVA–PVC and EVA–cellulose in various proportions were investigated under pyrolysis. A kinetic model with an independent pathway is proposed for the weight loss and compared with the experimental and theoretical results obtained in a previous study with individual polymers. The kinetic parameters were determined and online IR spectrometric analysis used to follow the evolution of the gaseous pyrolysis products versus the temperature. The result shows good agreement for the EVA–PS mixture and confirms the hypothesis of an independent pathway. However, in the case of EVA–PVC and EVA–cellulose mixtures, the polymers affect one other in the pyrolysis reaction.     

Dynamics of terrace formation in a nanostructured thin block copolymer film

We have used dynamic self-consistent field (DSCF) theory to investigate the structural evolution of an ABA block copolymer thin film placed between a solid substrate and a free surface. In line with the few existing theoretical studies for pure homopolymers and mixtures, the free interface is introduced by a void component. In our calculations, the free surface experiences surface roughening and eventually the formation of terraces, as in the experiments. The kinetic pathway of the microstructures was compared to findings of an existing detailed experimental study (Knoll, A.; Lyakhova, K. S.; Horvat, A.; Krausch, G.; Sevink, G. J. A.; Zvelindovsky, A. V.; Magerle, R. Nat. Mater. 2004, 3, 886) and was found to be equivalent in detail. This corroborates our assumption in this earlier work that the pathway due to changing film thickness is similar to a pathway due to changing surface energetics. Moreover, our calculations show for the first time that microstructural transitions are a driving force of polymer/air interface curving and the formation of terraces.     

Unique sugar metabolism and novel enzymes of hyperthermophilic archaea

Hyperthermophiles are a group of microorganisms that have their optimum growth temperature above 80 degrees C. More than 60 species of the hyperthermophiles have been isolated from marine and continental volcanic environments. Most hyperthermophiles belong to Archaea, the third domain of life, and are considered to be the most ancient of all extant life forms. Recent studies have revealed the presence of unusual sugar metabolic processes in hyperthermophilic archaea, for example, a modified Embden-Meyerhof pathway, that has so far not been observed in bacteria and eucarya. Several novel enzymes, such as ADP-dependent glucokinase, ADP-dependent phosphofructokinase, glyceraldehyde-3-phosphate ferredoxin oxidoreductase, phosphoenolpyruvate synthase, pyruvate : ferredoxin oxidoreductase, and ADP-forming acetyl-CoA synthetase, have been found to be involved in a modified Embden-Meyerhof pathway of the hyperthermophilic archaeon Pyrococcus furiosus. In addition, a unique mode of ATP regeneration has been postulated to exist in the pathway of P. furiosus. The metabolic design observed in this microorganism might reflect the situation at an early stage of evolution.     

A thermodynamic solution model for calcium carbonate: Towards an understanding of multi-equilibria precipitation pathways

Thermodynamic solubility calculations are normally only related to thermodynamic equilibria in solution. In this paper, we extend the use of such solubility calculations to help elucidate possible precipitation reaction pathways during the entire reaction. We also estimate the interfacial energy of particles using only solubility data by a modification of Mersmann’s approach. We have carried this out by considering precipitation reactions as a succession of small quasi-equilibrium states. Thus possible equilibrium precipitation pathways can be evaluated by calculating the evolution of surface charge, particle size and/or interfacial energy during the ongoing reaction. The approach includes the use of the Kelvin’s law to express the influence of particle size on the solubility constant of precipitates, the use of Nernst’s law to calculate surface potentials from solubility calculations and relate this to experimentally measured zeta potentials. Calcium carbonate precipitation and zeta potential measurements of well characterised high purity calcite have been used as a model system to validate the calculated values. The clarification of the change in zeta potential on titration illustrates the power of this approach as a tool for reaction pathway prediction and hence knowledge based tailoring of precipitation reactions.     

In situ activation and monitoring of the evolution of the intracellular caspase family

The evolution of the intracellular caspase family is crucial in cell apoptosis. To evaluate this process, a universal platform of in situ activation and monitoring of the evolution of intracellular caspase is designed. Using well-known gold nanostructure as a model of both nanocarrier and matter inducing the cell apoptosis for photothermal therapy, a nanoprobe is prepared by assembly of two kinds of dye-labelled peptides specific to upstream caspase-9 and downstream caspase-3 as the signal switch, and folic acid as a targeting moiety. The energy transfer from dyes to the gold nanocarrier at two surface plasmon resonance absorption wavelengths leads to their fluorescence quenching. Upon endocytosis of the nanoprobe to perform the therapy against cancer cells, the peptides are successively cleaved by intracellular caspase activation with the evolution from upstream to downstream, which lights up the fluorescence of the dyes sequentially, and can be used to quantify both caspase-9 and caspase-3 activities in cancer cells and to monitor their evolution in living mice. The recovered fluorescence could also be used to assess therapeutic efficiency. This work provides a novel powerful tool for studying the evolution of the intracellular caspase family and elucidating the biological roles of caspases in cancer cell apoptosis.     

Influence of photo-Fries reaction products on the photodegradation of bisphenol-A polycarbonate

The photodegradation of BPA polycarbonate (PC) can be described as an autoaccelerating process initiated by the formation of biphenol products arising from a formal photo-Fries reaction pathway. Evidence comes from spiking PC films with model compounds of photo-Fries reaction products, pre-exposure of films to generate photo-Fries products, and kinetic analysis. Published data on products formed during natural PC weathering are consistent with this pathway.     

A possible evolutionary role of formaldehyde

Formaldehyde is a compound which is believed to have had a role in evolutionary processes. On the other hand, the (methyl)glyoxalase pathway is a route being present in all biological organisms whereas its function has not yet been recognized in the biochemical machinery. In this article it is raised that (methyl)glyoxalase path might have functioned as a bridge between formose and archaic reductive citric acid cycles in surface metabolists at the early stage of evolution. According to the theory, formaldehyde was essential for the mentioned system as a raw molecule. Based on thermodynamic calculations a simple way of regulation is also shown. The simplicity of the theory may be in a good agreement with and an explanation of why the (methyl)glyoxalase system is of ubiquitous nature.     

Measuring the Electrode Kinetics of Vitamin B2 at a Constant Time Window of a Square Wave Voltammetric Experiment

The electrode kinetics of vitamin B2 was measured at a constant scan rate of a square‐wave (SW) voltammetric experiment by recently introduced method based on alteration of the height (amplitude) of the SW potential pulses. The electrode reaction mechanism was analyzed in the light of the simplified model considering two‐electron one step surface electrode mechanism, as well as to more appropriate EE surface reaction pathway consisting of two successive one‐electron quasireversible reactions. Theoretical analysis indicated that the evolution of the voltammetric response under variation of the SW amplitude enables estimation of the rate determining step of the EE mechanism.