Ion structural studies

Cooks, R. G., J. H. Beynon, and M. Bertrand. 1973. