Mathematical modeling and solution trajectories of complex chemical mechanism based on Monte Carlo methods

The main purpose of this article is introducing the method of Spectral Quasi Equilibrium Manifold taking different model, simple and complex mechanism to find solution curve. Before that discussing reaction kinetic, reduction of system, chemical equilibrium, QEM technique. As in complex reaction we need to split reaction mechanism in different route to reduce the complexity of higher dimensional system.in this article SQEM technique is apply to different route and comparison of route is also discussed. In previous years, the depiction of existing method based on chemical reaction kinetics has become a standard approach, for which estimation of involved parameters become challenge. For the model developments and standardization, Sensitivity analysis is powerful tool. Influence of parameters on target output is discussed through graphical results.     

Electrochemical reactions with protonations at equilibrium: Part VI. The homogeneous electron exchange reaction between a monoelectronic and A 1 e, 1 H+ system

The rate of homogeneous electron exchange between a 1 e redox couple and a 1 e, 1 H⁺ redox system is studied theoretically when the protonations are much faster than the electron exchange reactions, i.e. when they can be assumed to be at equilibrium. It is shown that the whole system is equivalent to a reaction between two simple 1 e couples, with apparent rate constants for the electron exchange. Variations of these constants are complex functions of the difference of the standard potentials of the monoelectronic system and those of the 1 e, 1 H⁺ system. They also vary with pH in a less complicated way. The reaction path and the reaction sequence (order of addition or loss of electrons and protons) are studied. A potential-pH diagram, which allows the results to be visualized, is given. It is shown that it is not possible to accelerate at the same time the reduction and oxidation of the members of the square scheme by the same monoelectronic system. Applications to redox polymer electrodes are discussed.     

燃料电池的机理模型及控制建模的研究

根据直接甲醇燃料电池(DNIFC)的组成结构、工作原理,并运用电化学,流体动力学、热力学等学科理论,建立了DNIFC电池性能数学模型,并结合DNIFC实验数据进行仿真,结果表明这种数学建模是合理和有效的。由于数学模型的复杂性难以满足工程上对PNIFC控制系统的设计特别是实时控制需要的情况,本文提出一种基于最小二乘支持向量机建模算法,用具有RBF核函数的LS-SVM离线建立DNIFC电堆的非线性模型;仿真和实验结果表明了该建模方法具有建模简单、模型精度高等优点,亦证明了该算法的有效性和优越性。研究结果对直接甲醇燃料电池控制系统的建模和控制具有一定的实用价值。     

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.     

HO+CH4→H2O+CH3反应的偏分势能面与散射共振态理论研究

用ab initio方法构建了该体系的偏分势能面, 并用其研究了该体系中散射共振态的形成机理, 估算了第一共振态寿命.     

A rate law model for the explanation of complex pH oscillations in the thiourea-iodate-sulfite flow system

In a continuous flow stirred tank reactor (CSTR), the reaction of thiourea-iodate-sulfite (TuIS) exhibits a rich variety of complex oscillations in pH. The transitions from 1(n) type oscillations to 1(3), 1(2) type and simple oscillations were observed on decreasing the flow rate gradually in small steps at 30.2 °C and 20.5 °C, respectively. The transitions from 1(n) type oscillations to 1(0)1(4), 1(0)1(3) type and simple oscillations were observed as well on increasing the temperature in small steps at a given flow rate. Based on the analogous iodate-sulfite-thiosulfate system a simple empirical rate law model is suggested to give a sound agreement between the experimental and simulated results on the complex oscillatory behaviour. A possible explanation of the emergence of the simple empirical rate law model from the mechanism of the individual reactions of the TuIS system is also discussed.     

Chelate complex formation as a basis for titration processes

Metal cations can be looked upon as LEWIS acids and their reaction with ligands during complex formation can be compared to the addition of the proton to a base. The complex formation reactions, however, lack sharp and definite endpoints and metal cations therefore cannot be titrated with ammonia, cyanide and other ligands in the same way as the hydrogen ion can be titrated alkalimetrically. The theoretical reason for this fact is discussed and it is shown that complex formations gain the characteristic properties of neutralisation reactions if the simple ligands are replaced by a polydentate group which is able to satisfy not only one, but several of the coordination points of the metal cation. A great number of titration processes can be based on such reactions.     

