Kinetic hierarchy

After the definition of a reaction type, a scheme for the evaluation of the given reaction type can follow in the reaction rule. An entire hierarchy of evaluations can be implemented, from no evaluation at all to a full-fledged estimation of reaction kinetics [12 ... 

As is well recognized, various macroscopic properties such as mechanical properties are controlled by microstructure, and the stability of a phase which consists of each microstructure is essentially the subject of electronic structure calculation and statistical mechanics of atomic configuration. The main subject focused in this article is configurational thermodynamics and kinetics in the atomic level, but we start with a brief review of the stability of microstructure, which also poses the configurational problem in the different hierarchy of scale. 

The reaction of eq. 16.9 will regenerate the antioxidant Arj-OH at the expense of the antioxidant At2-OH. Despite the fact that such regeneration reactions are not simple electron transfer reactions, the rate of reactions like that of eq. 16.9 has been correlated with the E values for the respective Ar-0. Thermodynamic and kinetic effects have not been clearly separated for such hierarchies, but for a number of flavonoids the following pecking order was established in dimethyl formamid (DMF) by a combination of electrolysis for generating the a-tocopherol and the flavonoid phenoxyl radicals and electron spin resonance (ESR) spectroscopy for detection of these radicals (Jorgensen et al, 1999) ... 

MORTENSEN A, SKIBSTED L H (1997) Relative stability of carotenoid radical cations and homologue tocopheroxyl radicals. A real time kinetic study of antioxidant hierarchy. FFBS Letters, 417, 261-6. 

As outlined in the previous section, there is a hierarchy of possible representations of metabolism and no unique definition what constitutes a true model of metabolism exists. Nonetheless, mathematical modeling of metabolism is usually closely associated with changes in compound concentrations that are described in terms of rates of biochemical reactions. In this section, we outline the nomenclature and the essential steps in constructing explicit kinetic models of metabolic networks. 

Hypothetical hierarchy of reactions (A) those that fail to yield amplification and (B) those that can achieve any level of amplification, depending only on the number of cycles and the kinetic parameters of the active enzymes formed by successive conversions of proenzyme into active enzymes. 

Kuzovkov and Kotomin [89-91] (see also [92, 93]) were the first to use the complete Kirkwood superposition approximation (2.3.62) in the kinetic calculations for bimolecular reaction in condensed media. This approximation allows us to cut off the infinite hierarchy of equations for the correlation functions describing spatial distribution of particles of the two kinds and to restrict ourselves to the treatment of minimal set of the kinetic equations which realistically could be handled (Fig. 2.21). In earlier studies [82, 84, 91, 94-97] a shortened superposition approximation was widely used... 

The kinetics of the diffusion-controlled reaction A + B —> 0 under study is defined by the initial conditions imposed on the kinetic equations. Let us discuss this point using the production of geminate particles (defects) as an example. Neglecting for the sake of simplicity diffusion and recombination (note that even the kinetics of immobile particle accumulation under steady-state source is not a simple problem - see Chapter 7), let us consider several equations from the infinite hierarchy of equations (2.3.43) ... 

Turning back now to the kinetics of the diffusion-controlled A + B —> 0 recombination, and neglecting reactant interaction, let us write down several equations from an infinite hierarchy of equations (2.3.37), (2.3.45), and (2.3.53) ... 

However, Waite s approach has several shortcomings (first discussed by Kotomin and Kuzovkov [14, 15]). First of all, it contradicts a universal principle of statistical description itself the particle distribution functions (in particular, many-particle densities) have to be defined independently of the kinetic process, but it is only the physical process which determines the actual form of kinetic equations which are aimed to describe the system s time development. This means that when considering the diffusion-controlled particle recombination (there is no source), the actual mechanism of how particles were created - whether or not correlated in geminate pairs - is not important these are concentrations and joint densities which uniquely determine the decay kinetics. Moreover, even the knowledge of the coordinates of all the particles involved in the reaction (which permits us to find an infinite hierarchy of correlation functions = 2,...,oo, and thus is... 

