Introduction

2006 ◽  
Author(s):  
John Ross ◽  
Igor Schreiber ◽  
Marcel O. Vlad
Keyword(s):  
Reaction Mechanism ◽  
Chemical Kinetics ◽  
Chemical Engineering ◽  
Reaction Pathway ◽  
Reaction System ◽  
Chemical Species ◽  
Pulse Method ◽  
Elementary Reaction ◽  
Elementary Reactions ◽  
Arbitrary Strength

Chemical kinetics as a science has existed for more than a century. It deals with the rates of reactions and the details of how a given reaction proceeds from reactants to products. In a chemical system with many chemical species, there are several questions to be asked: What species react with what other species? In what temporal order? With what catalysts? And with what results? The answers constitute the macroscopic reaction mechanism. The process can be described macroscopically by listing the reactants, intermediates, products, and all the elementary reactions and catalysts in the reaction system. The present book is a treatise and text on the determination of complex reaction mechanisms in chemistry and in chemical reaction systems that occur in chemical engineering, biochemistry, biology, biotechnology, and genomics. A basic knowledge of chemical kinetics is assumed. Several approaches are suggested for the deduction of information on the causal chemical connectivity of the species, on the elementary reactions among the species, and on the sequence of the elementary reactions that constitute the reaction pathway and the reaction mechanism. Chemical reactions occur by the collisions of molecules, and such an event is called an elementary reaction for specified reactant and product molecules. A balanced stoichiometric equation for an elementary reaction yields the number of each type of molecule according to conservation of atoms, mass, and charge. Figure 1.1 shows a relatively simple reaction mechanism for the decomposition of ozone by light, postulated to occur in a series of three elementary steps. (The details of collisions of molecules and bond rearrangements are not discussed.) All approaches are based on the measurements of the concentrations of chemical species in the whole reaction system, not on parts, as has been the practice. One approach is called the pulse method, in which a pulse of concentration of one or more species of arbitrary strength is applied to a reacting system and the responses of as many species as possible are measured. From these responses causal chemical connectivities may be inferred. The basic theory is explained, demonstrated on a model mechanism, and tested in an experiment on a part of glycolysis.

Determination of Complex Reaction Mechanisms

2006 ◽  
Author(s):  
John Ross ◽  
Igor Schreiber ◽  
Marcel O. Vlad
Keyword(s):  
Reaction Mechanism ◽  
Reaction Mechanisms ◽  
Reaction Pathway ◽  
Chemical Species ◽  
Rate Coefficients ◽  
Chemical System ◽  
Evolutionary Development ◽  
Complex Reaction ◽  
Oscillatory Reactions

In a chemical system with many chemical species several questions can be asked: what species react with other species: in what temporal order: and with what results? These questions have been asked for over one hundred years about simple and complex chemical systems, and the answers constitute the macroscopic reaction mechanism. In Determination of Complex Reaction Mechanisms authors John Ross, Igor Schreiber, and Marcel Vlad present several systematic approaches for obtaining information on the causal connectivity of chemical species, on correlations of chemical species, on the reaction pathway, and on the reaction mechanism. Basic pulse theory is demonstrated and tested in an experiment on glycolysis. In a second approach, measurements on time series of concentrations are used to construct correlation functions and a theory is developed which shows that from these functions information may be inferred on the reaction pathway, the reaction mechanism, and the centers of control in that mechanism. A third approach is based on application of genetic algorithm methods to the study of the evolutionary development of a reaction mechanism, to the attainment given goals in a mechanism, and to the determination of a reaction mechanism and rate coefficients by comparison with experiment. Responses of non-linear systems to pulses or other perturbations are analyzed, and mechanisms of oscillatory reactions are presented in detail. The concluding chapters give an introduction to bioinformatics and statistical methods for determining reaction mechanisms.

