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.     

Evaluation of kinetic parameters and mechanisms of complex reactions from thermal analysis data

A method is for TA data-processing: the method of exponential multipliers (MEM). The application of this method permits determination of the steps of the process, the type of the kinetic function, the type of the reaction and the kinetic parameters of the reaction steps. The method is simple and is easily carried out with the use of a mini-computer. The efficiency of the method is illustrated on the example of the thermal decomposition of ammonia copper chromate. The mechanism of the process and the kinetic constants were determined. They agree with available literature data.

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Zusammenfassung Ein Verfahren zur Verarbeitung von TA-Daten wurde entwickelt: das Verfahren exponentieller Multiplizierglieder (MEM). Die Anwendung dieses Verfahrens erlaubt die Bestimmung der Schritte eines Vorganges, des Typs der kinetischen Function, des Reaktionstypes und der kinetischen Parameter der Reaktionsschritte. Es handelt sich um eine einfache Methode, die auf einem Mini-Computer leicht verwirklicht werden kann. Die Wirksamkeit dieses Verfahrens wird am Beispiel der thermischen Zersetzung von Ammoniumkupferchromat gezeigt. Der Mechanismus und die kinetischen Konstanten des Prozesses wurden bestimmt, sie stimmen mit erreichbaren Literaturdaten überinen.

     

Simultaneous determination of kinetic and thermodynamic parameters from fast-reaction kinetic measurements

A combined stopped-flow temperature-jump apparatus interfaced with a dedicated microcomputer has been used to study the complexation reaction of iron(III) with thiocyanate in aqueous solution. Kinetic rate-constants (k(f) = 143 l.mole(-1) .sec(-1) from T-jump, k(f) = 150 l.mole(-1) .sec(-1) from stopped flow), equilibrium constants (K = 143 from T-jump, K = 150 from stopped flow) and the thermodynamic enthalpy change (DeltaH(c) = -6.7 kJ/mole) could be independently determined from the simultaneous application of the two techniques.     

The determination of kinetic parameters for the decomposition of complex substances from thermogravimetry data

A procedure for thermogravimetry data processing was suggested. It was based on treatment of a substance as a superposition of fractions, the decomposition of which occurred independently and could be described by first-order kinetics with the corresponding kinetic parameters, that is, activation energy and preexponential factor. The theoretical dependences of weight loss were constructed using exact solutions to kinetic equations. The results obtained by the determination of the kinetic parameters for two coal samples are presented.     

Determination of nitrite in food samples by second-order calibration of kinetic spectrophotometric data

A method for the determination of nitrite in soil and vegetable samples by UV-Vis spectroscopy was proposed. The kinetic UV-Vis data were collected during the reaction between nitrite and 4-amino-3-hydroxynaphthalene-1-sulfonic acid with concentration of 0.001 M and pH 1.6. Data were collected by standard addition method. Multivariate curve resolution-alternating least squares was employed to analyze data with non-negativity and three-way data structure constraints. The method can be used to solve matrix effect and unknown interferents in the determination of nitrite in complex samples. The proposed method was used to determine nitrite at low mg/L levels with satisfactory results in soil, lettuce, cabbage and cucumber samples.     

Modelling small-angle scattering data from micelles

Models for small-angle scattering of spherical micelles are briefly reviewed, considering both the intra-molecular form factor and the inter-molecular structure factor. Recent examples from the literature, where such approaches have been used to extract information on micellar structure and ordering, are then discussed. A particular emphasis is on micelles formed by block copolymers in solution.     

Kinetic data from DTA measurements

The theory of Borchardt and Daniels for the determination from the DTA curve of the fraction decomposed (α) is used. The probable mechanism, activation energy (E) and frequency factor (Z) can be found by the trial and error method from the plot ofα vs.T for a decomposition reaction which can be expressed by the equation $$\log g(\alpha ) = \log p(E/RT) + \frac{{ZE}}{{Rq}}$$ The use of tables of log g(α) for different mechanisms, and plots of the function logp(E/RT _α) vs. temperature for different activation energies is described. The influence is shown of the mechanism of the process, activation energy, frequency factor and heating rate (q) on the shape of the DTA curve. The kinetic data for the decomposition of several solids obtained by the described method are in good agreement with those obtained from literature sources.     

