Reaction Systems Research Articles

A framework for monitored dynamic slicing of reaction systems

AbstractReaction systems (RSs) are a computational framework inspired by biochemical mechanisms. A RS defines a finite set of reactions over a finite set of entities. Typically each reaction has a local scope, because it is concerned with a small set of entities, but complex models can involve a large number of reactions and entities, and their computation can manifest unforeseen emerging behaviours. When a deviation is detected, like the unexpected production of some entities, it is often difficult to establish its causes, e.g., which entities were directly responsible or if some reaction was misconceived. Slicing is a well-known technique for debugging, which can point out the program lines containing the faulty code. In this paper, we define the first dynamic slicer for RSs and show that it can help to detect the causes of erroneous behaviour and highlight the involved reactions for a closer inspection. To fully automate the debugging process, we propose to distil monitors for starting the slicing whenever a violation from a safety specification is detected. We have integrated our slicer in BioResolve, written in Prolog which provides many useful features for the formal analysis of RSs. We define the slicing algorithm for basic RSs and then enhance it for dealing with quantitative extensions of RSs, where timed processes and linear processes can be represented. Our framework is shown at work on suitable biologically inspired RS models.

Spectroelectrochemical Exploration of Biogenic Substrates for Electrosynthesis

AbstractSpectroelectrochemistry, especially ATR‐SEIRAS, is an emerging method to identify key descriptors for optimizing reaction systems in organic electrosynthesis. Here, the upgrading of biogenic acids via Kolbe electrolysis and reductive transformations was studied. The findings affirm acid group adsorption on electrodes, consistent with existing literature. The effectiveness of Kolbe reaction in suppressing the parasitic ethanol oxidation reaction was observed, whereas it faces stiff competition from the methanol oxidation reaction. Parallel reduction and reductive amination of levulinic acid were uncovered, both relying on adsorbed organic species rather than molecular H2. Intriguingly, the electrode's polarization influences the bond strength, enabling discrimination between acid and ketone species within levulinic acid.

Hydrodeoxygenation of Oxygen-Containing Aromatic Plastic Wastes into Cycloalkanes and Aromatics.

Chemical recycling and upcycling offer promising approaches for the management of plastic wastes. Hydrodeoxygenation (HDO) is one of the appealing ways for conversion of oxygen-containing plastic wastes, including PET, PBT, PC, PPO, and PEEK, into cyclic alkanes and aromatics in high yields under mild reaction conditions. The challenge lies in achieving C-O activation while preserving C-C bonds. In this review, we highlight the recent advancements in catalytic strategies and catalysts for the conversion of these oxygen-containing plastic wastes into cycloalkanes and aromatics. The reaction systems, including multi-step routes, direct HDO and transfer HDO methods, are exemplified. The design and performance of HDO catalysts are systematically summarized and compared. We comprehensively discuss the functions of the catalysts' components, reaction pathway and mechanism to gain insights into the HDO process for efficient valorization of oxygen-containing plastic wastes. Finally, we provide perspectives for this field, with specific emphasis on the non-noble metal catalyst design, selectivity control, reaction network and mechanism studies, mixed plastic wastes management and product functionalization. We anticipate that this review will inspire innovations on the catalytic process development and rational catalyst design for the HDO of oxygen-containing aromatic plastics to establish a low-emission circular economy.

Asymmetric Additions Empowered by OrganoCatalysts, Metal Catalysts, and Deep Natural Eutectic Solvents (NADES).

This article is a history of an industrial-academic partnership that started almost two decades ago and details the evolution of a relationship between a small academic research group and a spin-out company located in Portugal. Their activities have ranged from the development of new metal-based catalytic systems for asymmetric epoxidations, allylic alkylations, and arylations to the development of novel cinchona-based organocatalysts for asymmetric hydrosilylations and Michael additions. Current common interests are centered on the development of novel chiral Natural Deep Eutectic Solvent systems, which they are investigating in different types of reaction systems.