Experimental Test and Applications of Correlation Metric Construction

2006 ◽  
Author(s):  
John Ross ◽  
Igor Schreiber ◽  
Marcel O. Vlad
Keyword(s):  
Time Series ◽  
Steady State ◽  
Reaction Mechanism ◽  
Experimental Test ◽  
Reaction Pathway ◽  
Chemical Species ◽  
Reaction Network ◽  
Sampling Period ◽  
The Matrix ◽  
Time Lagged

In this chapter we present an experimental test case of the deduction of a reaction pathway and mechanism by means of correlation metric construction from time-series measurements of the concentrations of chemical species. We choose as the system an enzymatic reaction network, the initial steps of glycolysis. Glycolysis is central in intermediary metabolism and has a high degree of regulation. The reaction pathway has been well studied and thus it is a good test for the theory. Further, the reaction mechanism of this part of glycolysis has been modeled extensively. The quantity and precision of the measurements reported here are sufficient to determine the matrix of correlation functions and, from this, a reaction pathway that is qualitatively consistent with the reaction mechanism established previously. The existence of unmeasured species did not compromise the analysis. The quantity and precision of the data were not excessive, and thus we expect the method to be generally applicable. This CMC experiment was carried out in a continuous-flow stirred-tank reactor (CSTR). The reaction network considered consists of eight enzymes, which catalyze the conversion of glucose into dihydroxyacetone phosphate and glyceraldehyde phosphate. The enzymes were confined to the reactor by an ultrafiltration membrane at the top of the reactor. The membrane was permeable to all low molecular weight species. The inputs are (1) a reaction buffer, which provides starting material for the reaction network to process, maintains pH and pMg, and contains any other species that act as constant constraints on the system dynamics, and (2) a set of “control species” (at least one), whose input concentrations are changed randomly every sampling period over the course of the experiment. The sampling period is chosen such that the system almost, but not quite, relaxes to a chosen nonequilibrium steady state. The system is kept near enough to its steady state to minimize trending (caused by the relaxation) in the time series, but far enough from the steady state that the time-lagged autocorrelation functions for each species decay to zero over three to five sampling periods. This long decay is necessary if temporal ordering in the network is to be analyzed.

Lifetime and Transit Time Distributions and Response Experiments in Chemical Kinetics

2006 ◽  
Author(s):  
John Ross ◽  
Igor Schreiber ◽  
Marcel O. Vlad
Keyword(s):  
Reaction Mechanism ◽  
Stationary State ◽  
Linear Response ◽  
Reaction Pathway ◽  
Kinetic Equations ◽  
Chemical Species ◽  
Main Idea ◽  
Stable Stationary State ◽  
Probability Densities ◽  
Mathematical Techniques

We discussed some aspects of the responses of chemical systems, linear or nonlinear, to perturbations on several earlier occasions. The first was the responses of the chemical species in a reaction mechanism (a network) in a nonequilibrium stable stationary state to a pulse in concentration of one species. We referred to this approach as the “pulse method” (see chapter 5 for theory and chapter 6 for experiments). Second, we studied the time series of the responses of concentrations to repeated random perturbations, the formulation of correlation functions from such measurements, and the construction of the correlation metric (see chapter 7 for theory and chapter 8 for experiments). Third, in the investigation of oscillatory chemical reactions we showed that the responses of a chemical system in a stable stationary state close to a Hopf bifurcation are related to the category of the oscillatory reaction and to the role of the essential species in the system (see chapter 11 for theory and experiments). In each of these cases the responses yield important information about the reaction pathway and the reaction mechanism. In this chapter we focus on the design of simple types of response experiments that make it possible to extract mechanistic and kinetic information from complex nonlinear reaction systems. The main idea is to use “neutral” labeled compounds (tracers), which have the same kinetic and transport properties as the unlabeled compounds. In our previous work we have shown that by using neutral tracers a class of response experiments can be described by linear response laws, even though the underlying kinetic equations are highly nonlinear. The linear response is not the result of a linearization procedure, but it is due to the use of neutral tracers. As a result the response is linear even for large perturbations, making it possible to investigate global nonlinear kinetics by making use of linear mathematical techniques. Moreover, the susceptibility functions from the response law are related to the probability densities of the lifetimes and transit times of the various chemical species, making it easy to establish a connection between the response data and the mechanism and kinetics of the process.

