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"Kinetics"
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Correction: Growth and Nitrogen Uptake Kinetics in Cultured Prorocentrum donghaiense
[...]this work was supported by NOAA and NSF grants to MRM, and Natural Science Foundation of China (NSFC) (Grant Numbers 40776078, 40876074, 41176104, U1133003). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.”
Journal Article
Velocity-resolved kinetics of site-specific carbon monoxide oxidation on platinum surfaces
Catalysts are widely used to increase reaction rates. They function by stabilizing the transition state of the reaction at their active site, where the atomic arrangement ensures favourable interactions
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. However, mechanistic understanding is often limited when catalysts possess multiple active sites—such as sites associated with either the step edges or the close-packed terraces of inorganic nanoparticles
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–
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—with distinct activities that cannot be measured simultaneously. An example is the oxidation of carbon monoxide over platinum surfaces, one of the oldest and best studied heterogeneous reactions. In 1824, this reaction was recognized to be crucial for the function of the Davy safety lamp, and today it is used to optimize combustion, hydrogen production and fuel-cell operation
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,
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. The carbon dioxide products are formed in a bimodal kinetic energy distribution
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–
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; however, despite extensive study
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, it remains unclear whether this reflects the involvement of more than one reaction mechanism occurring at multiple active sites
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,
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. Here we show that the reaction rates at different active sites can be measured simultaneously, using molecular beams to controllably introduce reactants and slice ion imaging
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,
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to map the velocity vectors of the product molecules, which reflect the symmetry and the orientation of the active site
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. We use this velocity-resolved kinetics approach to map the oxidation rates of carbon monoxide at step edges and terrace sites on platinum surfaces, and find that the reaction proceeds through two distinct channels
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–
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: it is dominated at low temperatures by the more active step sites, and at high temperatures by the more abundant terrace sites. We expect our approach to be applicable to a wide range of heterogeneous reactions and to provide improved mechanistic understanding of the contribution of different active sites, which should be useful in the design of improved catalysts.
The catalytic oxidation of carbon monoxide over platinum proceeds through two distinct channels: it is dominated at low temperatures by the more active step sites and at high temperatures by the more abundant terrace sites of the platinum surface.
Journal Article
Standardized assays for determining the catalytic activity and kinetics of peroxidase-like nanozymes
Nanozymes are nanomaterials exhibiting intrinsic enzyme-like characteristics that have increasingly attracted attention, owing to their high catalytic activity, low cost and high stability. This combination of properties has enabled a broad spectrum of applications, ranging from biological detection assays to disease diagnosis and biomedicine development. Since the intrinsic peroxidase activity of Fe3O4 nanoparticles (NPs) was first reported in 2007, >40 types of nanozymes have been reported that possess peroxidase-, oxidase-, haloperoxidase- or superoxide dismutase–like catalytic activities. Given the complex interdependence of the physicochemical properties and catalytic characteristics of nanozymes, it is important to establish a standard by which the catalytic activities and kinetics of various nanozymes can be quantitatively compared and that will benefit the development of nanozyme-based detection and diagnostic technologies. Here, we first present a protocol for measuring and defining the catalytic activity units and kinetics for peroxidase nanozymes, the most widely used type of nanozyme. In addition, we describe the detailed experimental procedures for a typical nanozyme strip–based biological detection test and demonstrate that nanozyme-based detection is repeatable and reliable when guided by the presented nanozyme catalytic standard. The catalytic activity and kinetics assays for a nanozyme can be performed within 4 h.
Journal Article
DNA as a universal substrate for chemical kinetics
Molecular programming aims to systematically engineer molecular and chemical systems of autonomous function and ever-increasing complexity. A key goal is to develop embedded control circuitry within a chemical system to direct molecular events. Here we show that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of arbitrary systems of coupled chemical reactions. By using strand displacement reactions as a primitive, we construct reaction cascades with effectively unimolecular and bimolecular kinetics. Our construction allows individual reactions to be coupled in arbitrary ways such that reactants can participate in multiple reactions simultaneously, reproducing the desired dynamical properties. Thus arbitrary systems of chemical equations can be compiled into real chemical systems. We illustrate our method on the Lotka-Volterra oscillator, a limit-cycle oscillator, a chaotic system, and systems implementing feedback digital logic and algorithmic behavior.
