Extracting the mechanisms and kinetic models of complex reactions from atomistic simulation data

Determining reaction mechanisms and kinetic models, which can be used for chemical reaction engineering and design, from atomistic simulation is highly challenging. In this study, we develop a novel methodology to solve this problem. Our approach has three components: (1) a procedure for precisely identifying chemical species and elementary reactions and statistically calculating the reaction rate constants; (2) a reduction method to simplify the complex reaction network into a skeletal network which can be used directly for kinetic modeling; and (3) a deterministic method for validating the derived full and skeletal kinetic models. The methodology is demonstrated by analyzing simulation data of hydrogen combustion. The full reaction network comprises 69 species and 256 reactions, which is reduced into a skeletal network of 9 species and 30 reactions. The kinetic models of both the full and skeletal networks represent the simulation data well. In addition, the essential elementary reactions and their rate constants agree favorably with those obtained experimentally. © 2019 Wiley Periodicals, Inc.     

ANN-MATOPT hybrid algorithm: determination of kinetic and non-kinetic parameters in different reaction mechanisms

In this work we have applied the computational methodology based on Artificial Neural Networks (ANN) to the kinetic study of distinct reaction mechanisms to determine different types of parameters. Moreover, the problems of ambiguity or equivalence are analyzed in the set of parameters to determine in different kinetic systems when these parameters are from different natures. The ambiguity in the set of parameters show the possibility of existence of two possible set of parameter values that fit the experimental data. The deterministic analysis is applied to know beforehand if this problem occurs when rate constants of the different stages of the mechanism and the molar absorption coefficients of the species participating in the reaction are obtained together. Through the deterministic analysis we will analyze if a system is identifiable (unique solution or finite number of solutions) or if it is non-identifiable if it possesses infinite solutions. The determination of parameters of different nature can also present problems due to the different magnitude order, so we must analyze in each case the necessity to apply a second method to improve the values obtained through ANN. If necessary, an optimization mathematical method for improving the values of the parameters obtained with ANN will be used. The complete process, ANN and mathematical optimizations constitutes a hybrid algorithm ANN-MATOPT. The procedure will be applied first for the treatment of synthetic data with the purpose of checking the applicability of the method and after, it will be used in the case of experimental kinetic data.

     

Variable Time Normalization Analysis: General Graphical Elucidation of Reaction Orders from Concentration Profiles

The recent technological evolution of reaction monitoring techniques has not been paralleled by the development of modern kinetic analyses. The analyses currently used disregard part of the data acquired, thus requiring an increased number of experiments to obtain sufficient kinetic information for a given chemical reaction. Herein, we present a simple graphical analysis method that takes advantage of the data‐rich results provided by modern reaction monitoring tools. This analysis uses a variable normalization of the time scale to enable the visual comparison of entire concentration reaction profiles. As a result, the order in each component of the reaction, as well as k_obs , is determined with just a few experiments using a simple and quick mathematical data treatment. This analysis facilitates the rapid extraction of relevant kinetic information and will be a valuable tool for the study of reaction mechanisms.     

KINMODEL (AGDC): a multipurpose computational method for kinetic treatment

KINMODEL (AGDC) is a kinetic computational methodology that is valid for the treatment of any reaction mechanism and that allows the determination of different kinetic and non-kinetic parameters from the experimental data acquired by monitoring absorbance at one or several different wavelengths. It is a numerical computational model that can be applied to any reaction mechanism, with the advantage that on changing the treatment from one mechanism to another it is not necessary to modify even a single line of the program code since it automatically establishes and solves the set of differential rate equations. It is able to treat a broad set of reaction mechanisms in the individual and joint determination of the following groups of parameters (a) the individual rate constants of the different reaction mechanisms; (b) the values of the molar absorption coefficients (which are very valuable in the case of intermediate species and their identification) of all the species involved in the mechanism, and (c) the concentrations of the species participating in the mechanism. The program can be used by non-experts in the field and it is able to treat mechanisms involving ambiguities in the solutions and in the identification of parameters when kinetic constants and molar absorption coefficients are optimized together, and it allows a discrimination to be made between the possible mechanisms responsible for the course of the reaction after the residuals have been analyzed statistically, automatically choosing the one that best fits the kinetic data.     

Extent-based kinetic identification using spectroscopic measurements and multivariate calibration

Extent-based kinetic identification is a kinetic modeling technique that uses concentration measurements to compute extents and identify reaction kinetics by the integral method of parameter estimation. This article considers the case where spectroscopic data are used together with a calibration model to predict concentrations. The calibration set is assumed to be constructed from reacting data that include pairs of concentration and spectral data. Alternatively, one can use the concentration- and spectral contributions of the reactions and mass transfers, which are obtained by pretreatment in reaction- and mass-transfer-variant form. The extent-based kinetic identification using concentrations predicted from spectroscopic data is illustrated through the simulation of both a homogeneous and a gas–liquid reaction system.     

