Dynamic chromatography: A stochastic approach

During the chromatographic separation process, analyte reactions are often observed leading to band broadening and/or elution of peak clusters. For many different chemical compounds the reaction can be reduced to a simple isomerisation kinetic scheme where elution is the result of adsorption–desorption on the surface stationary phase coupled with a flipping two-level reaction system. In this paper, the chromatographic peak shape for a reacting analyte is calculated in frequency domain when the reaction follows a simple reversible first order scheme. Both reaction and dynamic chromatographic systems have been considered. The derived solutions are expressed in closed form in the Fourier domain. Several limit solutions obtained under conditions of very slow and moderately fast kinetics are exploited. The effects of both kinetics rate constants and retention time on the chromatographic peak shape are singled out.     

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.     

F+CH2CO的反应机理和动力学研究

用G3(MP2)方法对F与CH₂CO的反应进行研究,揭示了该反应的加成-消除机理.F原子首先与CH₂CO作用形成富能的中间体CH₂FCO^*,此加成反应为无势垒过程.富能的CH₂FCO^*可进一步发生解离或异构化反应生成各种可能的产物.其中CO和CH₂F可能为反应的主要产物.根据从头算的结果,用RRKM-TST理论计算该反应的速率常数.总包反应速率常数与温度存在弱的依赖关系,与总压力无关.     

Cholesterol study: Reaction plateau and kinetic determinations

A study has been described of a comparison between reaction plateaus and kinetic modes for measuring cholesterol. A similar investigation of bilirubin reactions under the same procedural conditions was also carried out because this compound is a major interference which is frequently encountered in abnormal serums. The findings indicate that bilirubin is a more sensitive reactant than cholesterol by LB reaction but that its effect as an interference can be lessened by a kinetic approach providing that the effect of H₂O on reaction velocity and molar absorptivity can be minimized. An iron reaction even though more sensitive proved less workable in the kinetic mode owing to reaction velocity and the presence of air bubbles. However, its reaction plateau characteristics were superior to the LB reaction because of a favorable ratio of colors generated for the two reacting constituents. Based on this study, it is predictable that a kinetic approach is quite workable for the LB reaction and could be made more workable for the iron reaction if, in the latter case, conditions perhaps such as temperature and reaction media, could be altered to slow the rate of color formation.     

Kinetics and mechanism of electron-induced splitting of a cyclobutane pyrimidine dimer with or without an electron acceptor

DNA repair has received heightened attention in recent years as ozone depletion threatens to significantly increase DNA damage by UVB radiation[1—6]. The major lesions formed in DNA by this radiation are cis-syn cyclobutane pyrimidine dimers, which are created by the linkage of two neighboring pyrimidine bases in DNA via C5-C5 and C6-C6 atoms by [2+2] cycloaddition[2,5—8]. This potentially lethal or mutagenic damage can be repaired either by the removal of the damaged bases by excisio…     

Thermodynamic Analysis of Chemically Reacting Mixtures and Their Kinetics: Example of a Mixture of Three Isomers

Thermodynamics provides consequences of and restrictions on chemically reacting mixtures, particularly their kinetics, which have not been fully explored. Herein, a comprehensive thermodynamic analysis is illustrated for a reacting mixture of three isomers. The rate equation is first derived on the basis of the results of nonequilibrium continuum thermodynamics of linear fluids, and is then subjected to the requirement of consistency with entropic inequality (the second law). This consistency test involves the correct representation of the reaction rate as a function of affinities. It is shown that entropic inequality restricts the signs or values of coefficients in the constitutive equations for reaction rates/rate constants. The use of reverse rate constants and the identification of thermodynamic and kinetic equilibrium constants are not necessary in this approach. Although the presented thermodynamic analysis works only for independent reactions, the rates of dependent reactions are not excluded from having effects on kinetics. It is shown that the rates of dependent reactions are combined from the rates of independent reactions differently than dependent reactions are combined from independent reactions. The results are compared to the classical mass‐action rate equations, and new restrictions on the values of the classical rate constants are derived.     