Journal Article
Bridging Disciplines in Enzyme Kinetics: Understanding Steady-State, Transient-State and Performance Parameters
Enzyme kinetics is fundamental across diverse fields—from enzymology and medicine to biocatalysis and metabolic engineering. Analyses of enzyme kinetics provide insights into catalytic rates, substrate affinities, inhibition patterns, productivities and mechanistic pathways, which are critical for areas such as drug development, industrial biocatalysis and mechanistic enzymology. However, each research field emphasizes different types of kinetic parameters, leading to challenges in establishing a common ground for understanding and interpreting enzyme properties. This review covers interpretation of enzyme kinetic parameters under three main categories—steady-state, transient-state and performance metrics—in a descriptive way and discusses their relevance with respect to different scientific and applied fields that investigate and utilize enzymes. By comparatively defining key kinetic and thermodynamic parameters, the review aims to help researchers interpret and report enzyme behavior more effectively, bridging gaps across interdisciplinary fields.
Journal Article
Optimizing the standardized assays for determining the catalytic activity and kinetics of peroxidase-like nanozymes
Nanozymes are nanomaterials with enzyme-like catalytic properties. They are attractive reagents because they do not have the same limitations of natural enzymes (e.g., high cost, low stability and difficult storage). To test, optimize and compare nanozymes, it is important to establish fundamental principles and systematic standards to fully characterize their catalytic performance. Our 2018 protocol describes how to characterize the catalytic activity and kinetics of peroxidase nanozymes, the most widely used type of nanozyme. This approach was based on Michaelis–Menten enzyme kinetics and is now updated to take into account the unique physicochemical properties of nanomaterials that determine the catalytic kinetics of nanozymes. The updated procedure describes how to determine the number of active sites as well as other physicochemical properties such as surface area, shape and size. It also outlines how to calculate the hydroxyl adsorption energy from the crystal structure using the density functional theory method. The calculations now incorporate these measurements and computations to better characterize the catalytic kinetics of peroxidase nanozymes that have different shapes, sizes and compositions. This updated protocol better describes the catalytic performance of nanozymes and benefits the development of nanozyme research since further nanozyme development requires precise control of activity by engineering the electronic, geometric structure and atomic configuration of the catalytic sites of nanozymes. The characterization of the catalytic activity of peroxidase nanozymes and the evaluation of their kinetics can be performed in 4 h. The procedure is suitable for users with expertise in nano- and materials technology.
Key points
Nanozymes are nanoparticles designed to have catalytic properties similar to those of natural enzymes. Design and optimization of nanozyme properties require analytical methods to characterize their physical properties as well as their catalytic activity and kinetics.
This is an updated protocol for measuring catalytic behavior that incorporates data from measured physical properties unique to each nanoparticle as well as density functional theory calculations into the Michaelis–Menten approach.
Developing optimal nanozymes requires standardized methods for measuring their catalytic activity and reaction kinetics. This protocol integrates enzyme based Michaelis–Menten kinetics with measured physical properties and computational methods.
Journal Article
Modified Arrhenius Equation in Materials Science, Chemistry and Biology
The Arrhenius plot (logarithmic plot vs. inverse temperature) is represented by a straight line if the Arrhenius equation holds. A curved Arrhenius plot (mostly concave) is usually described phenomenologically, often using polynomials of T or 1/T. Many modifications of the Arrhenius equation based on different models have also been published, which fit the experimental data better or worse. This paper proposes two solutions for the concave-curved Arrhenius plot. The first is based on consecutive A→B→C reaction with rate constants k1 ≪ k2 at higher temperatures and k1 ≫ k2 (or at least k1 > k2) at lower temperatures. The second is based on the substitution of the temperature T the by temperature difference T − T0 in the Arrhenius equation, where T0 is the maximum temperature at which the Arrheniusprocess under study does not yet occur.
Journal Article