Estimation of kinetic parameters from thermochemical data

A method is described by which kinetic parameters may be calculated from the measured temperature changes caused by the heat produced during a chemical reaction. An isoperibol titration calorimeter with an ampoule-breaking facility is used to obtain the temperature data. The temperature changes resulting from the reaction between tri-isopropyl phosphite and sulphur (S(8)) are used as an example to demonstrate the effectiveness of the method. The temperature changes are used to calculate an enthalpy of reaction. From the enthalpy of reaction and intermediate heats, instantaneous concentrations of the reactants may be calculated.     

The reproducible acquisition of comparative liquid chromatography/tandem mass spectrometry data from complex biological samples

An in-depth study of the reproducibility of data acquired for comparative proteomics analysis using a prototype two-stage heated laminar flow chamber fitted to a commercial high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) instrument was undertaken. The study is based on 24 replicate samples from four independent membrane preparations derived from two matched breast cancer cell lines. Variation and reproducibility in the data were evaluated at several levels highlighting the relative efficiency and variability of the acquisition routines used. Specifically, variation in the number and relative intensities of chromatographic peaks eluted from the LC column, precursor ion selection and sequence identification were evaluated. On average, approximately 6500 chromatographic peaks were generated for each acquisition with a corresponding coefficient of variance (CV) of less than 20%. Precursor ion selection and sequence identification averaged 1380 and 780 events per acquisition sample, respectively, with corresponding CVs of less than 10% for each. The reproducibility in the precursor ion selection was typically better than 60% between similar replicates. Using protein and peptide internal standards, it was found that the CV in retention time across the gradient between two acquisition pairs was typically less than 5%, whereas the average intensity ratio was 1.0 (expected) with a CV approaching 20%. An evaluation of the intensity ratios calculated from endogenous peptide sequences, identified across the acquisition set, indicated a CV of approximately 30%. Similarly, the CV associated with the top 1000 peptides indicated a mean and median of 28.4 and 26.95%. For a given acquisition pair it was also found that approximately 11% of the chromatographic peaks eluting from the column were linked to a sequence or identified. For these experiments, less than 10% of the peak pairs had absolute ratios greater than 2.0 and of those only approximately 10% had sequences linked to them. For each matched acquisition set on average 406 proteins were identified with a CV of less than 10%. Of the proteins that were identified approximately 30% had at least one predicted trans-membrane domain, indicating a four-fold increase over a crude homogenate sample with only minor enrichment. During these experiments it was found that the interface did not significantly alter the relative charge state distribution of ions, nor did it introduce significant interference from background ions. The interface was capable of 24-hour acquisition cycles.     

Rapid measurements of curcumin from complex samples coupled with magnetic biocompatibility molecularly imprinted polymer using electrochemical detection

Curcumin widely exists in food, and rapid selective and accurate detection of curcumin have great significance in chemical industry. In this experiment, a new magnetic biocompatibility molecularly imprinted polymer was prepared with nontoxic and biocompatible Zein to adsorb curcumin selectively. The polymer has high biocompatibility, good adsorption capacity, and specific adsorption for curcumin. Combined with portable electrochemical workstations, the polymer can be used to detect curcumin rapidly and cost‐effectively. Using curcumin as a template and Zein as the crosslinking agent, the polymers were synthesized on the surface of Fe₃O₄ particles for solid phase extraction. The experimental results showed that the polymer reached large adsorption capacity (32.12 mg/g) with fast kinetics (20 min). The adsorption characteristic of the polymer followed the Langmuir isotherm and pseudo‐second‐order kinetic models. Hexacyanoferrate was used as electrochemical probe to generate signals, and the linear range was 5–200 µg/mL for measuring curcumin. The experimental analysis showed that the polymer was an ideal material for selective accumulation of curcumin from complex samples. This approach has been successfully applied to the determination of curcumin in food samples with electrochemical detection, indicating that this is a feasible and practical technique.     

Analysis of isothermal kinetic data from solid-state reactions

In most solid state reactions the reaction velocity can be described as a product of two functionsK(T) andf(1?α) whereT is the temperature and α the degree of conversion of the solid reactant. The physical interpretation of these functions is discussed, and a systematic method is described by whichf(1?α) of a reaction is identified from its kinetic data.K(T) and the reaction mechanism are then determined. This method has been successfully applied to analyse the kinetics of the thermal decomposition of silver azide.     