利用减秩因子分析法同时优化确定化学反应级数和速率常数

通过对反应过程中在线测得的动力学谱-光谱二维数据矩阵进行主成分分析，可确定化学反应过程存在的组分数。提出用优化动力学参数-减秩因子分析法解析二维数据矩阵，对未知动力学模型的复杂反应可同时优化求解第一步反应的级数和速率常数。模拟二维数据验证了该方法的可行性。该方法用于高锰酸钾氧化溴化钠的反应过程中测得的二维数据的解析，结果表明：高锰酸钾的还原过程符合0级反应模型。     

N2O分解反应的蒙特卡罗模拟

N2O作为大气污染物之一早已受到人们的注意，许多人研究了N2O在金属氧化物上的分解反应得到了一些基本的实验事实[1]：（1）反应速率与原料气中N2O的分压近似成比例．(2)在反应初期，N2的生成速率由大变小，O2的生成速率由小变大，达到平衡时，N2生成速率是O2生成速率的二倍．(3)过渡应答法研究表明，把原料气由N2O和He的混合气体切换成纯He后，N2立即停止发生，而O2的生成仍能维持一段时间．基于上述实验事实，人们对Nzo的催化分解反应提出了一些可能的机理，主要有下面两种看法：另一方面，人们还发现几O的催化分解反应是一个振荡…     

Use of Nonlinear Frequency Response for Discriminating Adsorption Kinetics Mechanisms Resulting with Bimodal Characteristic Functions

One of the characteristic examples of the inability of the classical linear frequency response (FR) method to identify the correct kinetic mechanism is adsorption of some substances (p-xylene, 2-butane, propane or n-hexane) on silicalite-1. The linear FR resulted with bimodal FR characteristic functions, which fitted equally well to three different kinetic models: nonisothermal micropore diffusion, two independent isothermal diffusion processes, and an isothermal diffusion-rearrangement process. We show that the second order frequency response functions (FRFs), obtained from the nonlinear FR, can be used for discrimination among these three mechanisms. Starting from the nonlinear models, we derive the theoretical expressions for the first and second order FRFs corresponding to these three mechanisms and show that different shapes of the second order FRFs are obtained for each mechanism. This would enable identification of the real mechanism from nonlinear FR data.     

Kinetics of the water-gas shift reaction in Fischer-Tropsch synthesis over a nano-structured iron catalyst

Based on formate and direct oxidation mechanisms, three Langmuir-Hinshelwood-Hougen-Watson (LHHW) kinetic models of the water-gasshift (WGS) reaction over a nano-structured iron catalyst under Fischer-Tropsch synthesis (FTS) reaction conditions were derived and compared with those over the conventional catalyst. The conventional and nanostructured Fe/Cu/La/Si catalysts were prepared by co-precipitation of Fe and Cu nitrates in aqueous media and water-oil micro-emulsion, respectively. The WGS kinetic data were measured by experiments over a wide range of reaction conditions and comparisons were also made for various rate equations. WGS rate expressions based on the formate mechanism with the assumption that the formation of formate is rate determining step were found to be the best.     

Theory and application of cyclic voltammetry at a hemispherical microelectrode for a quasi-reversible reaction

The theory of cyclic voltammetry for a quasi-reversible reaction at a hemispherical microelectrode has been deduced. From the results calculated according to the theory, the heterogeneous rate constant and charge transfer coefficient can be measured with the cyclic voltammetric data obtained at an intermediate scan rate on a hemispherical microelectrode. To verify the theory, the kinetic constant for reduction of benzoquinone in acetonitrile has been determined. The result is coincident with that measured by a fast scan rate at a platinum microdisk electrode. The kinetic constant and charge transfer coefficient for reduction of 2,3,5,6-tetrachlorobenzoquinone have also been determined with the method described in this paper.     

Kinetic pathway investigations of three‐component photoinitiator systems for visible‐light activated free radical polymerizations

Three‐component photoinitiator systems generally include a light‐absorbing photosensitizer (PS), an electron donor, and an electron acceptor. To investigate the key factors involved with visible‐light activated free radical polymerizations involving three‐component photoinitiators and 2‐hydroxyethyl methacrylate, we used thermodynamic feasibility and kinetic considerations to study photopolymerizations initiated with either rose bengal or fluorescein as the PS. The Rehm–Weller equation was used to verify the thermodynamic feasibility for the photo‐induced electron transfer reaction. It was concluded that key kinetic factors for efficient visible‐light activated initiation process are summarized in two ways: (1) to retard back electron transfer and recombination reaction steps and (2) to use a secondary reaction step for consuming dye‐based radical and regenerating the original PS (dye). Using the thermodynamic feasibility and kinetic data, we suggest three different kinetic mechanisms, which are (i) photo‐reducible series mechanism, (ii) photo‐oxidizable series mechanism, and (iii) parallel‐series mechanism. Because the photo‐oxidizable series mechanisms most efficiently allow the key kinetic factors, this kinetic pathway showed the highest conversion and rate of polymerization. The kinetic data measured by near‐IR and photo‐differential scanning calorimeter verified that the photo‐oxidizable series mechanism provides the most efficient kinetic pathway in the visible‐light activated free radical polymerizations. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 887–898, 2009     

