Reaction Systems Research Articles

Simulating BRAFV600E-MEK-ERK signalling dynamics in response to vertical inhibition treatment strategies

In vertical inhibition treatment strategies, multiple components of an intracellular pathway are simultaneously inhibited. Vertical inhibition of the BRAFV600E–MEK-ERK signalling pathway is a standard of care for treating BRAFV600E-mutated melanoma where two targeted cancer drugs, a BRAFV600E-inhibitor, and a MEK inhibitor, are administered in combination. Targeted therapies have been linked to early onsets of drug resistance, and thus treatment strategies of higher complexities and lower doses have been proposed as alternatives to current clinical strategies. However, finding optimal complex, low-dose treatment strategies is a challenge, as it is possible to design more treatment strategies than are feasibly testable in experimental settings. To quantitatively address this challenge, we develop a mathematical model of BRAFV600E–MEK-ERK signalling dynamics in response to combinations of the BRAFV600E-inhibitor dabrafenib (DBF), the MEK inhibitor trametinib (TMT), and the ERK-inhibitor SCH772984 (SCH). From a model of the BRAFV600E–MEK–ERK pathway, and a set of molecular-level drug–protein interactions, we extract a system of chemical reactions that is parameterised by in vitro data and converted to a system of ordinary differential equations (ODEs) using the law of mass action. The ODEs are solved numerically to produce simulations of how pathway-component concentrations change over time in response to different treatment strategies, i.e., inhibitor combinations and doses. The model can thus be used to limit the search space for effective treatment strategies that target the BRAFV600E–MEK–ERK pathway and warrant further experimental investigation. The results demonstrate that DBF and DBF–TMT–SCH therapies show marked sensitivity to BRAFV600E concentrations in silico, whilst TMT and SCH monotherapies do not.

Charge Transfer Mechanism on a Cobalt-Polyoxometalate-TiO2 Photoanode for Water Oxidation in Acid.

We constructed a photoanode comprising the homogeneous water oxidation catalyst (WOC) Na8K8[Co9(H2O)6(OH)3(HPO4)2(PW9O34)3] (Co9POM) and nanoporous n-type TiO2 photoelectrodes (henceforth "TiO2-Co9POM") by first anchoring the cationic 3-aminopropyltrimethoxysilane (APS) ligand on a metal oxide light absorber, followed by treatment of the metal oxide-APS with a solution of the polyoxometalate WOC. The resulting TiO2-Co9POM photoelectrode exhibits a 3-fold oxygen evolution photocurrent enhancement compared to bare TiO2 in aqueous acidic conditions. Three-element (Co 2p, W 4f, and O 1s) X-ray photoelectron spectroscopy and Raman spectroscopy studies before and after use indicate that surface-bound Co9POM retains its structural integrity throughout all photoelectrochemical water oxidation studies reported here. Extensive charge-transfer mechanistic studies by photoelectrochemical techniques and transient absorption spectroscopy elucidate that Co9POM serves as an efficient WOC, extracting photogenerated holes from TiO2 on the picosecond time scale. This is the first comprehensive mechanistic investigation elucidating the roles of polyoxometalates in POM-photoelectrode hybrid oxygen evolution reaction systems.

Finding regulatory modules of chemical reaction systems

Within a cell, numerous chemical reactions form chemical reaction networks (CRNs), which are the origins of cellular functions. We previously developed a theoretical method called structural sensitivity analysis (SSA), which enables us to determine, solely from the network structure, the qualitative changes in the steady-state concentrations of chemicals resulting from the perturbations to a parameter. Notably, if a subnetwork satisfies specific topological conditions, it is referred to as a buffering structure, and the effects of perturbations to the parameter within the subnetwork are localized to the subnetwork (the law of localization). A buffering structure can be the origin of modularity in the regulation of cellular functions generated from CRNs. However, an efficient method to search for buffering structures in a large CRN has not yet been established. In this study, we prove the “inverse theorem” of the law of localization, which states that a certain subnetwork exhibiting a confined response range is always a buffering structure. In other words, we are able to identify buffering structures in terms of confined responses rather than the topological conditions. By leveraging this property, we develop an algorithm to enumerate all buffering structures for a given network by calculating responses. Additionally, we show that the hierarchy of perturbed response patterns corresponds to that of buffering structures, and present a method to illustrate the hierarchy. Our method will be a powerful tool for understanding the regulation of cellular functions generated from CRNs. Published by the American Physical Society 2024