三聚氰胺-甲醛加成反应的研究

The addition reaction between melamine and formaldehyde involves the conversion of melamine into nine different methylol melamines.The reaction mechanism of the complex system can be summarized in a simple reaction model as below:(这里有图片19890824-878-1.gif)The rate equations of above reactions are evaluated by using Runge-Kutta method, and the rate constants are determined by means of fitting them to reaction species concentrations at various times.The molecular distribution formula of methylol derivatives of polyamine, which we developed previously, is used to form simultaneous equations with reaction rate equations and the contents of various meth-ylol-melamine are calculated.The results are good in agreement with the experiment data.     

Palladium-Nanoparticle-Catalysed Ullmann Reactions in Ionic Liquids with Aldehydes as the Reductants: Scope and Mechanism

An efficient Ullmann-type reductive homocoupling of aryl, vinyl and heteroaryl halides can be promoted by an aldehyde in tetraalkylammonium ionic liquids under very mild reaction conditions. This simple procedure generates symmetrical biaryls under relatively mild conditions. The ionic liquid is crucial for this process because it behaves simultaneously as a base, ligand and reaction medium. The role of the aldehyde is also discussed and a general mechanism for this unusual reaction is proposed. These results open the way to a new efficient method of Pd-catalysed dehydrogenation of carbonyl compounds.     

Hydride-exchange reactions between NADH and NAD+ model compounds under non-steady-state conditions. Apparent and real kinetic isotope effects

The kinetics of the hydride exchange reaction between NADH model compound 10-methyl-9,10-dihydroacridine (MAH) and 1-benzyl-3-cyanoquinolinium (BQCN+) ion in acetonitrile were studied at temperatures ranging from 291 to 325 K. The extent of reaction-time profiles during the first half-lives are compared with theoretical data for the simple single-step mechanism and a 2-step mechanism involving initial donor/acceptor complex formation followed by unimolecular hydride transfer. The profiles for the reactions of MAH deviate significantly from those expected for the simple single-step mechanism with the deviation increasing with increasing temperature. The deviation from simple mechanism behavior is much less pronounced for the reactions of 10-methyl-9,10-dihydroacridine-10,10-d2 (MAD) which gives rise to extent of reaction dependent apparent kinetic isotope effects (KIEapp). Excellent fits of the experimental extent of reaction-time profiles with theoretical data for the 2-step mechanism, in the pre-steady-state time period, were observed in all cases. Resolution of the kinetics of the hydride exchange reaction into the microscopic rate constants over the entire temperature range resulted in real kinetic isotope effects for the hydride transfer step ranging from 40 (291 K) to 8.2 (325 K). That the reaction involves significant hydride tunnelling was verified by the magnitudes of the Arrhenius parameters; Ea D - EaH = 8.7 kcal mol-1 and AD/AH = 8 x 10(4). An electron donor acceptor complex (lambda max = 526 nm) was observed to be a reaction intermediate. Theoretical extent of reaction-time profile data are discussed for the case where a reaction intermediate is formed in a non-productive side equilibrium as compared to the case where it is a real intermediate on the reaction coordinate between reactants and products. The common assumption that the two cases are kinetically indistinguishable is shown to be incorrect.     

A quantum-chemical study of dinitrogen reduction at mononuclear iron-sulfur complexes with hints to the mechanism of nitrogenase

The mechanism of biological dinitrogen reduction is still unsolved, and the structure of the biological reaction center, the FeMo cofactor with its seven iron atoms bridged by sulfur atoms, is too complicated for direct attack by current sophisticated quantum chemical methods. Therefore, iron-sulfur complexes with biologically compatible ligands are utilized as models for studying particular features of the reduction process: coordination energetics, thermodynamic stability of intermediates, relative stability of isomers of N2H2, end-on versus side-on binding of N2, and the role of states of different multiplicity at a single iron center. From the thermodynamical point of view, the crucial steps are dinitrogen binding and reduction to diazene, while especially the reduction of hydrazine to ammonia is not affected by the transition metal complex, because the complex-free reduction reaction is equally favored. Moreover, the abstraction of coordinated ammonia can be easily achieved and the complex is recovered for the next reduction cycle. Our results are discussed in the light of studies on various model systems in order to identify common features and to arrive at conclusions which are of importance for the biological mechanism.     

Catalytic studies of the gaseous exchange Reaction H2/HDO using Platinum on Charcoal

In the gaseous exchange reaction H₂/HDO the catalyst (Pt/Charcoal) of concentration 0.4 gm Pt per 100 ml catalyst proved to be highly efficient. Its preparation is simple but precaution is needed to choose, optimum conditions in activating the charcoal prior to impregnation, the right grain size to reduce channelling, the proper reduction process and an efficient purification system to remove poisons. The regeneration of the catalyst is described. The kinetics and mechanism of this reaction are discussed.     

