Dynamic structure, reaction kinetics

Within physical chemistry, the long-lasting interest in IR spectroscopy lies in structural and dynamical characterization. Fligh resolution vibration-rotation spectroscopy in the gas phase reveals bond lengths, bond angles, molecular symmetry and force constants. Time-resolved IR spectroscopy characterizes reaction kinetics, vibrational lifetimes and relaxation processes. 

The simple pore structure shown in Figure 2.69 allows the use of some simplified models for mass transfer in the porous medium coupled with chemical reaction kinetics. An overview of corresponding modeling approaches is given in [194]. The reaction-diffusion dynamics inside a pore can be approximated by a one-dimensional equation... 

It is important to propose molecular and theoretical models to describe the forces, energy, structure and dynamics of water near mineral surfaces. Our understanding of experimental results concerning hydration forces, the hydrophobic effect, swelling, reaction kinetics and adsorption mechanisms in aqueous colloidal systems is rapidly advancing as a result of recent Monte Carlo (MC) and molecular dynamics (MO) models for water properties near model surfaces. This paper reviews the basic MC and MD simulation techniques, compares and contrasts the merits and limitations of various models for water-water interactions and surface-water interactions, and proposes an interaction potential model which would be useful in simulating water near hydrophilic surfaces. In addition, results from selected MC and MD simulations of water near hydrophobic surfaces are discussed in relation to experimental results, to theories of the double layer, and to structural forces in interfacial systems. 

Experimental work providing information on reaction kinetics— the time dependence of reactants and products under defined conditions—served indispensably to correlate structure-reactivity data and to provide estimates of transition state energies. Theory-based definitions of transition structures gave some clues as to how reactions might actually take place. But the dynamic aspects of chemical reactions remained inaccessible, or only poorly accessible. 

The solver is implemented in Fortran, using optimized treatment of diagonal-band matrices and analytical derivatives of reaction rates to minimize computation time. The software structure is modular, so that different reaction-kinetic modules for individual types of catalysts can be easily employed in the monolith channel model. The compiled converter models are then linked in the form of dynamic libraries into the common environment (ExACT) under Matlab/Simulink. Such combination enables fast and effective simulation of combined systems of catalytic monolith converters for automobile exhaust treatment. 

The main problem with predictions of kinetic preferences based on force-field calculations of relative stabilities of reaction intermediates arises from the fact that the energies of the competing intermediate structures usually differ by amounts smaller than the accuracy of the energy calculations. These calculations are inherently inexact, since the force-field parameters for the intermediates are mostly unknown (high-level ab initio calculations would be needed to determine them). Moreover, the probability that a reaction passes via a given intermediate depends not only on its enthalpy, but also on entropy thus, a dynamic description of the solvated intermediate would be required. Finally, even if we knew the structure of a reaction intermediate perfectly, it would always remain an approximation for the geometry of the transition state, whose free energy is the real determinant of the reaction kinetics. 

In this chapter, we will review the reaction dynamics studies which has been performed on supported model catalysts in order to unravel the elementary steps of heterogeneous catalytic reactions. In particular we will focus on the aspects that cannot be studied on extended surfaces like the effect of the size and shape of the metal particles and the role of the substrate in the reaction kinetics. In the first part we will describe the experimental methods and techniques used in these studies. Then we present an overview of the preparation and the structural characterization of the metal particle. Later, we will review the adsorption studies of NO, CO and 02. Finally, we will review the two reactions that have been investigated on the supported model catalysts the CO oxidation and the NO reduction by CO. 

Theoretical approaches to structural biophysics, like the theories of transport and reaction kinetics explored in other chapters of this book, are grounded in physical chemistry concepts. Here we explore a few problems in molecular structural dynamics using those concepts. The first two systems presented, helix-coil transitions and actin polymerization, introduce classic theories. The material in the remainder of the chapter arises from the study of macromolecular interactions and is motivated by current research aimed at uncovering and understanding how large numbers of proteins (hundreds to thousands) interact in cells [7],... 

First principles approaches are important as they avoid many of the pitfalls associated with using parameterized descriptions of the interatomic interactions. Additionally, simulation of chemical reactivity, reactions and reaction kinetics really requires electronic structure calculations [108]. However, such calculations were traditionally limited in applicability to rather simplistic models. Developments in density functional theory are now broadening the scope of what is viable. Car-Parrinello first principles molecular dynamics are now being applied to real zeolite models [109,110], and the combined use of classical and quantum mechanical methods allows quantum chemical methods to be applied to cluster models embedded in a simpler description of the zeoUte cluster environment [105,111]. 

It appears that the incorporation of metal adatoms into adsorbate structures stabilizes the reaction intermediates, and therefore, can be expected to be a general phenomenon on catalytic metal surfaces, at least for metal particles large enough to be considered as metallic. The dynamic processes of incorporation, release, and mass transport of metal adatoms may occur on the time scale of surface reactions and affect the reactive behavior of the intermediates, that is to say, the reaction kinetics. Indeed, STM studies have shown that the kinetic oscillation in some surface reactions can be partially attributed to the spatial organization of reactive species on the surfaces and the structural change in such complex surfaces on the time scale of reaction [69]. The structural complexity of the active surfaces and the origin of unusual surface reaction kinetics are of interest, and may be connected. Recently, such a relationship was established in the autocatalytic decomposition of formate and acetate on the Ni(llO) surface [21]. 

Reaction Kinetics as a Probe for the Dynamic Structure of Microemulsions... 

Jakobsen HA, Bourg I, Hjarbo KW, Svendsen HF (2001) Interaction Between Reaction Kinetics and Flow Structure in Bubble Column Reactors. In Jenssen CB et al (eds) Parallel Computational Fluid Dynamics - Trends and Applications, Elsevier Science B.V., pp 543-550, ISBN 0-444-50673-X... 

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