Formation and dissociation kinetics and crystal structures of nickel(II)-macrocyclic tetrathiaether complexes in acetonitrile. Comparison to nickel(II)-macrocyclic tetramines

Complex formation and dissociation rate constants have been independently determined for solvated nickel(II) ion reacting with eight macrocyclic tetrathiaether ligands and one acyclic analogue in acetonitrile at 25 degrees C, mu = 0.15 M. The macrocyclic ligands include 1,4,8,11-tetrathiacyclotetradecane ([14]aneS4) and seven derivatives in which one or both ethylene bridges have been substituted by cis- or trans-1,2-cyclohexane, while the acyclic ligand is 2,5,9,12-tetrathiatridecane (Me2-2,3,2-S4). In contrast to similar complex formation kinetic studies on Ni(II) reacting with corresponding macrocyclic tetramines in acetonitrile and N,N-dimethylformamide (DMF), the kinetics of complex formation with the macrocyclic tetrathiaethers show no evidence of slow conformational changes following the initial coordination process. The differing behavior is ascribed to the fact that such conformational changes require donor atom inversion, which is readily accommodated by thiaether sulfurs but requires abstraction of a hydrogen from a nitrogen (to form a temporary amide). The latter process is not facilitated in solvents of low protophilicity. The rate-determining step in the formation reactions appears to be at the point of first-bond formation for the acyclic tetrathiaether but shifts to the point of chelate ring closure (i.e., second-bond formation) for the macrocyclic tetrathiaether complexes. The formation rate constants for Ni(II) with the macrocyclic tetrathiaethers parallel those previously obtained for Cu(II) reacting with the same ligands in 80% methanol-20% water (w/w). By contrast, the Ni(II) dissociation rate constants show significant variations from the trends in the Cu(II) behavior. Crystal structures are reported for the Ni(II) complexes formed with all five dicyclohexanediyl-substituted macrocyclic tetrathiaethers. All but one are low-spin species.     

Kinetic analysis of sequential multistep reactions

Many processes in biology and chemistry involve multistep reactions or transitions. The kinetic data associated with these reactions are manifested by superpositions of exponential decays that are often difficult to dissect. Two major challenges have hampered the kinetic analysis of multistep chemical reactions: (1) reliable and unbiased determination of the number of reaction steps, and (2) stable reconstruction of the distribution of kinetic rate constants. Here, we introduce two numerically stable integral transformations to solve these two challenges. The first transformation enables us to deduce the number of rate-limiting steps from kinetic measurements, even when each step has arbitrarily distributed rate constants. The second transformation allows us to reconstruct the distribution of rate constants in the multistep reaction using the phase function approach, without fitting the data. We demonstrate the stability of the two integral transformations by both analytic proofs and numerical tests. These new methods will help provide robust and unbiased kinetic analysis for many complex chemical and biochemical reactions.     

Reaction of diisocyanates with alcohols. I. Uncatalyzed reactions

Because diisocyanates are widely used raw materials in the production of urethane elastomers and foams, it is of particular interest, to know the contribution of secondary reactions to the overall reaction between diisocyanates and polyether glycols, because of the well known influence of crosslinks on the physicochemical properties of polyurethanes. A mathematical method is suggested to calculate rate constants for the primary and secondary reactions, the hypothesis being that the allophanate group is the main secondary product. The method has been verified with experimental data obtained by reacting models. In addition, the influence of the [NCO]/[OH] ratio and of temperature on the formation of the allophanate group has been studied. The method has been applied to the reaction of 4,4′-diphenylmethane diisocyanate with poly(oxytetramethylene) glycol, a polyether glycol specifically designed for use in preparing polyurethanes. The results are in complete agreement with the experimental data.     

A macroscopic kinetic model for DNA polymerase elongation and high-fidelity nucleotide selection

The enzymatically catalyzed template-directed extension of ssDNA/primer complex is an important reaction of extraordinary complexity. The DNA polymerase does not merely facilitate the insertion of dNMP, but it also performs rapid screening of substrates to ensure a high degree of fidelity. Several kinetic studies have determined rate constants and equilibrium constants for the elementary steps that make up the overall pathway. The information is used to develop a macroscopic kinetic model, using an approach described by Ninio [Ninio J., 1987. Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabilities. Proc. Natl. Acad. Sci. U.S.A. 84, 663-667]. The principle idea of the Ninio approach is to track a single template/primer complex over time and to identify the expected behavior. The average time to insert a single nucleotide is a weighted sum of several terms, including the actual time to insert a nucleotide plus delays due to polymerase detachment from either the ternary (template-primer-polymerase) or quaternary (+nucleotide) complexes and time delays associated with the identification and ultimate rejection of an incorrect nucleotide from the binding site. The passage times of all events and their probability of occurrence are expressed in terms of the rate constants of the elementary steps of the reaction pathway. The model accounts for variations in the average insertion time with different nucleotides as well as the influence of G + C content of the sequence in the vicinity of the insertion site. Furthermore the model provides estimates of error frequencies. If nucleotide extension is recognized as a competition between successful insertions and time delaying events, it can be described as a binomial process with a probability distribution. The distribution gives the probability to extend a primer/template complex with a certain number of base pairs and in general it maps annealed complexes into extension products.     