Rolling circle enzymatic replication of a complex multi-crossover DNA nanostructure

Nature has evolved replicable biological molecules, such as DNA, as genetic information carriers. The replication process is tightly controlled by complicated cellular machinery. It is interesting to ask if artificial DNA nano-objects with a complex secondary structure can be replicated in the same way as simple DNA double helices. Here we demonstrate that paranemic crossover DNA, a structurally complicated multi-crossover DNA molecule, can be replicated successfully using Rolling Circle Amplification (RCA). The amplification efficiency is moderate with high fidelity, confirmed by native PAGE, thermal transition study, and Ferguson analysis. The structural details of the DNA structure after the full replication circle are verified by hydroxyl radical autofootprinting. We conclude that RCA can serve as a reliable method to replicate complex DNA structures. We also discuss the possibility of using viruses and bacteria to clone artificial DNA nano-objects. The findings that single stranded paranemic crossover DNA molecules can be replicated by DNA polymerase will not only be useful in nanotechnology but also may have implications for the possible existence of such complicated DNA structures in nature.     

Transport in Nanoporous Materials Including MOFs: The Applicability of Fick’s Laws

Diffusion in nanoporous host–guest systems is often considered to be too complicated to comply with such “simple” relationships as Fick’s first and second law of diffusion. However, it is shown herein that the microscopic techniques of diffusion measurement, notably the pulsed field gradient (PFG) technique of NMR spectroscopy and microimaging by interference microscopy (IFM) and IR microscopy (IRM), provide direct experimental evidence of the applicability of Fick’s laws to such systems. This remains true in many situations, even when the detailed mechanism is complex. The limitations of the diffusion model are also discussed with reference to the extensive literature on this subject.     

Controllability and observability of the photophysical system of intermolecular two-state excited-state processes

In this report, we focus on the consequences of controllability and observability on the number of distinct exponential terms in the fluorescence decay and on the identifiability analysis of the photophysical model of intermolecular two-state excited-state processes. Controllability and observability prove to be useful concepts in photophysics for exploring methodically the conditions under which intermolecular two-state excited-state processes lead to single-exponential fluorescence delta-response functions. A detailed discussion on the distinction of the possible origins of monoexponential fluorescence decays is presented. We also show that the similarity transformation approach to identifiability leads to erroneous conclusions concerning which model parameters can be identified if this photophysical system is not controllable or not observable. The results obtained for this relatively simple photophysical system can be extended in a systematic way to more complicated photophysical models.     

动力学方程控制表面反应的模拟模型和方法

提出了动力学方程控制表面反应的模拟模型和方法.该模型从最基本的质量作用定律出发,获得表面反应的动力学方程.而表面反应通过格子模拟反应器进行.通过表面催化样板反应"CO表面催化氧化"检验了该模拟模型和方法,与实验结果吻合.该模型可在其它复杂的表面催化反应体系中推广应用.     

四氮杂大环四烯镍(Ⅱ)配合物催化的化学振荡反应

化学振荡反应是化学反应体系中某些状态量随时间或空间周期性变化。四氮杂大环配合物与存在生物体内的一些含有卟吩环的金属酶结构相似。目前,可以催化化学振荡反应的四氮杂大环配合物并不多,文献报道了一种具有Ｃ＝Ｎ共轭双键的四烯型四氮杂大环配体（ＴＩＭ）的Ｎｉ 的配合物可以催化ＢＺ化学振荡反应［１－３］。然而以２,４,４,９．１１,１１一六甲基一１,５,８,１２－四氮杂环十四一１,５, ８, １２一四烯（Ｌ）镍配合物［ＮｉＬ（ＣＩＯ４）２］这种具有四个孤立 Ｃ＝Ｎ双键的四烯型四氮杂大环镍的配合物作为振荡反应催化…     

On the mechanism of the ion-molecule reaction CH3+ + CH4 = C2H5+ + H2

Experimental evidence supporting the “direct” reaction model and the “intermediate complex” model for the reaction CH₃⁺(CH₄, H₂)C₂H₅⁺ are analysed. It is shown that the evidence for the former can equally well be interpreted in terms of a proposed model of persistent complex formation and decay. The plausibility of a “direct” mechanism is discussed and is found to be poor.     

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.