Dynamic structure, reaction kinetics studies

A fundamental goal of chemical research has always been to understand the reaction mechanisms leading to specific reaction products. Reaction mechanisms, in turn, are a consequence of the structural dynamics of molecules participating in the chemical process, with atomic motions occurring on the ultrafast timescale of femtoseconds (10 s) and picoseconds (10" s). Although kinetic studies often allow reaction mechanisms as well as the kind and properties of reaction intermediates to be determined, the obtained information is not sufficient to deduce the ultrafast molecular dynamics. Because these ultrafast motions are the essence of every chemical process, detailed knowledge about their nature is of fundamental importance. 

Structural studies of the oxy-Cope catalytic antibody system reinforce the idea that conformational dynamics of both protein and substrate are intimately intertwined with enzyme catalysis, and consideration of these dynamics is essential for complete understanding of biologically catalyzed reactions. Indeed, recent single molecule kinetic studies of enzyme-catalyzed reactions also suggest that different conformations of proteins are associated with different catalytic rates (Xie and Lu, 1999). In addition, a number of enzymes are known to undergo conformational changes on binding of substrate (Koshland, 1987) that lead to enhanced catalysis two examples are hexokinase (Anderson and Steitz, 1975 Dela-Fuente and Sols, 1970) and triosephosphate isomerase (Knowles, 1991). 

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],... 

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]. 

Our recent studies on phenol oxidation by oxoiron(IV) and oxomanganese(IV) porphyrins in aqueous solution (pH 7.6) have shown that the initial step in these reactions is H atom abstraction to generate a phenoxyl radical (Scheme 3). e kinetic isotope effect measured in the present study indicates that H atom abstraction also occurs in the rate determining step of the oxidation of azonaphthol dyes by 1. However, although the structures of azonaphthol dyes are normally shown as azo compounds, in aqueous solution they are in a rapid dynamic equilibrium with their hydrazone tautomers the latter isomer being the dominant species (Scheme 4). This complicates kinetic studies on the dyes, since the substrate is in effect a mixture of two compounds. Consequently one or both the tautomers may be the active form of the substrate providing the H atom for the oxidant. It is important to note that, irrespective of which tautomer is the reactive substrate, H atom abstraction leads to a common azonaphthoxyl radical intermediate and subsequent reactions of this species should be independent of the initial tautomerism (Scheme 5). 

Theoretical chemistry is the discipline that uses quantum mechanics, classical mechanics, and statistical mechanics to explain the structures and dynamics of chemical systems and to correlate, understand, and predict their thermodynamic and kinetic properties. Modern theoretical chemistry may be roughly divided into the study of chemical structure and the study of chemical dynamics. The former includes studies of (1) electronic structure, potential energy surfaces, and force fields (2) vibrational-rotational motion and (3) equilibrium properties of condensed-phase systems and macromolecules. Chemical dynamics includes (1) bimolecular kinetics and the collision theory of reactions and energy transfer (2) unimolecular rate theory and metastable states and (3) condensed-phase and macromolecular aspects of dynamics. 

Probably the main utilization of low-temperature spectroscopic studies in biophysics has been to trap short-lived intermediate chemical states of a protein. Typically the chromophore alone is the object of study, and the protein is viewed basically as a structure which simply holds the chromophore in place or may contribute some critical amino acids in close proximity to the chromophore. The protein is not believed to play an overtly dynamic role, a dynamic role being one where the reaction process is steered by time-dependent protein conformational changes. Temperature is used to slow down or arrest the reaction kinetics occurring at the chromophore and perhaps to discover additional chemical states which have too short a lifetime to be observed at room temperature. Such kinds of kinetic arrest studies have been successfully used in studies of heme... 

---