Heuristic control of kinetic energy in dynamic reaction coordinate calculations

For the understanding and prediction of chemical reactions, detailed knowledge of the minimum energy path between reactants and transition state is of utmost importance. Stewart et al. (J. Comput. Chem. 1987, 8, 1117) proposed the usage of molecular trajectories calculated from Newton's equations of motion for an efficient reaction path following. Two operational modes are possible thereby: intrinsic (IRC) and dynamic reaction coordinate calculations (DRC). The technical difference between these modes is that in an IRC calculation the kinetic energy of the nuclei is quenched while the total energy is conserved in DRC calculations. In this work, a heuristic control methodology of atomic kinetic energies in DRC calculations using fuzzy logic is proposed. A diversified test set of 10 reactions has been collected to examine the performance of this approach. Fuzzy rule‐based models are found to be a convenient way to make the determination of accessible paths of chemical reactions computationally efficient. © 2013 Wiley Periodicals, Inc.     

In Situ Mass Spectrometric and Kinetic Investigations of Soai's Asymmetric Autocatalysis

Chemical reactions that lead to a spontaneous symmetry breaking or amplification of the enantiomeric excess are of fundamental interest in explaining the formation of a homochiral world. An outstanding example is Soai's asymmetric autocatalysis, in which small enantiomeric excesses of the added product alcohol are amplified in the reaction of diisopropylzinc and pyrimidine-5-carbaldehydes. The exact mechanism is still in dispute due to complex reaction equilibria and elusive intermediates. In situ high-resolution mass spectrometric measurements, detailed kinetic analyses and doping with in situ reacting reaction mixtures show the transient formation of hemiacetal complexes, which can establish an autocatalytic cycle. We propose a mechanism that explains the autocatalytic amplification involving these hemiacetal complexes. Comprehensive kinetic experiments and modelling of the hemiacetal formation and the Soai reaction allow the precise prediction of the reaction progress, the enantiomeric excess as well as the enantiomeric excess dependent time shift in the induction period. Experimental structural data give insights into the privileged properties of the pyrimidyl units and the formation of diastereomeric structures leading to an efficient amplification of even minimal enantiomeric excesses, respectively.     

A fitting formula for the falloff curves of unimolecular reactions,II: Tunneling effects

By taking into account effects of tunneling on the shape of the falloff curves of unimolecular reaction rate constants based on Troe's weak collision integral, a fitting formula for these curves is developed and then examined for several tunneling‐affected reactions. It is demonstrated that, compared to the widely used Troe's formula, the present expression not only substantially enhances the accuracy in fitting for tunneling‐affected reactions, but it is also computationally more efficient in its evaluation. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 43: 31–42, 2011     

A comparative study of the master equation approach and the discrete galerkin method for the simulation of free radical polymerization

The present article deals with the mathematical treatment of free radical polymerization reactions. As a typical example the synthesis of poly(methyl methacrylate) under realistic experimental conditions is investigated. Since the mathematical treatment of the kinetic rate equations raises severe numerical problems, alternative approaches are required. In this paper two of these methods, i.e. the discrete Galerkin method and the master equation approach, are compared. The discrete Galerkin method circumvents difficulties encountered by the direct integration of the kinetic rate equations but requires much a priori knowledge of the chemical reaction system. Within the framework of the master equation approach the polymerization reaction is regarded as a stochastic process. For the simulation of this stochastic process a modified algorithm is presented. The example of the polymerization of methyl methacrylate shows that the master equation approach is an efficient tool in the simulation of free radical polymerization reactions.     