Deciphering complexity in Pd–catalyzed cross-couplings

Understanding complex reaction systems is critical in chemistry. While synthetic methods for selective formation of products are sought after, oftentimes it is the full reaction signature, i.e., complete profile of products/side-products, that informs mechanistic rationale and accelerates discovery chemistry. Here, we report a methodology using high-throughput experimentation and multivariate data analysis to examine the full signature of one of the most complicated chemical reactions catalyzed by palladium known in the chemical literature. A model Pd-catalyzed reaction was selected involving functionalization of 2-bromo-N-phenylbenzamide and multiple bond activation pathways. Principal component analysis, correspondence analysis and heatmaps with hierarchical clustering reveal the factors contributing to the variance in product distributions and show associations between solvents and reaction products. Using robust data from experiments performed with eight solvents, for four different reaction times at five different temperatures, we correlate side-products to a major dominant N-phenyl phenanthridinone product, and many other side products.

Development and evaluation of time-resolved rapid immunofluorescence test for detection of TSOL18 specific antibody in porcine cysticercosis infections

BackgroundPorcine cysticercosis, a serious zoonotic parasitic disease, is caused by the larvae of Taenia solium and has been acknowledged by the World Organization for Animal Health. The current detection methods of Cysticercus cellulosae cannot meet the needs of large-scale and rapid detection in the field. We hypothesized that the immunofluorescence chromatography test strip (ICS) for detecting Cysticercus cellulosae, according to optimization of a series of reaction systems was conducted, and sensitivity, specificity, and stability testing, and was finally compared with ELISA. This method utilizes Eu3+-labeled time-resolved fluorescent microspheres (TRFM) coupled with TSOL18 antigen to detect TSOL18 antibodies in infected pig sera.ResultsICS and autopsy have highly consistent diagnostic results (n = 133), as determined by Cohen’s κ analysis (κ = 0.925). And the results showed that the proposed ICS are high sensitivity (0.9459) with specificity (0.9792). The ICS was unable to detect positive samples of other parasites. It can be stored for at least six months at 4℃.ConclusionsIn summary, we established a TRFM-ICS method with higher sensitivity and specificity than indirect ELISA. Results obtained from serum samples can be read within 10 min, indicating a rapid, user-friendly test suitable for large-scale field detection.

Best Practices for Experiments and Reports in Photocatalytic Methane Conversion.

Efficiently converting methane into valuable chemicals via photocatalysis under mild condition represents a sustainable route to energy storage and value-added manufacture. Despite continued interest in this area, the achievements have been overshadowed by the absence of standardized protocols for conducting photocatalytic methane oxidation experiments as well as evaluating the corresponding performance. In this review, we present a structured solution aimed at addressing these challenges. Firstly, we introduce the norms underlying reactor design and outline various configurations in the gas-solid and gas-solid-liquid reaction systems. This discussion helps choosing the suitable reactors for methane conversion experiments. Subsequently, we offer a comprehensive step-by-step protocol applicable to diverse methane-conversion reactions. Emphasizing meticulous verification and accurate quantification of the products, this protocol highlights the significance of mitigating contamination sources and selecting appropriate detection methods. Lastly, we propose the standardized performance metrics crucial for evaluating photocatalytic methane conversion. By defining these metrics, the community could obtain the consensus of assessing the performance across different studies. Moving forward, the future of photocatalytic methane conversion necessitates further refinement of stringent experimental standards and evaluation criteria. Moreover, development of scalable reactor is essential to facilitate the transition from laboratory proof-of-concept to potentially industrial production.

Best Practices for Experiments and Reports in Photocatalytic Methane Conversion

AbstractEfficiently converting methane into valuable chemicals via photocatalysis under mild condition represents a sustainable route to energy storage and value‐added manufacture. Despite continued interest in this area, the achievements have been overshadowed by the absence of standardized protocols for conducting photocatalytic methane oxidation experiments as well as evaluating the corresponding performance. In this review, we present a structured solution aimed at addressing these challenges. Firstly, we introduce the norms underlying reactor design and outline various configurations in the gas–solid and gas–solid–liquid reaction systems. This discussion helps choosing the suitable reactors for methane conversion experiments. Subsequently, we offer a comprehensive step‐by‐step protocol applicable to diverse methane‐conversion reactions. Emphasizing meticulous verification and accurate quantification of the products, this protocol highlights the significance of mitigating contamination sources and selecting appropriate detection methods. Lastly, we propose the standardized performance metrics crucial for evaluating photocatalytic methane conversion. By defining these metrics, the community could obtain the consensus of assessing the performance across different studies. Moving forward, the future of photocatalytic methane conversion necessitates further refinement of stringent experimental standards and evaluation criteria. Moreover, development of scalable reactor is essential to facilitate the transition from laboratory proof‐of‐concept to potentially industrial production.