由热重数据计算动力学参数

热重法(TG)是一种动态测量技术,可在程序升温或降温情况下对给定物质或体系提供一个连续的,以温度或时间为函数的重量变化曲线,所以由它跟踪反应能给出反应动力学的有关信息。这种非等温法与早期使用的等温法相比,有快速、连续和需要较少实验数据等优点,近年来在动力学研究方面得到广泛应用,但还只限于研究下列几种类型的简单     

Analysis of dynamic kinetic data from solid-state reactions

The kinetics of heterogeneous reactions, involving one reactant in the solid phase, usually follow the lawα=K _∞ exp(?E/kT)f(1?α), where α is the degree of conversion of the solid, andK _∞ andE are the kinetic constants. A critical examination is given of the various methods which are currently used to analyse dynamic experimental data. The limitations of these methods and their insensitivity to the form off(1-α) are pointed out. An alternative approach free from these limitations is suggested. In this,f(1?α) is determined from isothermal experiments, and then the dynamic data are accurately analyzed to obtain the values of the kinetic constants. A case study is given to elucidate the applicability of the approach.     

The use of free energy relationships to rationalize kinetic data in complex solvent mixtures

The electron transfer reaction [(NH₃)₄CO^III(μ-pzCO₂)Fe^II(CN)₅]⁻ → [(NH₃)₄CO^II(μ-pzCO₂)Fe^III (CN)₅]⁻ has been studied in water-cosolvent mixtures at ionic strength of I = 0.5 mol dm⁻³ (NaClO₄). A multiparameter regression coefficients have been compared to those obtained for the same reaction to a different ionic strength (I = 2.8 10⁻³ mol dm⁻³). The magnitude of these coefficients changes with the ionic strength. An explanation is given for this behavior. © 1996 John Wiley & Sons, Inc.     

Untargeted metabolite discovery in kinetic data from multi-dose intervention studies

A new strategy for biomarker discovery is presented that is based on multi-dose kinetic metabolomics data. Gas chromatography-mass spectrometry (GC-MS) data sets recorded in the full scan mode are scanned for compounds showing a meaningful trend following the different doses and sampling time points. From a biological point of view, a meaningful trend denotes a compound that responds similarly at all doses and follows a smooth trend along the time points. This type of information can be used to distinguish relevant metabolites from those compounds not following the expected trends. The method is based on analysing the time and dosage trends of each compound via principal component analysis. As only local information is analysed at a time (meaning no correlation with other metabolites is taken into account), the proposed model flags relevant metabolites even if their trend is different from that of any other compound. The new method is therefore an attractive way to reduce the long list of detected compounds in a metabolomics sample set to include only those having the expected smooth time profile that is common for all doses. The new strategy is tested on a sample set obtained from a gut fermentation study of a polyphenol-rich diet. For this study, the initial list of over 25,000 potentially interesting features was reduced to less than 250, thus significantly reducing the expensive and time-consuming manual examination.     

Nitric oxide measurements in biological samples

The crucial role of nitric oxide (NO) in controlling many physiological functions in mammals is now established. To aid understanding this crucial role, sensitive and selective methods for its in vivo and in vitro detection are vital. The unique chemical and physical properties of NO set the tone for its detection strategies. This review summarizes different techniques and methodologies used in measuring NO in biological samples. Those include gas and liquid phase chemiluminescence, electron spin resonance spectroscopy, UV-visible spectroscopy, fluorescence, electrochemical sensors, and reporter cell assay. The principles, applications, merits, and limitations of each technique are discussed.     

Comparative results of kinetic data obtained with different methods for complex decomposition steps

A comparative kinetic analysis on the thermal decomposition of tartaric acid and potassium tartrate under non-isothermal conditions was performed. The non-isothermal kinetic parameters were determined by the following four methods: integral isoconversional method suggested by Flynn-Wall-Ozawa (FWO method); differential isoconversional method suggested by Friedman; Budrugeac-Segal method and Non-Parametric-Kinetic (NKP) method suggested by Sempere and Nomen and modified by Vlase and Doca. The comparison of the results obtaining by these methods leads to interesting conclusions. The experimental data were obtained in dynamic nitrogen atmosphere at heating rates of 5, 7, 10, 12 and 15 K min⁻¹. The less speculative kinetic analysis was possible by the NPK method.     

Analyses of three-way data from equilibrium and kinetic investigations

In kinetic or equilibrium investigations it is common to measure two-way multiwavelength data, e.g. absorption spectra as a function of time or reagent addition. Often it is advantageous to acquire experimental data at various initial conditions or even on different instruments. A collection of these measurements can be arranged in three-dimensional arrays, which can be analysed as a whole under the assumption of a superimposed function, e.g. a kinetic model, and/or common properties of the subsets, such as molar absorptivity. As we show on selected formation equilibria (Zn²⁺/phen) and kinetic studies (Cu²⁺/cyclam) from our own research, an appropriate combination of multivariate data can lead to an improved analysis of the investigated systems.