Collisional energy transfer in the reactions I + NO + M → INO + M and I + NO2 + M → INO2 + M

The low-pressure recombination rate constants of the reactions I + NO + M → INO + M (with 14 different M) and I + NO₂ + M → INO₂ + M (with 26 different M) have been measured at 330°K by laser flash photolysis. The collision efficiencies β_c are analyzed and compared with other thermal activation systems. Whereas β_c increases in one reaction with an increasing number of atoms in M, practically no such effect is found when, for the same M, different reactions with varying complexities of the reacting molecules are considered.     

Multidimensional vibrational spectroscopy for tunneling processes in a dissipative environment

Simulating tunneling processes as well as their observation are challenging problems for many areas. In this study, we consider a double-well potential system coupled to a heat bath with a linear-linear (LL) and square-linear (SL) system-bath interactions. The LL interaction leads to longitudinal (T1) and transversal (T2) homogeneous relaxations, whereas the SL interaction leads to the inhomogeneous dephasing (T2*) relaxation in the white noise limit with a rotating wave approximation. We discuss the dynamics of the double-well system under infrared (IR) laser excitations from a Gaussian-Markovian quantum Fokker-Planck equation approach, which was developed by generalizing Kubo's stochastic Liouville equation. Analytical expression of the Green function is obtained for a case of two-state-jump modulation by performing the Fourier-Laplace transformation. We then calculate a two-dimensional infrared signal, which is defined by the four-body correlation function of optical dipole, for various noise correlation time, system-bath coupling parameters, and temperatures. It is shown that the bath-induced vibrational excitation and relaxation dynamics between the tunneling splitting levels can be detected as the isolated off-diagonal peaks in the third-order two-dimensional infrared (2D-IR) spectroscopy for a specific phase matching condition. Furthermore, this spectroscopy also allows us to directly evaluate the rate constants for tunneling reactions, which relates to the coherence between the splitting levels; it can be regarded as a novel technique for measuring chemical reaction rates. We depict the change of reaction rates as a function of system-bath coupling strength and a temperature through the 2D-IR signal.     

Derivation of rate constant ratios for consecutive second‐order irreversible reactions

The determination of rate constants for consecutive irreversible reactions is a difficult and time‐consuming problem, especially when the research extends up to many subsequent products. Thus, the derivation of proper mathematical expressions would greatly facilitate the determination of these rate constants when only the rate constant of the first consecutive reaction is known. Many authors have dealt with this problem in the past but the issue is still of interest to the scientific community judging from recent publications. This paper aims at extending our knowledge of mathematical expressions for rate constant ratios of consecutive reactions to more than three reactions, as is the situation now, and offering a simple graphical estimation of the rate constant ratios exploiting the maxima of each intermediate product. Furthermore, the method extends to the derivation of a generic formula for the estimation of the rate constant ratios based on this graphical approach. This approach for the estimation of rate constant ratios based on mathematical expressions and graphical estimations was validated against experimental data found in the literature.     

Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase

The ability of using wave function propagation approaches to simulate isotope effects in enzymes is explored, focusing on the large H/D kinetic isotope effect of soybean lipoxygenase-1 (SLO-1). The H/D kinetic isotope effect (KIE) is calculated as the ratio of the rate constants for hydrogen and deuterium transfer. The rate constants are calculated from the time course of the H and D nuclear wave functions. The propagations are done using one-dimensional proton potentials generated as sections from the full multidimensional surface of the reacting system in the protein. The sections are obtained during a classical empirical valence bond (EVB) molecular dynamics simulation of SLO-1. Since the propagations require an extremely long time for treating realistic activation barriers, it is essential to use an effective biasing approach. Thus, we develop here an approach that uses the classical quantum path (QCP) method to evaluate the quantum free energy change associated with the biasing potential. This approach provides an interesting alternative to full QCP simulations and to other current approaches for simulating isotope effects in proteins. In particular, this approach can be used to evaluate the quantum mechanical transmission factor or other dynamical effects, while still obtaining reliable quantized activation free energies due to the QCP correction.     

High temperature molecular beam source reactor

Small low residence time flow tube reactors made of alumina and used as molecular beam sources are described. In these reactors, gas mixtures are rapidly heated and brought to reaction. The composition of the gas leaving the reactor is analyzed by molecular beam mass spectroscopy. For quantitative simulation of the reacting gas flow, the theory of one-dimensional compressible flow with friction, heat transfer, and chemical reaction is brought into a form suitable for practical computation. The system has been applied to study the thermal decompositions of O₃ and N₂O. The experimental results on both reactions can be well modeled by homogeneous reaction mechanisms with accepted rate constants. Heterogeneous reaction steps are shown to be unimportant.     

