SciCombinator

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Concept: Chemical kinetics

147

A chemiluminescence (CL) amplification platform based on HCC/Lucigenin&GOx (HLG) film was developed. Hollow structural calcium carbonate (HCC) particles were used as alternative materials for carrying both enzyme and CL reagent. The model enzyme (GOx), immobilized in confined space of HCC particles, exhibited an improved biocatalysis. The Michaelis constant (Km) and the enzymatic rate constant (kcat) were determined to be 0.209 μM and 2.21 s(-1), respectively, which are much better than those of either free GOx in aqueous solution or the GOx immobilized on common nanomaterials. Based on the HLG platform, CL signal was effectively amplified and visualized after adding trace glucose, which could be attributed to the HCC particles' high biocompatibility, large specific surface area, attractive interfacial properties and efficient interaction with analyses. The visual CL bioplatform showed an excellent performance with high selectivity, wide linear range and low detection limit for sensing trace glucose. Because it eliminates the need of complicated assembly procedure and enables visualization by the naked eye, the sensitive and selective CL bioplatform would provide wide potential applications in disease diagnosis and food safety.

Concepts: Chemical kinetics, Glucose, Calcium carbonate, Glucose meter, Signal transduction, Specific surface area, Catalysis, Enzyme

80

Sensing reaction mechanism is crucial for enhancing the sensing performance of semiconductor-based sensing materials. Here we show a new strategy to enhancing sensing performance of SnO2 nanocrystals by increasing the density of unsaturated Sn atoms with dangling bonds at the SnO2 surface through hydrogenation. A concept of the surface unsaturated Sn atoms serving as active sites for the sensing reaction is proposed, and the sensing mechanism is described in detail at atomic and molecule level for the first time. Sensing properties of other metal oxide sensors and catalytic activity of other catalysts may be improved by using the hydrogenation strategy. The concept of the surface unsaturated metal atoms serving as active sites may be very useful for understanding the sensing and catalytic reaction mechanisms and designing advanced sensing sensors, catalysts and photoelectronic devices.

Concepts: Chemical kinetics, Oxygen, Solid, Nitrogen, Chemistry, Hydrogenation, Catalysis, Hydrogen

30

A possible mechanistic pathway related to an enzyme-catalyzed [4+2] cycloaddition reac-tion was studied by theoretical calculations at density functional (B3LYP, O3LYP, M062X) and semiempirical levels (PM6-DH2, PM6) performed on a model system. The calculations were carried out for the key [4+2] cycloaddition step considering enzyme-catalyzed biosynthesis of Spinosyn A in a model reaction, where a reliable example of a biological Diels-Alder reaction was reported experimentally. In the present study it was demonstrated that the [4+2] cycloaddition reaction may benefit from moving along the energetically balanced reaction coordinate, which enabled the catalytic rate enhancement of the [4+2] cycloaddition pathway involving a single transition state. Modeling of such a system with coordination of three amino acids indicated a reliable decrease of activation energy by ~18.0 kcal/mol as compared to a non-catalytic transformation.

Concepts: Amine, Chemical kinetics, Computational chemistry, Model, Chemical reaction, Catalysis, Amino acid, Transition state

30

Hierarchical zeolites are a class of microporous catalysts and adsorbents that also contain mesopores, which allow for fast transport of bulky molecules and thereby enable improved performance in petrochemical and biomass processing. We used repetitive branching during one-step hydrothermal crystal growth to synthesize a new hierarchical zeolite made of orthogonally connected microporous nanosheets. The nanosheets are 2 nanometers thick and contain a network of 0.5-nanometer micropores. The house-of-cards arrangement of the nanosheets creates a permanent network of 2- to 7-nanometer mesopores, which, along with the high external surface area and reduced micropore diffusion length, account for higher reaction rates for bulky molecules relative to those of other mesoporous and conventional MFI zeolites.

Concepts: Mesoporous material, Synthesis, Zeolite, Chemical engineering, Chemical kinetics, Petroleum, Adsorption, Chemical reaction