Stability of solutions to a reaction diffusion system based upon chemical reaction kinetics

In this paper, we deal with the stability problem to some mathematical models that describe chemical reaction kinetics. One is a set of ordinary differential equations induced by one reversible chemical reaction mechanism containing three chemical species. The other is a set of reaction diffusion equations based on the same chemical reaction. We show that all solutions of the model are asymptotically stable by applying the Liapunov method. We thus find that the concentration of each species has certain limits as time proceeds.      

Kinetic Evidence for a Non‐Langmuir‐Hinshelwood Surface Reaction: H/D Exchange over Pd Nanoparticles and Pd(111)

The mechanism of hydrogen recombination on a Pd(111) single crystal and well‐defined Pd nanoparticles is studied using pulsed multi‐molecular beam techniques and the H₂/D₂ isotope exchange reaction. The focus of this study is to obtain a microscopic understanding of the role of subsurface hydrogen in enhancing the associative desorption of molecular hydrogen. HD production from H₂ and D₂ over Pd is investigated using pulsed molecular beams, and the temperature dependence and reaction orders are obtained for the rate of HD production under various reaction conditions designed to modulate the amount of subsurface hydrogen present. The experimental data are compared to the results of kinetic modeling based on different mechanisms for hydrogen recombination. We found that under conditions where virtually no subsurface hydrogen species are present, the HD formation rate can be described exceptionally well by a classic Langmuir–Hinshelwood model. However, this model completely fails to reproduce the experimentally observed high HD formation rates and the reaction orders under reaction conditions where subsurface hydrogen is present. To analyze this phenomenon, we develop two kinetic models that account for the role of subsurface hydrogen. First, we investigate the possibility of a change in the reaction mechanism, where recombination of one subsurface and one surface hydrogen species (known as a breakthrough mechanism) becomes dominant when subsurface hydrogen is present. Second, we investigate the possibility of the modified Langmuir–Hinshelwood mechanism with subsurface hydrogen lowering the activation energy for recombination of two hydrogen species adsorbed on the surface. We show that the experimental reaction kinetics can be well described by both kinetic models based on non‐Langmuir–Hinshelwood‐type mechanisms.     

Enzyme catalyzed reactions: From experiment to computational mechanism reconstruction

The traditional experimental practice in enzyme kinetics involves the measurement of substrate or product concentrations as a function of time. Advances in computing have produced novel approaches for modeling enzyme catalyzed reactions from time course data. One example of such an approach is the selection of appropriate chemical reactions that best fit the data. A common limitation of this approach resides in the number of chemical species considered. The number of possible chemical reactions grows exponentially with the number of chemical species, which makes difficult to select reactions that uniquely describe the data and diminishes the efficiency of the methods. In addition, a method’s performance is also dependent on several quantitative and qualitative properties of the time course data, of which we know very little. This information is important to experimentalists as it could allow them to setup their experiments in ways that optimize the network reconstruction. We have previously described a method for inferring reaction mechanisms and kinetic rate parameters from time course data. Here, we address the limitations in the number of chemical reactions by allowing the introduction of information about chemical interactions. We also address the unknown properties of the input data by determining experimental data properties that maximize our method’s performance. We investigate the following properties: initial substrate–enzyme concentration ratios; initial substrate–enzyme concentration variation ranges; number of data points; number of different experiments (time courses); and noise. We test the method using data generated in silico from the Michaelis–Menten and the Hartley–Kilby reaction mechanisms. Our results demonstrate the importance of experimental design for time course assays that has not been considered in experimental protocols. These considerations can have far reaching implications for the computational mechanism reconstruction process.     

对化学反应数据分类获取反应知识的新方法

尽管已有大量化学反应数据可供使用,但化学家仍常常感到很难便捷地从中得到所需的信息.这主要是由于反应数据库基于结构的检索方法与化学家解决问题的方法相去甚远.为解决这一问题而发展了一种通过对反应进行二级分类得到精细描述反应知识的层次模型的方法.第一次分类时不同的同类反应都在由一组普适性好的称作反应结构一级描述符构成的空间中进行.在第一次分类结果的基础上,得到每一类反应的公共结构特征作为第二次分类的结构描述符,利用它们进行更精细的分类,即可从原始反应数据中得到所需的基核反应.由特定反应、基核反应和基型反应就可将反应知识更合理地组织在同类反应知识库中,使它们得到更好的利用.     