Formation of Volatile Pyrazinones in the Asparagine Maillard Reaction Systems and Novel Pyrazinone Formation Pathways in the Amidated-Alanine Maillard Reaction Systems.

Maillard reaction (MR) plays a pivotal role in the food flavor industry, including a cascade of reactions starting with the reaction between amino compounds and reducing sugars, and thus provides various colors and flavors. A new group of volatile compounds called pyrazinones found in MR are now getting more attention. In this study, eight volatile pyrazinones were found in the asparagine MR systems, in which 3,5-dimethyl- and 3,6-dimethyl-2(1H)-pyrazinones were reported for the first time. The major formation pathways were the reactions between asparagine and α-dicarbonyls, with decarboxylation as a critical step. Besides, novel alternative pathways involving alanine amidation and successive reactions with α-dicarbonyls were explored and successfully formed eight pyrazinones. The major differences between alanine-amidated pathways and decarboxylation pathways are the amidation step and absence of the decarboxylation step. For the alanine-amidated pathways, the higher the temperature, the better the amidation effect. The optimal amidation temperature was 200 °C in this study. The reaction between the alanine amide and α-dicarbonyls after amidation can happen at low temperatures, such as 35 and 50 °C, proposing the possibility of pyrazinone formation in real food systems. Further investigations should be conducted to investigate volatile pyrazinones in various food systems as well as the biological effects and kinetic formation differences of the volatile pyrazinones.

New insight into molecular mechanisms of different polyphenols affecting Sirtuin 3 deacetylation activity.

Multiple phenolic substances have been shown to promote SIRT3 expression, however, few studies have focused on the effects of these phenolics on SIRT3 enzyme activity. This study constructed a variety of reaction systems to elucidate the mechanisms by which different polyphenols affect SIRT3 enzyme activity. The results showed that acP53317-320 was the most suitable substrate among the five acetylated peptide substrates (Kcat/Km = 74.85 ± 1.86 M-1•s-1). All the phenolic compounds involved in the experiment inhibited the enzymatic activity of SIRT3, and the lowest IC50 among them was quercetin (0.12 ± 0.01 mM) and the highest was piceatannol (1.29 ± 0.08 mM). Their inhibition types were mainly competitive and mixed. In addition, piceatannol was found to be a natural SIRT3 agonist by enzyme kinetic analysis and validation of deacetylation efficiency. This study will provide a useful reference for polyphenol modulation of SIRT3 dosage, as well as the development and application of polyphenol-based SIRT3 activators and agonists.

Periodic Precipitation in a Confined Liquid Layer.

Pattern formation is a ubiquitous phenomenon in animate and inanimate systems generated by mass transport and reaction of chemical species. The Liesegang phenomenon is a self-organized periodic precipitation pattern always studied in porous media such as hydrogels and aerogels for over a century. The primary consideration of applying the porous media is to prevent the disintegration of the precipitation structures due to the sedimentation of the precipitate and induced fluid flow. Here, we show that the periodic precipitation patterns can be engineered using a Hele-Shaw cell in a confined liquid phase, restricting hydrodynamic instability. The patterns generated in several precipitation reaction systems exhibit spatiotemporal properties consistent with patterns obtained in solid hydrogels. Furthermore, analysis considering the Rayleigh-Darcy number emphasizes the crucial role of fluidity in generating periodic precipitation structures in a thin liquid film. This exploration promises breakthroughs at the intersection of fundamental understanding and practical applications.

