Characterization of structures and reactions

Hendrickson, J.B. (1971) A Systematic Characterization of Structures and Reactions for Use in Organic Synthesis. Journal of the American Chemical Society, 93, 6847-6854. 

A less empirical approach to synthesis analysis has been taken by Hendrickson He recognizes the need for a system of characterization of structures and reactions that is specifically designed for use in synthesis. Obviously such a system should derive from the fundamentals of structure, and should be general enough to allow the inclusion of new reactions without collapse of the system. It should convey the information a chemist looks for first when he considers a molecule that is to be synthesized, i.e. the carbon skeleton and functionality. Finally, the system should be so designed that it takes into account, at least implicitly, all possible synthetic routes to a given compound. 

Stationary hanging mercury drop electrodes (h.m.d.e.) are suitable for evaluating a slow equilibrium of adsorption and subsequent reduction. Solid metal or graphite electrodes are used mainly for oxidation. From the molecular biophysical point of view such measurements are performed for characterization of structural and conformational transitions caused by physical and electrochemical influences, such as heat, light, electrical fields, solvents, ions, and other ligands. In all cases, one can distinguish between reversible (allosteric and conformational modifications) and irreversible (denaturation, strand break, enzyme reactions) processes. Besides these investigations, biochemical analysis, clinical tests, and electrochemical synthesis are fruitful applications. 

Huang, H.-H., Glaser, R.H., and Wilkes, G.L. (1987) Structure-property behavior of new hybrid materials incorporating organic oligomeric species into sol—gel glasses. IV. Characterization of structure and extent of reaction. Proc. PMSE ACS Div., 56, 85812. 

STM has particularly great potential for in situ chemical studies. While our present knowledge of the atomic structure of catalyst surfaces is largely limited to those structures which are stable in ultra-high vacuum before and after reaction, STM may provide an insight into both adsorbate and catalyst surface structure in situ during the reaction. The following issues to be characterized by STM may be most relevant to characterization of catalysts and catalysis ... 

The kinetics of ethylene hydrogenation on small Pt crystallites has been studied by a number of researchers. The reaction rate is invariant with the size of the metal nanoparticle, and a structure-sensitive reaction according to the classification proposed by Boudart [39]. Hydrogenation of ethylene is directly proportional to the exposed surface area and is utilized as an additional characterization of Cl and NE catalysts. Ethylene hydrogenation reaction rates and kinetic parameters for the Cl catalyst series are summarized in Table 3. The turnover rate is 0.7 s for all particle sizes these rates are lower in some cases than those measured on other types of supported Pt catalysts [40]. The lower activity per surface... 

Enzymes that catalyze redox reactions are usually large molecules (molecular mass typically in the range 30-300 kDa), and the effects of the protein environment distant from the active site are not always well understood. However, the structures and reactions occurring at their active sites can be characterized by a combination of spectroscopic methods. X-ray crystallography, transient and steady-state solution kinetics, and electrochemistry. Catalytic states of enzyme active sites are usually better defined than active sites on metal surfaces. 

Lipases belong to the subclass of serine hydrolases, and their structure and reaction mechanism are well understood. Their common a/p-hydrolase enzyme fold is characterized by an a-helix that is connected with a sharp turn, referred to as the nucleophilic elbow, to the middle of a P-sheet array. All lipases possess an identical catalytic triad consisting of an Asp or Gin residue, a His and a nucleophilic Ser [14]. The latter residue is located at the nucleophilic elbow and is found in the middle of the highly conserved Gly—AAl—Ser—AA2—Gly sequence in which amino acids AAl and AA2 can vary. The His residue is spatially located at one side of the Ser residue, whereas at the opposite side of the Ser a negative charge can be stabilized in the so-called oxyanion hole by a series of hydrogen bond interactions. The catalytic mechanism of the class of a/P-hydrolases is briefly discussed below using CALB as a typical example, since this is the most commonly applied lipase in polymerization reactions [15]. 

There are many excellent books and reviews on the structure and reactions of secondary radical ions generated in radiolytic and photolytic reactions. Common topics include the means and kinetics of radical ion production, techniques for matrix stabilization, electronic and atomic structure, ion-molecule reactions, structural rearrangements, etc. On the other hand, the studies of primary radical ions, viz. solvent radical ions, have not been reviewed in a systematic fashion. In this chapter, we attempt to close this gap. To this end, we will concentrate on a few better-characterized systems. (There have been many scattered pulse radiolysis studies of organic solvents most of these studies are inconclusive as to the nature of the primary species.)... 

PKSs are characterized by their ability to catalyze the formation of polyketide chains from the sequential condensation of acetate units from malonate thioesters. In plants they produce a range of natural products with varied in vivo and pharmacological properties. PKSs of particular note include acridone synthase, bibenzyl synthase, 2-pyrone synthase, and stilbene synthase (STS). STS forms resveratrol, a plant defense compound of much interest with regard to human health. STS shares high sequence identity with CHS, and is considered to have evolved from CHS more than once. ° Knowledge of the molecular structure of the CHS-like enzymes has allowed direct engineering of CHS and STS to alter their catalytic activities, including the number of condensations carried out (reviewed in Refs. 46, 51, 52). These reviews also present extensive, and superbly illustrated, discussions of CHS enzyme structure and reaction mechanism. 

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