Before discussing mathematical formalism we should stress here that the Kirkwood approximation cannot be used for the modification of the drift terms in the kinetics equations, like it was done in Section 6.3 for elastic interaction of particles, since it is too rough for the Coulomb systems to allow us the correct treatment of the charge screening [75], Therefore, the cut-off of the hierarchy of equations in these terms requires the use of some principally new approach, keeping also in mind that it should be consistent with the level at which the fluctuation spectrum is treated. In the case of joint correlation functions we use here it means that the only acceptable for us is the Debye-Htickel approximation [75], equations (5.1.54), (5.1.55), (5.1.57). 

Of special interest in the recent years was the kinetics of defect radiation-induced aggregation in a form of colloids-, in alkali halides MeX irradiated at high temperatures and high doses bubbles filled with X2 gas and metal particles with several nanometers in size were observed [58] more than once. Several theoretical formalisms were developed for describing this phenomenon, which could be classified as three general categories (i) macroscopic theory [59-62], which is based on the rate equations for macroscopic defect concentrations (ii) mesoscopic theory [63-65] operating with space-dependent local concentrations of point defects, and lastly (iii) discussed in Section 7.1 microscopic theory based on the hierarchy of equations for many-particle densities (in principle, it is infinite and contains complete information about all kinds of spatial correlation within different clusters of defects). 

With Eq. (3.37) for Fn it is possible to write a kinetic equation for F, that describes the formation and the decay of two-particle bound states in three-particle collisions. Introducing (3.37) into the first equation of the hierarchy (1-29), we obtain in a similar way as in Section III.2 a kinetic equation for the density operator of free particles. This equation may be written in the following form ... 

In science, there is a hierarchy of questions (i) what , (ii) how , and (iii) why . The report of a given fact, e.g., the determination of a series of products and their yields, only answers the question what . Additional kinetic studies raise our level of understanding, as it answers the question how . The ultimate scientific question, why , has as yet rarely been answered, but this level of knowledge is a prerequisite for being able to predict a certain reaction without too many flanking experiments. Thus, it will be one of the main goals of future research to strive for an in-depth theoretical understanding. This, of course, has to be based on our present (and future) experimental data, and it is one of the intentions of this book to provide the necessary information in a compact form. 

Figure 2. Multiscale modeling hierarchy. AIMD ab initio molecular dynamics, MD molecular dynamics, KMC kinetic Monte Carlo modeling, and FEA finite element analysis.

In a recent survey [19] it was noted that a realistic model for catalytic oxidation reactions must include equations describing the evolution of at least two concentrations of surface substances and account for the slow variation in the properties of the catalyst surface (e.g. oxidation-reduction). For the synchronization of the dynamic behaviour for various surface domains, it is necessary to take into consideration changes in the concentrations of gas-phase substances and the temperature of the catalyst surface. It is evident that, in the hierarchy of modelling levels, such models must be constructed and tested immediately after kinetic models. On the one hand, the appearance of such models is associated with the experimental data on self-oscillations in reactors with noticeable concentration variations of the initial substances and products (e.g. ref. 74) on the other hand, there was a gap between the comprehensively examined non-isothermal models with simple kinetics and those for the complex heterogeneous catalytic reactions... 

For this reason, the local concentrations of the B components will vary and, consequently, the concentrations of the A and V components will also vary. The indicated change in the structure of the system of equations relates to all the levels of the hierarchy. For instance, in a point model with restricted mobility of the B component, the kinetic equation for the function 0 (1) will be written as follows ... 

The relative power of DMG (Table 1), established by experiments at low temperature and short reaction times and thus crudely representative of kinetic control conditions, may vary with inter- and intramolecular competition, conditions, and sometimes results are conflicting. Nevertheless, for synthetic practice this hierarchy follows a qualitative order consistent with CIPE and serves as a useful predictive chart. For thermodynamic control conditions, the pchart of Fraser of 12 DMG [27], determined by equilibrium deprotonation using LiTMP (pka=37.8), is a guide for lithium dialkylamide DoM reactions. 

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