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.

Concealed fluorescent anti-counterfeiting paper prepared by loading perovskite and lead-metal-organic framework on cellulose fibers

Counterfeiting has caused great concern all over the world. What's more, the fluorescent materials play an important role in technological research and development for high-security. In this work, lead-metal-organic framework (Pb-MOF) and perovskite (MAPbBr3) were used in papers to achieving fluorescence counterfeiting. Pb-MOF, as the template or precursor of MAPbBr3, were in-situ generated on the surface of cellulose fibers (CFs) to preparing into hand sheets (Pb-MOF@CFs). Through the analysis of experimental results, it was found that ligands, reaction systems, addition sequences of drugs, time, etc. would affect the deposition of Pb-MOF on the surface of CFs. Using CH3NH3Br (MABr) as the anti-counterfeiting ink to write on Pb-MOF@CFs, the orange writing leaped across the paper, which caused by Pb in Pb-MOF chemically reacting with MABr forming MAPbBr3. The orange writing displayed green fluorescence under 365 nm ultraviolet lamp excitation. The orange writing with green fluorescence could be extinguished and reconstructed, which had promise for reuse. In addition, fluorescent security papers (MAPbBr3@Pb-MOFs@CFs) were prepared by immersing Pb-MOF@CFs in MABr solution. The fluorescence of MAPbBr3@Pb-MOFs@CFs opened when the surface of it was scraped under 365 nm ultraviolet lamp. This unique fluorescence property was very important in improving the security of products. Consequently, the ongoing research on perovskite and MOFs materials is of great significance.

The computational molecular technology for complex reaction systems: The Red Moon approach

The computational molecular technology for complex reaction systems: The Red Moon approach

Unveiling kinetics post Rate-Determining step in Brønsted Acid-Catalyzed reactions of Fructose: A strategy for 5-Hydroxymethylfurfural production from concentrated feedstock

The development of high-yielding catalytic systems is pivotal in biomass upgrading. However, the investigation of kinetics in these complex reaction systems is often highly challenging, especially when reactions leading to byproduct formation are obscured by a preceding, slow rate-determining step. In this work, we introduce a unique approach to kinetic analysis that enables the investigation of reactions occurring post rate-determining step. The technique was applied to the conversion of sugars to 5-hydroxymethylfurfural (HMF), an important platform molecule for sustainable chemical production. Screening experiments were carried out to identify a catalytic solvent system that achieves a balance between solvent stability, HMF yield, and cost-effectiveness. Our kinetic analysis on the identified system reveals that the fructose reactant undergoes a rate-determining dehydration step to form an unstable reactive intermediate. The post rate-determining step kinetics show multiple competitive reactions between the slow-forming unstable intermediate and other reactive species, such as the hexose reactants or the HMF product, ultimately lowering the HMF selectivity. The calculated relative activation energies of reactions post rate-determining step provide intuitive insights into the effects of temperature, co-existing reactive species, as well as the previously unexplained effect of feed concentration on HMF selectivity. Additionally, we propose a novel reaction strategy that significantly enhances HMF yield when compared to a traditional batch synthesis. Notably, a high HMF yield of 74 % was achieved with an extreme 55 wt% fructose loading on an aqueous basis (20 wt% loading on a total weight basis) in a low-boiling 80 wt% dioxane/water mixture using an HCl catalyst at 393 K.

Functional Equivalence and a Cover Relation for Reaction Systems

Functional Equivalence and a Cover Relation for Reaction Systems

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.

Photocatalytic coproduction of hydrogen peroxide and Aldehydic/Keto acid on carbon nitride

Photocatalytic H2O2 production is emerging as an alternative technology to contribute H2O2-based advanced oxidation applications. However, the present reaction systems rarely consider the selective oxidation of sacrificial agent along with oxygen reduction reaction. Herein, we design a reaction system by using hydroxycarboxylic acids as additives to boost photocatalytic H2O2 production. More importantly, hydroxycarboxylic acids could simultaneously be dehydrogenated into aldehydic/keto acids with high selectivity. Lactic acid as one of the typical hydroxycarboxylic acids reveals the feasibility of this hypothesis, delivering 6.56 mM/h of H2O2 generation along with > 70 % pyruvic acid selectivity. The universality of this reaction system is demonstrated by using other hydroxycarboxylic acids. This works sheds new light on coupling H2O2 generation with value-added chemicals production by mild photocatalytic approach.

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.