Slag Electrical Conductivity and Its Effect on Mass Transport and Interfacial Reaction Kinetics

Pyrometallurgical refining typically involves slag–metal reactions which are commonly controlled by transport of reactants in the slag or metal phase. For the simplicity of analysis, mass transport in slag is generally treated on a phenomenological basis as transport of molecules. Although this approach works well for many of the reaction systems over narrow ranges of conditions, it can fail when extrapolated over a wide range of conditions. In many refining processes, transport of oxygen in slag determines the kinetics of major reactions. Transport of oxygen in slag is strongly influenced by the electrical conductivity of slag. Whilst this has been well understood since the 1950s, there have been relatively few attempts to quantify the effects of slag electrical properties on the refining kinetics. Herein, an overview is presented focusing on the electrical properties of slags and their effects on the transport kinetics in steelmaking reactions. An analysis is conducted based on a modified version of the approach taken by Wagner to describe oxygen transport in solid oxides. Data from the literature including work from the authors’ laboratory is discussed in an evaluation of literature oxygen transport in CaO–SiO2–FetO, CaO–SiO2–Al2O3–FetO, and PbO–Fe2O3 slags.

Modeling phase or chemical reaction equilibrium with an equation of state, an unrealistic modeling

The traditional chemical thermodynamics considered the chemical potential then fugacity of a component in a single-phase, open system is just the one of the component in a co-existing phase of an equilibrium, multi-component, multi-phase system or in an equilibrium, chemical reaction system and the fugacity can be calculated with the equation of state of the single-phase, open system. Therefore, the most common method to model phase or chemical reaction equilibrium is with an equation of state. Obviously, modeling phase or chemical reaction equilibrium with an equation of state requires to the single-phase, open system is equivalent to the co-existing phase or the equilibrium, chemical reaction system. However, there are significant differences in the thermodynamics properties between the single-phase, open system and the co-existing phase or the equilibrium, chemical reaction system. Therefore, the chemical potential then fugacity of a component in the single-phase, open system is impossible the one of the component in the co-existing phase or in the equilibrium, chemical reaction system. That is, the calculated fugacity of a component in a single-phase, open system with the equation of state of the single-phase, open system is impossibly the fugacity of the component in a co-existing phase of an equilibrium, multi-component, multi-phase system or in an equilibrium, chemical reaction system. Therefore, it is unrealistic to model phase or chemical reaction equilibrium with an equation of state. For this, we establish the chemical potential differential formula of a component in a co-existing phase and in an equilibrium, chemical reaction system to calculate phase or chemical reaction equilibrium. The calculated values of solubility in molar concentration within the framework of the present theory equals exactly the measured values of solubility in molar concentration by the experiments.

Global structure of competing model with flocculation in a reaction–diffusion chemostat

In this paper, we study a system of reaction–diffusion equations arising from the competition of two competing species for a single limited nutrient with flocculation in an unstirred chemostat. By the conservation principle, we reduce the dimension of the system by eliminating the equation for the nutrient. Then the global structure of the reduced system is studied by the bifurcation theory in its feasible domain. Finally, we use numerical simulation to verify and supplement our theoretical results.

Efficient Synthesis of (S)-Nornicotine using Co-Immobilized IRED and GDH in Batch and Continuous Flow Reaction Systems

Efficient Synthesis of (<i>S</i>)-Nornicotine using Co-Immobilized IRED and GDH in Batch and Continuous Flow Reaction Systems

Aqueous-Phase Photoreactions of Mixed Aromatic Carbonyl Photosensitizers Yield More Oxygenated, Oxidized, and less Light-Absorbing Secondary Organic Aerosol (SOA) than Single Systems.