均相催化反应在任一给定形状微电极上的稳态电化学行为

根据反应层的概念对在任一给定形状微电极上进行的准一级和二级均相催化反应机理(EC'')的稳态电化学行为进行了研究。本方法简便易行,不需要解复杂方程的数学技巧。利用推导出的这些方程,可计算准一级和二级均相催化反应的动力学常数。     

An Efficient Stereoselective Synthesis of Key Fragments of Elaiophylin

The stereoselective synthesis of key fragments 3 and 7 of elaiophylin has been accomplished from readily available epichlorohydrin as the starting material. The key reactions involved are Jacobsen's kinetic resolution, Prins cyclization, pyridinium chlorochromate‐mediated oxidative cleavage, Grignard reaction, and cross‐metathesis reaction.     

Study on ketalization reaction of poly(vinyl alcohol) by ketones. IX. Kinetic study on acetalization and ketalization reaction of 1,3-butanediol as a model compound for poly(vinyl alcohol)

A kinetic study was carried out on the acetalization reaction of 1,3-butanediol, as a model compound for poly(vinyl alcohol) (PVA), in water, under acidic conditions. Since these equilibrium constants of ketalization reaction of 1,3-butanediol and ethylene glycol are so small, the kinetic parameters were estimated from the hydrolysis reactions of the corresponding ketals. It was made clear that these reactions proceed in the reversible bimolecular reaction, and the heat of reaction and activation energy are nearly equal to that of PVA. The rate constants of hydrolysis reaction (k′s) of model compounds were calculated on the basis of value of acetone ketal, Hammett-Taft's equation log k′s/k′so – 0.54(n – 6) = ρ^*σ^* was established, and the value of ρ^* was obtained (3.60), which coincided with the value of PVA. Therefore, it was made clear that the hydrolysis reactions of acetals and ketals are electrophilic reaction (SE II reaction) and the step of rate determination is the formation of hemiacetal and hemiketal. The rate constants of hydrolysis reaction of 1,3-butanediol acetals and ketals were approximately 10–20 larger, and those of ethylene glycol were approximetly 50–80 larger except for ketals, and those of ethanol were roughly 2000–10,000 larger compared with that of high-molecular weight compound (PVA). It can be well explained that these differences in the rate constant depend on their entropy and the mobility of molecules. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35 : 1719–1931, 1997     

On the application of an oxygen probe in chemical kinetics: The influence of the probe response on kinetic measurement

Membrance covered oxygen probes are frequently used to monitor the progress of chemical reactions involving dissolved oxygen. For reactions that are comparable in rate to the response of the oxygen probe it is difficult to obtain the correct kinetic constants directly from the probe signal with traditional kinetic data manipulation methods. In this article, we apply the method of impulse response function to describe the probe signal of an oxygen probe for three different types of simple chemical reactions. The impulse response function is obtained experimentally. Using the impulse response function we have obtained the relationships between the probe signal and the kinetic parameters of these reactions. The slow response of the probe has two effects on the kinetic curves of the reaction studied: a time-lag and distortion of the shape of the kinetic curve throughout the reaction. The latter effect becomes significant when the reaction is fast. Procedures to obtain the correct kinetic information from the oxygen probe signal are described. © 1995 John Wiley & Sons, Inc.     

Modulation of molecular and kinetic properties of enzymes upon immobilization

Pea seedling glutamate dehydrogenase(EC 1.4.1.2) and Jack bean urease (EC 3.5.1.5) were immobilized on aminoethyl cellulose by cross-linking in a two-step reaction with glutaral dehyde. Specific activities of the immobilized dehydrogenase and urease were about 14% and 87%, respectively, of the original material in free solution. Both immobilized enzymes show no appreciable change in their pH dependence, whereas a less efficient binding of the substrates is suggested by the increased apparent Michaelis constants (K_m app.). Sigmoid kinetics were observed for both enzymes when reactions were carried out in a packed bed. Diffusional effects are considered responsible for producing these anomalous kinetics. The implications of these perturbations in terms of the catalytic efficiency of the enzymes, as well as the practical problems involved in the analysis of the kinetic data, are discussed.     

