2. Making things happen—catalysis

2020 ◽  
pp. 12-26
Author(s):  
Paul Engel
Keyword(s):  
Chemical Reactions ◽  
Chemical Reaction ◽  
Living Systems ◽  
Chemical Catalysis

‘Making things happen—catalysis’ examines chemical catalysis, considering what makes a reaction go or not go and how enzymes catalyse particular chemical reactions. This process is not unique to living systems, although enzymes are both more potent and more selective than catalysts encountered elsewhere in chemistry. A catalyst is an agent that speeds up a chemical reaction but remains unchanged itself at the end of the process. Since a catalyst is not altered or used up, it can be used over and over again.

scholarly journals Protein dynamics and catalysis: the problems of transition state theory and the subtlety of dynamic control

2006 ◽  
Vol 361 (1472) ◽  
pp. 1433-1438 ◽  
Author(s):  
J.R.E.T Pineda ◽  
S.D Schwartz
Keyword(s):  
Lactate Dehydrogenase ◽  
Transition State ◽  
Protein Dynamics ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Condensed Phase ◽  
Transition State Theory ◽  
State Theory ◽  
Ongoing Research ◽  
Chemical Catalysis

This manuscript describes ongoing research on the nature of chemical reactions in enzymes. We will investigate how protein dynamics can couple to chemical reaction in an enzyme. We first investigate in some detail why transition state theory cannot fully describe the dynamics of chemical reactions catalysed by enzymes. We describe quantum theories of chemical reaction in condensed phase including studies of how the symmetry of coupled vibrational modes differentially affects reaction dynamics. We make reference to previous work in our group on a variety of condensed phase chemical reactions (liquid and crystalline) and a variety of enzymatically catalysed reactions including the reactions of lactate dehydrogenase and purine nucleoside phosphorylase. All the protein motions we have studied have been quite rapid. We will propose methods to find motions over a broad range of time-scales in enzymes that couple to chemical catalysis. We report recent findings which show that conformational fluctuations in lactate dehydrogenase can strongly affect its ability to catalyse reactions through protein motion, and that only a tiny minority of conformations appear to be catalytically competent.

Normal approximations for distributions arising in the stochastic approach to chemical reaction kinetics

1981 ◽  
Vol 18 (01) ◽  
pp. 263-267 ◽  
Author(s):  
F. D. J. Dunstan ◽  
J. F. Reynolds
Keyword(s):  
Reaction Kinetics ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Stochastic Approach ◽  
Algebraic Functions ◽  
Chemical Reaction Kinetics ◽  
Normal Approximations ◽  
Formal Solutions

Earlier stochastic analyses of chemical reactions have provided formal solutions which are unsuitable for most purposes in that they are expressed in terms of complex algebraic functions. Normal approximations are derived here for solutions to a variety of reactions. Using these, it is possible to investigate the level at which the classical deterministic solutions become inadequate. This is important in fields such as radioimmunoassay.

scholarly journals Mapping the Space of Chemical Reactions using Attention-Based Neural Networks

2020 ◽  
Author(s):  
Philippe Schwaller ◽  
Daniel Probst ◽  
Alain C. Vaucher ◽  
Vishnu H Nair ◽  
David Kreutter ◽  
...  
Keyword(s):  
Neural Networks ◽  
Reaction Center ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Classification Accuracy ◽  
Similarity Searching ◽  
Reaction Space ◽  
Fine Grained ◽  
Visual Clustering ◽  
Better Than

<div><div><div><p>Organic reactions are usually assigned to classes grouping reactions with similar reagents and mechanisms. Reaction classes facilitate communication of complex concepts and efficient navigation through chemical reaction space. However, the classification process is a tedious task, requiring the identification of the corresponding reaction class template via annotation of the number of molecules in the reactions, the reaction center and the distinction between reactants and reagents. In this work, we show that transformer-based models can infer reaction classes from non-annotated, simple text-based representations of chemical reactions. Our best model reaches a classification accuracy of 98.2%. We also show that the learned representations can be used as reaction fingerprints which capture fine-grained differences between reaction classes better than traditional reaction fingerprints. The unprecedented insights into chemical reaction space enabled by our learned fingerprints is illustrated by an interactive reaction atlas providing visual clustering and similarity searching. </p><p><br></p><p>Code: https://github.com/rxn4chemistry/rxnfp</p><p>Tutorials: https://rxn4chemistry.github.io/rxnfp/</p><p>Interactive reaction atlas: https://rxn4chemistry.github.io/rxnfp//tmaps/tmap_ft_10k.html</p></div></div></div>

scholarly journals Mass transfer with complex reversible chemical reactions—I. Single reversible chemical reaction