Aromatic carbonyls have been mainly probed as photosensitizers for aqueous secondary organic aerosol (aqSOA) and light-absorbing organic aerosol (i.e., brown carbon or BrC) formation, but due to their organic nature, they can also undergo oxidation to form aqSOA and BrC. However, photochemical transformations of aromatic carbonyl photosensitizers, particularly in multicomponent systems, are understudied. This study explored aqSOA formation from the irradiation of aromatic carbonyl photosensitizers in mixed and single systems under cloud/fog conditions. Mixed systems consisting of phenolic carbonyls only (VL + ActSyr + SyrAld: vanillin [VL] + acetosyringone [ActSyr] + syringaldehyde [SyrAld]) and another composed of both nonphenolic and phenolic carbonyls (DMB + ActSyr + SyrAld: 3,4-dimethoxybenzaldehyde [DMB], a nonphenolic carbonyl, + ActSyr + SyrAld) were compared to single systems of VL (VL*) and DMB (DMB*), respectively. In mixed systems, the shorter lifetimes of VL and DMB indicate their diminished capacity to trigger the oxidation of other organic compounds (e.g., guaiacol [GUA], a noncarbonyl phenol). In contrast to the slow decay and minimal photoenhancement for DMB*, the rapid photodegradation and significant photoenhancement for VL* indicate efficient direct photosensitized oxidation (i.e., self-photosensitization). Relative to single systems, the increased oxidant availability promoted functionalization in VL + ActSyr + SyrAld and accelerated the conversion of early generation aqSOA in DMB + ActSyr + SyrAld. Moreover, the increased availability of oxidizable substrates countered by stronger oxidative capacity limited the contribution of mixed systems to aqSOA light absorption. This suggests a weaker radiative effect of BrC from mixed photosensitizer systems than BrC from single photosensitizer systems. Furthermore, more oxygenated and oxidized aqSOA was observed with increasing complexity of the reaction systems (e.g., VL* < VL + ActSyr + SyrAld < VL + ActSyr + SyrAld + GUA). This work offers new insights into aqSOA formation by emphasizing the dual role of organic photosensitizers as oxidant sources and oxidizable substrates.

Formation of Volatile Pyrazinones in Amadori Rearrangement Products and Maillard Reaction Systems and the Major Formation Pathways.

Amadori rearrangement products (ARPs) are gaining more attention for their potential usage in the food flavor industry. Peptide-ARPs have been studied, but pyrazinones that were theoretically found in the Maillard reaction (MR) have not been reported to be formed from small peptide-ARPs. This study found four pyrazinones: 1-methyl-, 1,5-dimethyl-, 1,6-dimethyl-, and 1,5,6-trimethyl-2(1H)-pyrazinones in both MR and ARP systems. It was the first time 1-methyl-2(1H)-pyrazinone was reported, along with 1,5-dimethyl- and 1,5,6-trimethyl-2(1H)-pyrazinones being purified and analyzed by nuclear magnetic resonance for the first time. The primary formation routes of the pyrazinones were also proven as the reaction between diglycine and α-dicarbonyls, including glyoxal, methylglyoxal, and diacetyl. The pyrazinones, especially 1,5-dimethyl-2(1H)-pyrazinone, have strong fluorescence intensity, which may be the reason for the increase of fluorescence intensity in MR besides α-dicarbonyls. Cytotoxicity analysis showed that both Gly-/Digly-/Trigly-ARP and the three pyrazinones [1-methyl-, 1,5-dimethyl-, and 1,5,6-trimethyl-2(1H)-pyrazinones] showed no prominent cytotoxicity in the HepG2 cell line below 100 μg/mL, further suggesting that ARPs or pyrazinones could be used as flavor additives in the future. Further research should be conducted to investigate pyrazinones in various systems, especially the peptide-ARPs, which are ubiquitous in real food systems.

Effect of interaction between resveratrol and myofibrillar protein on the production of bound heterocyclic amines

To elucidate the pathways and mechanisms by which polyphenols inhibit protein-bound heterocyclic amines (HAs), the influence of resveratrol on bound/free HAs and the structure changes of myofibrillar proteins (MP) in the system of creatinine/MP/glucose model was studied. The results demonstrate that resveratrol significantly reduced bound and free HAs in the reaction systems (P < 0.05), and facilitates the transition from bound to free HAs. In addition, resveratrol altered the secondary structure of MP and had a static quenching effect on MP fluorescence. The strong interactions between resveratrol and MP are mainly hydrogen bonding and hydrophobic interactions. Furthermore, the results of molecular docking demonstrated that resveratrol exposed more hydrophobic amino acids (Ala, Lys and Pro) at the 556–578 amino acid sites of myosin. These results indicate that resveratrol controls the formation of bound HAs by reducing exposure to amino acids involved in the HAs reaction and promoting exposure to non-precursor amino acids.