Effect of brownian diffusion on chemical kinetics

A new method of theoretical prediction of the kinetic rate constants of fast chemical reactions in solutions is presented. It takes into account the effect of finite diffusive displacements of the reacting molecules. The approach is based on the solution of the steady-state Fokker–Planck equation by the moments method of Grad developed in the theory of coagulation of aerosol particles. A comparison of the predicted rate constants with the experimental data provided by Schuh and Fischer for the self-reaction of tert-butyl radicals in n-alkanes shows a good correspondence.     

Room-temperature synthesis of manganese oxide monosheets

Preparation of single-layer manganese oxide nanosheets (monosheets) comprised of edge-shared MnO(6) octahedra has relied on multistep processing involving a high-temperature solid-state synthesis of bulk templates, and ion-exchange and exfoliation reactions in solutions, requiring high cost and long processing time. Here we demonstrate the first single-step approach to directly access the MnO(2) monosheets, by the chemical oxidation of Mn(2+) ions in the presence of tetramethylammonium cations in an aqueous solution. Of importance is that this template-free reaction readily proceeds within a day at room temperature. The ability of the MnO(2) monosheets to self-assemble allows aggregation, to form layered structures with potassium cations and cationic tetrathiafulvalene analogues as intercalants. Furthermore, Langmuir-Blodgett (LB) films composed of the MnO(2) monosheets were successfully fabricated by the LB deposition method, in which about one layer of the monosheets was deposited for each process.     

Reactivity of tris(trimethylsilyl)silane toward diarylaminyl radicals

Absolute rate constants for the reaction of tri-tert-butylphenoxyl radical (ArO*) with (TMS)(3)SiH were measured spectrophotometrically in the temperature range 321-383 K. Rate constants for the hydrogen abstraction from (TMS)(3)SiH by diarylaminyl radicals of type (4-X-C(6)H(4))(2)N* were determined by using a method in which the corresponding amines catalyze the reaction of ArO* with (TMS)(3)SiH. At 364.2 K, rate constants are in the range of 2-50 M(-)(1) s(-)(1) for X = H, CH(3), CH(3)O, and Br, whereas the corresponding value for ArO* is 3 orders of magnitude lower. A common feature of these reactions is the low preexponential factor [log(A/M(-1)s(-1)) of 4.4 and 5.2 for ArO* and Ph(2)N*, respectively], which reflects high steric demand in the transition state. A semiempirical approach based on intersecting parabolas suggests that the observed reactivity is mainly related to the enthalpy of the reaction and allowed to estimate activation energies for the reaction of (4-X-C(6)H(4))(2)N* and ArO* radicals with a variety of silicon hydrides.     

Quantum chemical prediction of reaction pathways and rate constants for dissociative adsorption of CO(x) and NO(x) on the graphite (0001) surface

We present predictions of reaction rate constants for dissociative adsorption reactions of CO(x) (x = 1, 2) and NO(x) (x = 1, 2) molecules on the basal graphite (0001) surface based on potential energy surfaces (PES) obtained by the integrated ONIOM(B3LYP:DFTB-D) quantum chemical hybrid approach with dispersion-augmented density functional tight binding (DFTB-D) as low level method. Following an a priori methodology developed in a previous investigation of water dissociative adsorption reactions on graphite, we used a C(94)H(24) dicircumcoronene graphene slab as model system for the graphite surface in finite-size molecular structure investigations, and single adsorbate molecules reacting with the pristine graphene sheet. By employing the ONIOM PES information in RRKM theory we predict reaction rate constants in the temperature range between 1,000 and 5,000 K. We find that among CO(x) and NO(x) adsorbate species, the dissociative adsorption reactions of CO(2) and both radical species NO and NO(2) are likely candidates as a cause for high temperature oxidation and erosion of graphite (0001) surfaces, whereas reaction with CO is not likely to lead to long-lived surface defects. High temperature quantum chemical molecular dynamics simulations (QM/MD) at T = 5,000 K using on-the-fly DFTB-D energies and gradients confirm the results of our PES study.     

利用目标试验因子分析法确定化学反应的级数及速率常数

利用目标试验因子分析(TTFA)结合数值遗传算法(NGA).解析反应过程中在线测得的动力学谱-光谱数据矩阵,可在未知各组分纯光谱及动力学模型情况下同时求解出各组分的纯光谱、反应级数及速率常数。提出用近似计算法计算各组分的动力学谱,使该方法能适用于任意反应级数的体系。针对两步连续反应模型,对反应物、中间体和最终产物均有吸收及某一种组分没有吸收的体系的模拟实验数据矩阵进行了处理,表明该方法均能适用。利用该方法对邻苯二甲酸二甲酯在碱性介质中的水解反应及日落黄水溶液的电解降解反应过程中测得的数据矩阵进行解析,均获得了可靠结果。