Correlation Metric Construction: Theory of Statistical Construction of Reaction Mechanisms

2006 ◽  
Author(s):  
John Ross ◽  
Igor Schreiber ◽  
Marcel O. Vlad
Keyword(s):  
Time Series ◽  
Chemical Reactions ◽  
Reaction Pathway ◽  
Reaction System ◽  
Chemical Species ◽  
Biochemical Networks ◽  
Statistical Dependence ◽  
Nand Gate ◽  
Regulatory Structure ◽  
Genome Study

In chapter 5, we studied the responses of chemical species in a reaction system to pulse perturbations and showed the deduction of direct, causal connectivities by chemical reactions—the reaction pathway—and the reaction mechanism from such measurements. The causal connectivites give the information on how the chemical species are connected by chemical reactions. In this chapter we turn to another source of information about chemical species in a reaction system, that of correlations among the species. Correlations of concentrations are measures of the statistical dependence of the concentration of one species on that of one or more of the other species in the system. Such correlations can be determined from measurements of time series of concentrations collected around a stationary state (nonequilibrium or equilibrium). We shall show that from concentration correlations it is possible to construct a skeletal diagram of the reaction system that gives a graphical measure of strong control and regulatory structure in reaction networks, gives some information on connectivity, leads to information on the reaction pathway and mechanism, and may simplify the analysis of such networks by identifying possible, nearly separable subsystems. We begin with the demonstration and explanation of this approach by analyzing some abstract reaction models. In chapter 8 we show the utility of this “correlation metric construction” (CMC) with application to time-series measurements on a part of glycolysis, and in chapter 13 on an extensive genome study. Consider a chemical system as shown in fig. 7.1. Mechanisms of this type are common in biochemical networks. For example, the subnetwork of fig. 7.1 containing S3 to S5 is based on a simple model of fructose interconversion in glycolysis and the subnetwork composed of S6 to S7 is similar to the phosphorylation/dephosphorylation cycles found in cyclic cascades. As an aside, this mechanism performs the function of a biochemical NAND gate, another example of a chemical computational function (see chapter 4).

A Paramedic Treatment for Modeling Explicitly Solvated Chemical Reaction Mechanisms

2018 ◽  
Author(s):  
Yasemin Basdogan ◽  
John Keith
Keyword(s):  
Reaction Mechanism ◽  
Chemical Reaction ◽  
Reaction Mechanisms ◽  
Reaction Pathway ◽  
Optimization Procedure ◽  
Cost Effective ◽  
Chemical Reaction Mechanisms ◽  
Solvent Molecules ◽  
Dynamics Simulations ◽  
Mbh Reaction

<div> <div> <div> <p>We report a static quantum chemistry modeling treatment to study how solvent molecules affect chemical reaction mechanisms without dynamics simulations. This modeling scheme uses a global optimization procedure to identify low energy intermediate states with different numbers of explicit solvent molecules and then the growing string method to locate sequential transition states along a reaction pathway. Testing this approach on the acid-catalyzed Morita-Baylis-Hillman (MBH) reaction in methanol, we found a reaction mechanism that is consistent with both recent experiments and computationally intensive dynamics simulations with explicit solvation. In doing so, we explain unphysical pitfalls that obfuscate computational modeling that uses microsolvated reaction intermediates. This new paramedic approach can promisingly capture essential physical chemistry of the complicated and multistep MBH reaction mechanism, and the energy profiles found with this model appear reasonably insensitive to the level of theory used for energy calculations. Thus, it should be a useful and computationally cost-effective approach for modeling solvent mediated reaction mechanisms when dynamics simulations are not possible. </p> </div> </div> </div>

scholarly journals Detailed Derivations of Formulas for Heat Release Rate Calculations Revisited: A Pedagogical and Systematic Approach

2019 ◽  
Vol 124 ◽  
Author(s):  
Jiann C. Yang
Keyword(s):  
Oxygen Consumption ◽  
Heat Release ◽  
Heat Release Rate ◽  
Release Rate ◽  
Chemical Engineering ◽  
Chemical Species ◽  
Flow Process ◽  
Generalized Framework ◽  
Oxygen Consumption Calorimetry ◽  
Engineering Practices