1989 ◽  
Vol 44 (10) ◽  
pp. 2295-2310 ◽  
Author(s):  
G.F. Versteeg ◽  
J.A.M. Kuipers ◽  
F.P.H. Van Beckum ◽  
W.P.M. Van Swaaij
Keyword(s):  
Mass Transfer ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Reversible Chemical Reaction

Kinetic study of key species and reactions of atmospheric pressure pulsed corona discharge in humid air

2021 ◽  
Author(s):  
Yongkang Peng ◽  
Xiaoyue Chen ◽  
Yeqiang Deng ◽  
Lan Lei ◽  
Zhan Haoyu ◽  
...  
Keyword(s):  
Chemical Reactions ◽  
Chemical Reaction ◽  
Atmospheric Pressure ◽  
Discharge Plasma ◽  
Reaction Rates ◽  
Global Model ◽  
Discharge Process ◽  
Humid Air ◽  
Pressure Discharge ◽  
Atmospheric Pressure Discharge

Abstract The traditional corona discharge fluid model considers only electrons, positive and negative ions, and the discharge parameters are determined using the simplified weighting method involving the partial pressure ratio. Atmospheric pressure discharge plasma in humid air involves three main neutral gas molecule types: N2, O2, and H2O(g). However, in these conditions, the discharge process involves many types of particles and chemical reactions, and the charge and substance transfer processes are complex. At present, the databases of plasma chemical reaction equations are still expanding based on scholarly research. In this study, we examined the key particles and chemical reactions that substantially influence plasma characteristics. In summarizing the chemical reaction model for the discharge process of N2–O2–H2O(g) mixed gases, 65 particle types and 673 chemical reactions were investigated. On this basis, a global model of atmospheric pressure humid air discharge plasma was developed, with a focus on the variation of charged particles densities and chemical reaction rates with time under the excitation of a 0–200 Td pulsed electric field. Particles with a density greater than 1% of the electron density were classified as key particles. For such particles, the top ranking generation or consumption reactions (i.e., where the sum of their rates was greater than 95% of the total rate of the generation or consumption reactions) were classified as key chemical reactions On the basis of the key particles and reactions identified, a simplified global model was derived. A comparison of the global model with the simplified global model in terms of the model parameters, particle densities, reaction rates (with time), and calculation efficiencies demonstrated that both models can adequately identify the key particles and chemical reactions reflecting the chemical process of atmospheric pressure discharge plasma in humid air. Thus, by analyzing the key particles and chemical reaction pathways, the charge and substance transfer mechanism of atmospheric pressure pulse discharge plasma in humid air was revealed, and the mechanism underlying water vapor molecules’ influence on atmospheric pressure air discharge was elucidated.

Chemical Reaction Kinetics in Solution

2004 ◽  
Author(s):  
W. Ronald Fawcett
Keyword(s):  
Reaction Kinetics ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Physical Property ◽  
Theoretical Description ◽  
Time Range ◽  
Chemical Changes ◽  
Elementary Reactions ◽  
Chemical Reaction Kinetics ◽  
Liquid Solutions

The kinetics of chemical reactions were first studied in liquid solutions. These experiments involved mixing two liquids and following the change in the concentration of a reactant or product with time. The concentration was monitored by removing a small sample of the solution and stopping the reaction, for example, by rapidly lowering the temperature, or by following a physical property of the system in situ, for example, its color. Although the experiments were initially limited to slow reactions, they established the basic laws governing the rate at which chemical changes occur. The variables considered included the concentrations of the reactants and of the products, the temperature, and the pressure. Thus, the reacting system was examined using the variables normally considered for a system at equilibrium. Most reactions were found to be complex, that is, to be made up of several elementary steps which involved one or two reactants. As the fundamental concepts of chemical kinetics developed, there was a strong interest in studying chemical reactions in the gas phase. At low pressures the reacting molecules in a gaseous solution are far from one another, and the theoretical description of equilibrium thermodynamic properties was well developed. Thus, the kinetic theory of gases and collision processes was applied first to construct a model for chemical reaction kinetics. This was followed by transition state theory and a more detailed understanding of elementary reactions on the basis of quantum mechanics. Eventually, these concepts were applied to reactions in liquid solutions with consideration of the role of the non-reacting medium, that is, the solvent. An important turning point in reaction kinetics was the development of experimental techniques for studying fast reactions in solution. The first of these was based on flow techniques and extended the time range over which chemical changes could be observed from a few seconds down to a few milliseconds. This was followed by the development of a variety of relaxation techniques, including the temperature jump, pressure jump, and electrical field jump methods. In this way, the time for experimental observation was extended below the nanosecond range.

scholarly journals VIII. On the apparent change in weight during chemical reaction