The interaction between lipid oxidation and the Maillard reaction model of lysine-glucose on aroma formation in fragrant sesame oil

The formation mechanism behind the sophisticated aromas of sesame oil (SO) has not been elucidated. The interaction effects of the Maillard reaction (MR) and lipid oxidation on the aroma formation of fragrant sesame oil were investigated in model reaction systems made of l-lysine (Lys) and d-glucose (Glc) with or without fresh SO (FSO) or oxidized SO (OSO). The addition of OSO to the Lys-Glc model increased the MR browning at 294 nm and 420 nm and enhanced the DPPH radical scavenging activity greater than the addition of FSO (p < 0.05). The presence of lysine and glucose inhibited the oxidation of sesame oil, reduced the loss of γ-tocopherol, and facilitated the formation of sesamol (p < 0.05). The Maillard-lipid interaction led to the increased concentrations of some of the alkylpyrazines, alkylfurans, and MR-derived ketones and acids (p < 0.05) while reducing the concentrations of other pyrazines, lipid-derived furans, aliphatic aldehydes, ketones, alcohols, and acids (p < 0.05). The addition of FSO to the MR model enhanced the characteristic roasted, nutty, sweet, and fatty aromas in sesame oil (p < 0.05), while excessive lipid oxidation (OSO) brought about an unpleasant oxidized odor and reduced the characteristic aromas. This study helps to understand the sophisticated aroma formation mechanism in sesame oil and provides scientific instruction for precise flavor control in the production of sesame oil.

Variation in the relationship between odd isotopes of tin in mass-independent fractionation induced by the magnetic isotope effect

Experimental results are presented showing the variation in the relationship between odd isotopes of tin (Sn) in mass-independent fractionation caused by the magnetic isotope effect (MIE), which has previously only been observed for mercury. These results are consistent with the trend predicted from the difference between the magnitudes of nuclear magnetic moments of odd isotopes with a nuclear spin. However, the correlation between odd isotopes in fractionation induced by the MIE for the reaction system used in this study (solvent extraction using a crown ether) was different from that reported for the photochemical reaction of methyltin. This difference between the two reaction systems is consistent with a theoretical prediction that the correlation between odd isotopes in fractionation induced by the MIE is controlled by the relationship between the spin conversion time and radical lifetime. The characteristic changes in the correlation between odd isotopes in fractionation induced by the MIE observed for Sn in this study provide a guideline for quantitatively determining fractionation patterns caused by the MIE for elements that have multiple isotopes with a nuclear spin. These results improve our understanding of the potential impact of the MIE on mass-independent fractionation observed in natural samples, such as meteorites, and analytical artifacts of high-precision isotope analysis for heavy elements.

TEMPO-Grafted Polystyrene/Polymethacrylate Organosiloxane Janus Nanohybrids as Efficient Pickering Interfacial Catalyst for Selective Aerobic Oxidation of Cinnamyl Alcohol.

The novel 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) groups immobilized on functional polymers or nanoparticles emerged as potential Pickering interfacial catalysts (PICs) for effective catalysis in biphasic systems. In this study, a snowman-shaped Janus-structured polymer with TEMPO-anchored nanohybrid particles (SM-JPP-TEMPO) was prepared and employed as a potential PIC in the Anelli-Montanari system for the selective oxidation of alcohol. The amphiphilic character of SM-JPP-TEMPO particles plays a dual role as an emulsifier and catalyst in the Pickering emulsion. As a result, it enables smaller droplets (102 μm) at the water-in-oil (W/O) interface and reduces the interfacial tension from 26.58 to 17.38 mN/m, which improves the stability of the Pickering emulsion system. This constructed Pickering emulsion microreactor offers a larger interface contact area and shortens the mass transfer distance of the substrate of cinnamyl alcohol, which significantly enhances the catalytic conversion at the Anelli-Montanari oxidation system, thus achieving remarkable conversion efficiency of (92.3%) with excellent selectivity (99%) in static (stirring-free) condition. It was found that the Janus nanohybrid catalyst (SM-JPP-TEMPO) enhanced 1.29-fold catalytic efficiency compared to the TEMPO grafted spherical polystyrene nanoparticle (PS-NPs-TEMPO) catalyst (72%). Moreover, after seven consecutive cycles, the Janus nanocatalyst (SM-JPP-TEMPO) maintained the conversion significantly. Hence, these results collectively highlight that the amphiphilic SM-JPP-TEMPO catalyst provides an efficient and eco-friendly strategy for the intensification of liquid-liquid biphasic reaction systems for potential applications in industries.