Evaluation of the kinetics and mechanisms of hybriding reactions

A scheme for a kinetic study of the hydriding reactions of metals is presented. This scheme is based on a combined kinetic and metallographic study of hydride formation in metallic samples with well defined geometrical shapes.Since the directly measured kinetic quantity (which is the overall reaction rate) depends also on parameters which are not related to the intrinsic nature of the reaction (i.e., on the geometrical shape of the sample and on the topochemistry of the product development) an intrinsic kinetic parameter IKP, should be evaluated in order to characterize uniquely a given reacting system. The choices for these intrinsic parameters and the methods for their evaluation are presented.Different theoretical models for the hydriding reactions are summarized and the predicted pressure-temperature dependence of the IKP's are discussed in light of these models. In some cases the comparison between the experimental and theoretical pressure-temperature behavior may elucidate the mechanisms controlling the respective reactions.     

Parallel replica dynamics with a heterogeneous distribution of barriers: application to n-hexadecane pyrolysis

Parallel replica dynamics simulation methods appropriate for the simulation of chemical reactions in molecular systems with many conformational degrees of freedom have been developed and applied to study the microsecond-scale pyrolysis of n-hexadecane in the temperature range of 2100-2500 K. The algorithm uses a transition detection scheme that is based on molecular topology, rather than energetic basins. This algorithm allows efficient parallelization of small systems even when using more processors than particles (in contrast to more traditional parallelization algorithms), and even when there are frequent conformational transitions (in contrast to previous implementations of the parallel replica algorithm). The parallel efficiency for pyrolysis initiation reactions was over 90% on 61 processors for this 50-atom system. The parallel replica dynamics technique results in reaction probabilities that are statistically indistinguishable from those obtained from direct molecular dynamics, under conditions where both are feasible, but allows simulations at temperatures as much as 1000 K lower than direct molecular dynamics simulations. The rate of initiation displayed Arrhenius behavior over the entire temperature range, with an activation energy and frequency factor of E(a) = 79.7 kcal/mol and log A/s(-1) = 14.8, respectively, in reasonable agreement with experiment and empirical kinetic models. Several interesting unimolecular reaction mechanisms were observed in simulations of the chain propagation reactions above 2000 K, which are not included in most coarse-grained kinetic models. More studies are needed in order to determine whether these mechanisms are experimentally relevant, or specific to the potential energy surface used.     

Kinetics and mechanism of the chain reaction between <Emphasis Type="Italic">N</Emphasis>-phenyl-1,4-benzoquinone monoimine and thiophenol

The kinetics of the reaction between N-phenyl-1,4-benzoquinone monoimine (quinone monoimine) and thiophenol is studied in chlorobenzene at 343 K. The reaction has the same mechanism proposed earlier for a similar reaction involving N,N'-diphenyl-1,4-benzoquinone diimine (quinone diimine). This mechanism has two paths: chain and nonchain. An important difference between the kinetics of the two reactions is the apparent reversible nature of the chain reaction in the quinone monoimine + thiophenol system. This nature reveals itself when the concentrations of thiophenol are comparable to or slightly higher than the concentrations of quinone imine. In light of this, kinetic research is conducted under conditions where the concentrations of thiophenol are significantly higher than those of quinone monoimine, allowing us to simplify the kinetic features and obtain interpretable data. The rate constants of the reaction’s elementary steps are estimated and found to be three to five times lower for the reaction involving quinone monoamine than for the one involving quinone diimine. Both reactions have relatively short chains whose lengths do not exceed several tens of units.     