1913 ◽  
Vol 212 (484-496) ◽  
pp. 227-260
Keyword(s):  
Chemical Reactions ◽  
Chemical Reaction ◽  
Experimental Work ◽  
Total Mass ◽  
Apparent Change ◽  
Chemically Reacting

During the year 1890 the late Prof. Landolt inaugurated his prolonged researches upon the apparent alteration in the total mass of chemically reacting substances. From the time of its inception until it was brought to a conclusion in 1907, the experimental work was freely varied both as regards the conditions and the nature of the chemical reactions involved. The methods and precautions adopted, together with the final results obtained, are to be found embodied and set forth in detail in Landolt’s important memoir, “Über die Erhaltung der Masse hei Chemischen Umsetzungen.”* Before proceeding to deal with my own investigations in this field of research, it may not be inappropriate first very briefly to recall the chief features of Landolt’s work and conclusions.

Chemical Reactions in Rubber Compounds. I. Reactions between Pine Tar and Litharge

1929 ◽  
Vol 2 (4) ◽  
pp. 567-570
Author(s):  
W. H. Reece
Keyword(s):  
Chemical Reactions ◽  
Chemical Reaction ◽  
Rubber Compounds

Abstract The results of the experiments indicate that when litharge and pine tar are present in a rubber mixing, a chemical reaction takes place which does not appear to differ from that which occurs between litharge and pine tar in the absence of rubber. The figures obtained are also in agreement with the assumption that the reaction is one in which the acids present in the pine tar react with the litharge to form soaps. It has been shown that the pine tar contained 46.9 per cent of acids which reacted with litharge to produce 2.45 per cent of water.

Mechanism of Rubber Vulcanization with Sulfur

1938 ◽  
Vol 11 (1) ◽  
pp. 107-130
Author(s):  
W. K. Lewis ◽  
Lombard Squires ◽  
Robert D. Nutting
Keyword(s):  
Natural Rubber ◽  
Temperature Coefficient ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Reaction Rate ◽  
Complex Behavior ◽  
Double Bonds ◽  
Irreversible Reaction ◽  
Sulfur Addition

Abstract THAT vulcanization of rubber with sulfur always involves a chemical reaction consisting in the addition of sulfur to the double bonds of the rubber molecule has been conclusively established (18, 28). The facts indicate that this addition of sulfur to rubber is an irreversible reaction (31). The temperature coefficient of the reaction is high, increasing about 2.65 fold per 10° C. at ordinary curing temperatures (31). Furthermore, the reaction is apparently exothermic (4, 24). It is noteworthy that catalysts are apparently necessary, since synthetic rubbers prepared from pure materials add sulfur slowly, if at all. The proteins and perhaps the resins in natural rubber undoubtedly serve as accelerators. The curves for combined sulfur vs. time of cure for typical mixes are shown in Figures 1 and 2. Figure 1 is taken from the data of Kratz and Flower (16); the composition and temperature of cure for this mix are shown in Cranor's Table I (9). Figure 2, curve 1, is from Table I of Eaton and Day (10), and curve 2 from data obtained in this laboratory (27, Table I). Superficial inspection of these curves shows extraordinary divergence of type. Figure 1 is a typical fadeaway curve, characteristic of most chemical reactions, where the reaction rate decreases with decreasing concentration of the reacting materials. Curve 1, Figure 2, is an entirely different type, where the rate of sulfur addition is constant until nearly 70 per cent of the initial sulfur has reacted. Curve 2, Figure 2, shows even more complex behavior. Again the rate is constant in the initial portions of the cure. However, following this period, the rate increases markedly but later falls off, approaching zero, to give an S-shaped eurve.

scholarly journals Grip on complexity in chemical reaction networks

2017 ◽  
Vol 13 ◽  
pp. 1486-1497 ◽  
Author(s):  
Albert S Y Wong ◽  
Wilhelm T S Huck
Keyword(s):  
Complex Networks ◽  
Chemical Reaction ◽  
Biological Networks ◽  
Chemical Reaction Networks ◽  
Living Systems ◽  
Reaction Networks ◽  
Natural Systems ◽  
Systems Chemistry ◽  
Single Chemical ◽  
And Control

A new discipline of “systems chemistry” is emerging, which aims to capture the complexity observed in natural systems within a synthetic chemical framework. Living systems rely on complex networks of chemical reactions to control the concentration of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. To truly understand how living systems function, we need a complete understanding of how chemical reaction networks (CRNs) create function. We propose the development of a bottom-up approach to design and construct CRNs where we can follow the influence of single chemical entities on the properties of the network as a whole. Ultimately, this approach should allow us to not only understand such complex networks but also to guide and control their behavior.

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