On the spectrum between reaction systems and string rewriting

On the spectrum between reaction systems and string rewriting

Counter-regulatory RAS peptides: new therapy targets for inflammation and fibrotic diseases?

The renin-angiotensin system (RAS) is an important cascade of enzymes and peptides that regulates blood pressure, volume, and electrolytes. Within this complex system of reactions, its counter-regulatory axis has attracted attention, which has been associated with the pathophysiology of inflammatory and fibrotic diseases. This review article analyzes the impact of different components of the counter-regulatory axis of the RAS on different pathologies. Of these peptides, Angiotensin-(1-7), angiotensin-(1-9) and alamandine have been evaluated in a wide variety of in vitro and in vivo studies, where not only they counteract the actions of the classical axis, but also exhibit independent anti-inflammatory and fibrotic actions when binding to specific receptors, mainly in heart, kidney, and lung. Other functional peptides are also addressed, which despite no reports associated with inflammation and fibrosis to date were found, they could represent a potential target of study. Furthermore, the association of agonists of the counter-regulatory axis is analyzed, highlighting their contribution to the modulation of the inflammatory response counteracting the development of fibrotic events. This article shows an overview of the importance of the RAS in the resolution of inflammatory and fibrotic diseases, offering an understanding of the individual components as potential treatments.

Surface wettability control and electron transport regulation in zerovalent iron for enhanced removal of emerging polystyrene microplastics-heavy metal contaminants

Emerging microplastics-heavy metal (MPs-HM) contaminants in wastewaters pose an emerging health and environmental risk due to their persistence and increasing ecological risks (e.g., “Trojan horse” effect). Hence, removing MPs in solution and preventing secondary releases of HM has become a key challenge when tackling with MPs pollution. Leveraging the hydrophobic nature of MPs and the electron transfer efficiency from Fe0 to HM, we demonstrate an alkylated and sulfidated nanoscale zerovalent iron (AS-nZVI) featuring a delicate “core-shell-hydrophobic film” nanostructure. Exemplified by polystyrene (PS) MPs-Pb(II) removal, the three nanocomponents offer synergistic functions for the rapid separation of MPs, as well as the reduction and stabilization of Pb(II). The outmost hydrophobic film of AS-nZVI greatly improves the anticorrosion performance of nanoscale zerovalent iron and the enrichment abilities of hydrophilic MPs, achieving a maximum removal capacity of MPs to 2725.87 mgMPs·gFe−1. This MPs enrichment promotes the subsequent reductive removal of Pb(II) through the electron transfer from the iron core of AS-nZVI to Pb(II), a process further strengthened by the introduced sulfur. When considering the inevitable aging of MPs in wastewaters due to mechanical wear or microbial degradation, our study concurrently examines the efficiencies and behaviors of AS-nZVI in removing virgin-MPs-Pb(II) and aged-MPs-Pb(II). The batch results reveal that AS-nZVI has an exceptional ability to remove above 99.6 % Pb(II) for all reaction systems. Overall, this work marks a pioneering effort in highlighting the importance of MPs-toxin combinations in dealing with MPs contamination and in demonstrating the utility of nZVI techniques for MPs-contaminated water purification.