Vilsmeier–Haack formylation of coumarin derivatives. A solvent dependent kinetic study

A kinetic study of the reaction of coumarin derivatives with Vilsmeier-Haack (VH) reagent (1:1 DMF-POCl₃) in various solvent media revealed second-order kinetics with a first-order in [Substrate] and first-order in [VH reagent]. The reaction rates altered nonlinearly with an increase in the dielectric constant of the medium and the data did not fit completely well with either Amis or Kirkwood's theories of ion (SINGLEBOND) dipole and dipole (SINGLEBOND) dipole type reactions. On the basis of kinetic and spectroscopic results, participation of VH-adduct and coumarin molecule in the rate limiting step, has been proposed. Kinetic and activation parameters have been evaluated and discussed in terms of isokinetic relationship and as a function of solvent compositions. Linearity of Leffler's and Exner's plots indicate a similar type of mechanism to be operative in different dielectric media at all temperatures. © 1996 John Wiley & Sons, Inc.     

The application of symbolic computing to chemical kinetic reaction schemes

Given a reaction mechanism we show how a symbolic computation approach can be used to develop the kinetic equations by identifying the reaction scheme with an equivalent matrix. Our method is also applicable in cases where the stoichiometric matrix approach fails. The specific algorithm that is written applies to schemes where individual reactions are at most ternary, but the way to generalize the procedure is also discussed. By using symbolic computing it is possible to determine general properties of the system. We demonstrate this by showing how to use the matrix to determine the system's conservation laws, which in turn can be used to reduce the number of equations in the system. As another application it is shown how to determine some of the species which have a zero equilibrium state. To illustrate the procedure, example reaction schemes are investigated.     

Automation of the Batch Method for Reaction Kinetic Studies Using Flow Injection Analysis. Kinetic Study of Hydrolysis Of N4-Acetylsulfanilamide,Acetylsalicylic Acid and Phenyl Phosphate

Abstract

The automation of the discontinuous (batch) method for kinetic stucfies using flow-injection analysis (FIA) is described. Aliquots of the reaction mixture are automatically injected in an appropriate manifold and the kinetic profile of the reaction is obtained as a series of absorbance peaks. Observed reaction rate constants are calculated using the Guggenheim and non-linear fitting approaches. The new method is evaluated in the kinetic study of the acid hydrolysis of N⁴-acetylsulfanilamide by colorimetric monitoring of sulfanilamide, the alkaline hydrolysis of acetylsalicylic acid (aspirin) by colorimetric monitoring of salicylate, and the enzymic hydrolysis of phenyl phosphate with alkaline phosphatase by colorimetric monitoring of phosphate. The automated flow-injection batch method can be used in kinetic studies of reactions with t_1/2 greater than 200 s.     

Dinitrogen Fixation: Rationalizing Strategies Utilizing Molecular Complexes

Dinitrogen (N₂) is the most abundant gas in Earth's atmosphere, but its inertness hinders its use as a nitrogen source in the biosphere and in industry. Efficient catalysts are hence required to ov. ercome the high kinetic barriers associated to N₂ transformation. In that respect, molecular complexes have demonstrated strong potential to mediate N₂ functionalization reactions under mild conditions while providing a straightforward understanding of the reaction mechanisms. This Review emphasizes the strategies for N₂ reduction and functionalization using molecular transition metal and actinide complexes according to their proposed reaction mechanisms, distinguishing complexes inducing cleavage of the N≡N bond before (dissociative mechanism) or concomitantly with functionalization (associative mechanism). We present here the main examples of stoichiometric and catalytic N₂ functionalization reactions following these strategies.     

Controlled Preparation of Hydrangea-like 0.3Zn-0.15Sn/CuO Catalysts for the Rochow-Müller Reaction by Microwave-Assisted Liquid-Phase Synergistic Impregnation

In catalytic reactions, trace amounts of promoters can make up for the low activity of a catalyst and significantly affect the physicochemical properties of the catalyst. Exploring a simple and efficient composite Cu-based catalyst is essential to the Rochow-Müller reaction. In this work, monodisperse, a hydrangea-like 0.3Zn-0.15Sn/CuO composite catalyst in the Rochow-Müller reaction. The composite was synthesized via a microwave-assisted liquid-phase synergistic impregnation method in which Sn and Zn were used to dope the CuO surface to create strong Si interaction points. A significant increase in the catalytic activity of CuO was observed after Sn and Zn doping, attributed to the rearrangement of charges on the CuO surface and increase in the Cu atom's core electron density. This work provided a novel and efficient method for preparing efficient Cu-based catalysts for the Rochow-Müller reaction.     

