It has been thought that reactions, dynamic in nature, have only a little connection with crystallography which deals with static matter. This article, however, discusses the capability of the diffraction crystallography for the study of chemical reactions. Reactivity is closely related to the electron distribution in the reactant molecule and its geometry. Structures of the reaction intermediates which correspond to the local minima between those for the reactants and products in the potential energy hypersurf ace is important in establishing the reaction mechanism. Some correlation observed in structural fragments suggests the reaction path frozen by the different crystalline fields. Thermal parameters provide the information on the neighbourhood of the potential minima. Studies on the solid state reaction will also be helpful in discussing the reactions in solution or more complicated system, because the surrounding molecules in crystal limit the valley of the potential hypersurf ace, which is reaction path.
The recnt advances in X-ray determination of electron distribution in transition metal complexes are summarized in connection with possible applications of the technique to studies on mechanisms of chemical reactions. The effects of the ligand field symmetry on the d electron distribution were already observed in crystals of CoAl2O4, γ-Fe2SiO4 and FeS2 with the X-ray diffraction method. Using the aspherical scattering factors (ASF) of electrons in 3dyz, 3dxy, 3dz2and 3dx2-y2orbitals, the spin-states of transition metals in KMnF3and KCoF3crystals were determined equivocally. The wave functions for 3d electrons of the Cu atom in Jahn-Teller distorted KCuF3 crystals wese determined with ASF in a good approximation. These successes imply that the X-ray analysis with ASF can be effectively applied to the studies on chemical reactions, such as oxidation-reduction reactions where changes of the spin states are essential and catalytic reactions of transition metals where the spatial relations of the a electron lobes are important, and so on.
Based on the molecular structures of the reaction products determined by X-ray analysis, correlations between molecular structures and reaction mechanism are reported in this article. High selectivity for electrophilic addition of Br2 or BrOH and Michael addition of dimethyl malonate to the chiral sulf inyl compounds are explained in terms of the established configurations and conformations of the products. A study on a series of the compounds produced by Bipolar additions to thiadizoles and thiadizoline reveals that a bond switch takes place at the π-hypervalent sulfur atom during these reactions. In the last section recent topics on a relationship between reaction paths and molecular structures proposed by Burgi are reviewed.
Solid state reactions of organic compounds have been extensively studied for the last decade. It is proved that the crystal structure analysis is a very powerful tool in the elucidation of the reaction mechanism. The control of the reactions by the crystal. line field has been insisted by many investigators. We have found the crystalline-state racemization of cobaloxime complexes by X-ray exposure. The chiral group bonded to the cobalt atom in a single crystal is racemized without degradation of the crystallinity. Three types of the racemization have been found till now. We have defined the cavity for the reacting group, and concluded that the rate of the reaction is closely related tc the volume and the shape of the cavity at different temperatures or in different crys-tals. These findings will serve to elucidate the mechanisms not only in the solid state reaction but also in the reactions of the clathrate compounds and enzymes.
Based on X-ray single crystal analyses of α-, β-, and γ-cyclodextrins inclusion compounds, relation between structure and reactivity is demonstrated, especially focusing on molecular structure of the inclusion complexes.
Protein crystallography is one of the most powerful techniques for observing the interactions of enzymes with other molecules, especially small ones, at atomic resolution. This article, taking up a group of serine proteases as an example, outlines the way crystallography has been useful for elucidating the enzymatic reation mechanisms. Finally, we introduce “X-ray cryoenzymology” or “low temperture protein crystallography”, the apparently most effective technique for determining the details of the interaction of enzymes with their actual substrates, which will be a popular method in no distant future.
The advantages of nuclear magnetic resonance analyses for studying conformations and dynamical properties of protein molecules in aqueous solution are reviewed. For erabutoxin b, a short neurotoxin, and for α-cobratoxin, a long neurotoxin, the local environments and proximity relations of amino acid residues have been elucidated. The conformations of these molecules in neutral aqueous solution are different, in part, from those in crystal. From the analyses of the deuterium exchange rates of amide protons, the long neurotoxins are found to be less flexible than short neurotoxins, corresponding to the lower dissociation/association rates of long toxins for acetylcholin receptor proteins.
Many studies on topotactic decomposition of minerals have so far been carried out by many people, and the results were reviewed in this paper. Formation of intermedi-ate phases in the course of reactions were reported for some minerals, and the importance of the analyses of the intermediate phases was pointed out. Insitu observations of talc have been made using a high temperature X-ray camera and an electron microscope equipped with a heating stage. The results are also briefly reported.
The vapor phase silicon epitaxial reaction is taken as an example of chemical reactions in the crystal growth. As growth rates are mainly controlled by gas phase mass transfer, it is particularly shown that gas concentrations near the crystal surface are affected by surface processes and thermal diffusion. Futhermore, theoretical chemical equillibrium data including the calculation method and experimental gas concentration distributions of multicomponent species are cited from references. At low pressure epitaxy the main species is simply SiCl2 of the chemical condensation type. In this case, there is the metastable region on the supersaturation diagram where homoepitaxy proceeds preferentially than hetro-epitaxy. Finally, substrate orientation effects on growth rates are illustrated from the surface kinetics.