The derivations of the formulas for heat release rate calculations are revisited based on the oxygen consumption principle. A systematic, structured, and pedagogical approach to formulate the problem and derive the generalized formulas with fewer assumptions is used. The operation of oxygen consumption calorimetry is treated as a chemical flow process, the problem is formulated in matrix notation, and the associated material balances using the tie component concept commonly used in chemical engineering practices are solved. The derivation procedure described is intuitive and easy to follow. Inclusion of other chemical species in the measurements and calculations can be easily implemented using the generalized framework developed here.

Elementary reaction mechanism of diamond growth from acetylene

1994 ◽  
Vol 98 (1) ◽  
pp. 8-11 ◽  
Author(s):  
Sergei Skokov ◽  
Brian Weiner ◽  
Michael Frenklach
Keyword(s):  
Reaction Mechanism ◽  
Elementary Reaction ◽  
Diamond Growth

Computationally Efficient Simulation of Multi-Component Fuel Combustion Using a Sparse Analytical Jacobian Chemistry Solver and High-Dimensional Clustering

2013 ◽  
Author(s):  
Federico Perini ◽  
Anand Krishnasamy ◽  
Youngchul Ra ◽  
Rolf D. Reitz
Keyword(s):  
Reaction Mechanism ◽  
Chemical Kinetics ◽  
Internal Combustion Engines ◽  
Combustion Engine ◽  
Engine Performance ◽  
Internal Combustion ◽  
Point Of View ◽  
High Dimensional ◽  
Computational Point ◽  
Fuel Surrogates

The need for more efficient and environmentally sustainable internal combustion engines is driving research towards the need to consider more realistic models for both fuel physics and chemistry. As far as compression ignition engines are concerned, phenomenological or lumped fuel models are unreliable to capture spray and combustion strategies outside of their validation domains — typically, high-pressure injection and high-temperature combustion. Furthermore, the development of variable-reactivity combustion strategies also creates the need to model comprehensively different hydrocarbon families even in single fuel surrogates. From the computational point of view, challenges to achieving practical simulation times arise from the dimensions of the reaction mechanism, that can be of hundreds species even if hydrocarbon families are lumped into representative compounds, and thus modeled with non-elementary, skeletal reaction pathways. In this case, it is also impossible to pursue further mechanism reductions to lower dimensions. CPU times for integrating chemical kinetics in internal combustion engine simulations ultimately scale with the number of cells in the grid, and with the cube number of species in the reaction mechanism. In the present work, two approaches to reduce the demands of engine simulations with detailed chemistry are presented. The first one addresses the demands due to the solution of the chemistry ODE system, and features the adoption of SpeedCHEM, a newly developed chemistry package that solves chemical kinetics using sparse analytical Jacobians. The second one aims to reduce the number of chemistry calculations by binning the CFD cells of the engine grid into a subset of clusters, where chemistry is solved and then mapped back to the original domain. In particular, a high-dimensional representation of the chemical state space is adopted for keeping track of the different fuel components, and a newly developed bounding-box-constrained k-means algorithm is used to subdivide the cells into reactively homogeneous clusters. The approaches have been tested on a number of simulations featuring multi-component diesel fuel surrogates, and different engine grids. The results show that significant CPU time reductions, of about one order of magnitude, can be achieved without loss of accuracy in both engine performance and emissions predictions, prompting for their applicability to more refined or full-sized engine grids.

Elementary Reaction Mechanism for Benzene Oxidation in Supercritical Water†

2000 ◽  
Vol 104 (45) ◽  
pp. 10576-10586 ◽  
Author(s):  
Joanna L. DiNaro ◽  
Jack B. Howard ◽  
William H. Green ◽  
Jefferson W. Tester ◽  
Joseph W. Bozzelli
Keyword(s):  
Reaction Mechanism ◽  
Supercritical Water ◽  
Elementary Reaction ◽  
Benzene Oxidation
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