氧族元素间共价单键参与的无机反应机理

结合一些热力学数据和动力学过程,运用亲电和亲核的概念,初步阐释了一些O―O键、S―S键参与的氧化还原反应的机理,并利用Gaussian09程序的计算对一些已有的机理和猜想进行了验证,以此说明无机反应机理的一些规律。     

Database of atomistic reaction mechanisms with application to kinetic Monte Carlo

Kinetic Monte Carlo is a method used to model the state-to-state kinetics of atomic systems when all reaction mechanisms and rates are known a priori. Adaptive versions of this algorithm use saddle searches from each visited state so that unexpected and complex reaction mechanisms can also be included. Here, we describe how calculated reaction mechanisms can be stored concisely in a kinetic database and subsequently reused to reduce the computational cost of such simulations. As all accessible reaction mechanisms available in a system are contained in the database, the cost of the adaptive algorithm is reduced towards that of standard kinetic Monte Carlo.     

A Chemical Kinetic Mechanism for 2‐Bromo‐3,3,3‐trifluoropropene (2‐BTP) Flame Inhibition

In this work, we report a detailed chemical kinetic mechanism to describe the flame inhibition chemistry of the fire‐suppressant 2‐bromo‐3,3,3‐trifluoropropene (2‐BTP), under consideration as a replacement for CF₃Br. Under some conditions, the effectiveness of 2‐BTP is similar to that of CF₃Br; however, like other potential halon replacements, it failed an U.S. Federal Aviation Authority (FAA) qualifying test for its use in cargo bays. Large overpressures are observed in that test and indicate an exothermic reaction of the agent under those conditions. The kinetic model reported herein lays the groundwork to understand the seemingly conflicting behavior on a fundamental basis. The present mechanism and parameters are based on an extensive literature review supplemented with new quantum chemical calculations. The first part of the present article documents the information considered and provides traceability with respect to the reaction set, species thermochemistry, and kinetic parameters. In additional work, presented more fully elsewhere, we have combined the 2‐BTP chemical kinetic mechanism developed here with several other submodels from the literature and then used the combined mechanism to simulate premixed flames over a range of fuel/air stoichiometries and agent loadings. Overall, the modeling results qualitatively predicted observations found in cup‐burner tests and FAA Aerosol Can Tests, including the extinguishing concentrations required and the lean‐to‐rich dependence of mixtures. With these data in hand, in a second phase of the present work, we perform a reaction path analysis of major species under several modeled conditions. This analysis leads to a qualitative understanding of the ability of 2‐BTP to act as both an inhibitor and a fuel, depending on the conditions and suggests areas of the kinetic model that should be further investigated and refined.     

关于副本交换分子动力学模拟复杂化学反应的研究

本文研究用温度副本交换分子动力学(T-REMD)和哈密顿副本交换分子动力学(H-REMD)方法模拟复杂化学反应的问题。使用具有不同活化能和反应能的简单置换反应模型,我们检验了上述两种方法用来预测反应平衡产物的效率和应用范围。T-REMD方法对具有适度活化能(约< 20 kcal·mol^-1)或者反应能量(< 3 kcal·mol^-1)的放热反应是有效的。由于在相空间的不完整采样,对于同时具有高活化能和反应能量的反应其模拟效率有严重障碍,并且对于吸热反应问题更为显着。另一方面,H-REMD对一系列具有不同活化能的反应能的模型表现出色,与T-REMD相比,H-REMD可以使用更少的副本获得优异的结果。     

Linear compartmental systems. III. Application to enzymatic reactions

In this paper we extend to enzyme systems the results previously obtained in paper I of this series for linear compartmental systems. We obtain the time course equations for both the enzyme and ligand species involved in the reaction mechanisms, which fit a general enzyme system model when the connections between the different enzyme species are of first or pseudofirst order. The kinetic equations obtained here for a given species, enzyme or ligand have the advantage over all previous equations described in the literature, in that they are in the most simplified form possible, since they only contain the kinetic parameters and initial concentrations of the enzymatic reaction which really have some influence on the time progress curves of the species under study. These kinetic equations are denominated optimized equation to distinguish them from the others, which shall call non-optimized equations. We discuss those cases when both types of equation coincide and we show how, when they do not coincide, the non-optimized equations can be simplified to the optimized ones. Therefore, we show that the optimized equations could be used in all cases to avoid the need of subsequent simplifications to eliminate the parameters that play no role in the corresponding time equations. To illustrate the use of this procedure we will apply it to two simple examples of enzymatic reactions.