Kinetics and mechanism of the defluorination of 8-fluoropurine nucleosides in basic and acidic media

For investigating the stability of C(8)-fluorine bond in 8-fluoropurine nucleosides some protected 8-fluoroguanosine, 8-fluoroinosine and 8-fluoroadenosine derivatives were prepared by direct fluorination of acetyl-protected purine nucleosides with elemental fluorine in solvents such as chloroform, acetonitrile and nitromethane. Fluorination reactions conducted in chloroform medium gave better yields of 8-fluoropurines. The fluorination yields were slightly lower when acetonitrile or nitromethane was used as solvent, but the product purification was found to be much easier. When the synthesized, protected fluoronucleosides were subjected to standard basic (NH₃ in methanol or 2-propanol) and acidic (HCl in methanol) deprotection conditions relevant to nucleoside chemistry, an efficient defluorination reaction took place. The kinetics of these defluorination reactions were conveniently followed, under pseudo-first-order reaction conditions, using ¹⁹F NMR spectroscopy. ¹H NMR, LC-MS and mass spectroscopy identified the products of the kinetic reaction mixtures. The defluorination reaction rate constants (k_obs) in basic media depended upon the electron density at C(8) while the k_obs data in acidic medium were determined by the pK_a of N⁷. An addition-elimination based mechanism (S_NAr) has been proposed for the defluorination reactions of these 8-fluoropurine nucleosides.     

Experimental study and kinetic modeling of kerosene thermal cracking

Thermal cracking of kerosene for producing ethylene and propylene has been studied in an experimental setup. A set of experiments were designed using Response Surface Design (Box Behnken) method. In these experiments, the coil outlet temperature (COT), residence time and steam ratio varied from 795 °C, 0.13 s and 0.6 to 838 °C, 0.27 s and 1.0, respectively. Obtained maximum ethylene and propylene yield in these experiments were 32 and 16.9 wt.%, respectively. In next step of studies, we tried to develop an applicable kinetic model to predict yield distribution of products of the kerosene thermal cracking. Therefore, a reaction mechanism is generated on the basis of major reactions classes in the pyrolysis and feed compounds using some simplification assumptions in the model. This semi-mechanistic kinetic model contains 172 reactions, 22 molecular and 29 radical species. A sensitivity analysis was done on kinetic model and controlling reactions identified. An objective function was defined and used to tune the model with experimental data. Finally, the calculated model results were compared with the experimental data. Scatter diagrams showed good agreement between model and experimental data.     

On the role of transport in the combustion kinetics of a steady-state premixed laminar CO + H2 + O2 flame

The role of mechanistic steps, diffusion, and their interrelation is explored in a steady-state premixed laminar CO + H₂ + O₂ flame using a numerical model. Sensitivity coefficients and Green's functions calculated for this system offer systematic characterization of the role of diffusion and exothermicity in carbon monoxide oxidation kinetics. The results reveal that the uncertainties in transport parameters are as important to the model predictions as those in the kinetic steps. The rate controlling steps of the CO + H₂ + O₂ reaction are found to be different for adiabatic and nonadiabatic premixed flames, and also for systems with and without transport. In particular, the reactions of the hydroperoxyl radical with hydrogen, oxygen, and hydroxyl radicals are found to be important at all temperatures in the fuel lean (40 torr) adiabatic flame studied here. The diffusive mixing of chemical species from the low and the high temperature portions of the flame and the larger heats of reaction associated with the hydroperoxyl radicals are found to be responsible for the increased importance of these reactions. © 1994 John Wiley & Sons, Inc.