28

The conversion of the prion protein (PrP) into scrapie PrP (PrP(Sc)) is a central event in prion diseases. Several molecules work as cofactors in the conversion process, including glycosaminoglycans (GAGs). GAGs exhibit a paradoxical effect, as they convert PrP into protease-resistant PrP (PrP-res) but also exert protective activity. We compared the stability and aggregation propensity of PrP and the heparin-PrP complex through the application of different in vitro aggregation approaches, including real-time quaking-induced conversion (RT-QuIC). Transmissible spongiform encephalopathy-associated forms from mouse and hamster brain homogenates were used to seed RT-QuIC-induced fibrillization. In our study, interaction between heparin and cellular PrP (PrP©) increased thermal PrP stability, leading to an 8-fold decrease in temperature-induced aggregation. The interaction of low-molecular-weight heparin (LMWHep) with the PrP N- or C-terminal domain affected not only the extent of PrP fibrillization but also its kinetics, lowering the reaction rate constant from 1.04 to 0.29 s(-1) and increasing the lag phase from 12 to 19 h in RT-QuIC experiments. Our findings explain the protective effect of heparin in different models of prion and prion-like neurodegenerative diseases and establish the groundwork for the development of therapeutic strategies based on GAGs.-Vieira, T. C. R. G., Cordeiro, Y., Caughey, B., Silva, J. L. Heparin binding confers prion stability and impairs its aggregation.

Concepts: Fatal familial insomnia, Chemical kinetics, Heparin, Protein, Prion, Reaction rate, Bovine spongiform encephalopathy, Transmissible spongiform encephalopathy

28

N-Nitroso compounds are a versatile class of organic structures that allow expedient access to a diversity of synthetically useful architectures through demonstrated reactivities. We report herein the development of a Rh(III)-catalyzed N-nitroso-directed methodology for the ortho-olefination of arenes. The heightened reactivity endowed by the N-nitroso group translates to mild reaction conditions, high reaction yields, and synthetic compatibility of otherwise elusive substrates (e.g., an unactivated olefin, 1-octene). Comprehensive mechanistic studies on the electronic effect, deuterium exchange, kinetic isotope effect, kinetic profile, and numerous Rh(III) complexes have established [RhCp*]2+ as the catalyst resting state, electrophilic C-H activation as the turnover-limiting step, and a five-membered rhodacycle as a catalytically competent intermediate. The ability to elaborate the N-nitroso moiety to an amine functionality provides a seminal example of the innumerable synthetic possibilities offered by this transformable directing group.

Concepts: Alkene, Physical organic chemistry, Chemical kinetics, Nitro compound, Isotope, Deuterium, Functional group, Kinetic isotope effect

28

Ferrate [Fe(VI); FeO(4)(2-)] is an emerging oxidizing agent capable of controlling chemical and microbial water contaminants. Here, inactivation of MS2 coliphage by Fe(VI) was examined. The inactivation kinetics observed in individual batch experiments was well described by a Chick-Watson model with first-order dependences on disinfectant and infective phage concentrations. The inactivation rate constant k(i) at a Fe(VI) dose of 1.23 mgFe/L (pH 7.0, 25 °C) was 2.27(±0.05) L/(mgFe × min), corresponding to 99.99% inactivation at a Ct of ∼4 (mgFe × min)/L. Measured k(i) values were found to increase with increasing applied Fe(VI) dose (0.56-2.24 mgFe/L), increasing temperature (5-30 °C), and decreasing pH conditions (pH 6-11). The Fe(VI) dose effect suggested that an unidentified Fe byproduct also contributed to inactivation. Temperature dependence was characterized by an activation energy of 39(±6) kJ mol(-1), and k(i) increased >50-fold when pH decreased from 11 to 6. The pH effect was quantitatively described by parallel reactions with HFeO(4)(-) and FeO(4)(2-). Mass spectrometry and qRT-PCR analyses demonstrated that both capsid protein and genome damage increased with the extent of inactivation, suggesting that both may contribute to phage inactivation. Capsid protein damage, localized in the two regions containing oxidant-sensitive cysteine residues, and protein cleavage in one of the two regions may facilitate genome damage by increasing Fe(VI) access to the interior of the virion.

Concepts: Chemical kinetics, Chemical reaction, Walter Fiers, Enzyme, RNA, Bacteriophage MS2, Bacteriophage, Microbiology

28

Mathematical modeling is used as a Systems Biology tool to answer biological questions, and more precisely, to validate a network that describes biological observations and predict the effect of perturbations. This article presents an algorithm for modeling biological networks in a discrete framework with continuous time. BACKGROUND: There exist two major types of mathematical modeling approaches: (1) quantitative modeling, representing various chemical species concentrations by real numbers, mainly based on differential equations and chemical kinetics formalism; (2) and qualitative modeling, representing chemical species concentrations or activities by a finite set of discrete values. Both approaches answer particular (and often different) biological questions. Qualitative modeling approach permits a simple and less detailed description of the biological systems, efficiently describes stable state identification but remains inconvenient in describing the transient kinetics leading to these states. In this context, time is represented by discrete steps. Quantitative modeling, on the other hand, can describe more accurately the dynamical behavior of biological processes as it follows the evolution of concentration or activities of chemical species as a function of time, but requires an important amount of information on the parameters difficult to find in the literature. RESULTS: Here, we propose a modeling framework based on a qualitative approach that is intrinsically continuous in time. The algorithm presented in this article fills the gap between qualitative and quantitative modeling. It is based on continuous time Markov process applied on a Boolean state space. In order to describe the temporal evolution of the biological process we wish to model, we explicitly specify the transition rates for each node. For that purpose, we built a language that can be seen as a generalization of Boolean equations. Mathematically, this approach can be translated in a set of ordinary differential equations on probability distributions. We developed a C++ software, MaBoSS, that is able to simulate such a system by applying Kinetic Monte-Carlo (or Gillespie algorithm) on the Boolean state space. This software, parallelized and optimized, computes the temporal evolution of probability distributions and estimates stationary distributions. CONCLUSIONS: Applications of the Boolean Kinetic Monte-Carlo are demonstrated for three qualitative models: a toy model, a published model of p53/Mdm2 interaction and a published model of the mammalian cell cycle. Our approach allows to describe kinetic phenomena which were difficult to handle in the original models. In particular, transient effects are represented by time dependent probability distributions, interpretable in terms of cell populations.

Concepts: Model, Quantitative research, Markov chain, Continuous-time Markov process, Chemical kinetics, Differential equation, Qualitative research, Mathematics

27

The reaction of OH with dimethyl ether (CH3OCH3) has been studied from 195 - 850 K using laser flash photolysis coupled to laser induced fluorescence detection of OH radicals. The rate coefficient from this work can be parameterised by the modified Arrhenius expression k = (1.23 ± 0.46) × 10-12 (T/298)2.05±0.23 exp((257 ± 107)/T) cm3 molecule-1 s-1. Including other recent literature data (923 - 1423 K) gives a modified Arrhenius expression of k1 = (1.54 ± 0.48) × 10-12 (T/298K)1.89±0.16 exp((184 ± 112)/T) cm3 molecule-1 s-1 over the range 195 - 1423 K. Various isotopomeric combinations of the reaction have also been investigated with deuteration of dimethyl ether leading to a normal isotope effect. Deuteration of the hydroxyl group leads to a small inverse isotope effect. To gain an insight into the reaction mechanisms and to support the experimental work, theoretical studies have also been undertaken calculating the energies and structures of the transition states and complexes using high level ab initio methods. The calculations also identify pre and post-reaction complexes. The pre reaction complex (binding energy of ~22 kJ mol-1) may contribute to the kinetics of the reaction, especially at low temperatures, but there is no direct evidence of this occurring under our experimental conditions, although the Arrhenius plot for the rate coefficient shows considerable curvature. The experimental data have been modelled using the recently developed MESMER (Master Equation Solver for Multi Energy Well Reactions) code giving good agreement. The calculations qualitatively reproduce the observed isotope effects closely above ~600 K but overestimate them at low temperatures, which may derive from an inadequate treatment of tunnelling and of an enhanced role of an outer transition state leading to the pre-reaction complex.

Concepts: Fluorescence, Hydroxide, Ab initio, Mathematics, Transition state, Dimethyl ether, Reaction rate, Chemical kinetics

27

Formaldehyde (HCHO) is a major indoor pollutant and long-term exposure to HCHO may cause health problems such as nasal tumors and skin irritation. Photocatalytic oxidation is considered as the most promising strategy for the decomposition of HCHO. Herein, for the first time, a direct g-C3N4-TiO2 Z-scheme photocatalyst without an electron mediator was prepared by a facile calcination route utilizing affordable P25 and urea as the feedstocks. Photocatalytic activities of the as-prepared samples were evaluated by the photocatalytic oxidation decomposition of HCHO in air. It was shown that the photocatalytic activity of the prepared Z-scheme photocatalysts was highly dependent on the g-C3N4 content. At the optimal g-C3N4 content (sample U100 in this study), the apparent reaction rate constant was 7.36 × 10(-2) min(-1) for HCHO decomposition, which exceeded that of pure P25 (3.53 × 10(-2) min(-1)) by a factor of 2.1. The enhanced photocatalytic activity could be ascribed to the formation of a g-C3N4-TiO2 Z-scheme photocatalyst, which results in the efficient space separation of photo-induced charge carriers. Considering the ease of the preparation method, this work will provide new insights into the design of high-performance Z-scheme photocatalysts for indoor air purification.

Concepts: Rate equation, Irritation, Nitrogen, Photocatalytic water splitting, Reaction rate constant, Chemical kinetics, Reaction rate, Photocatalysis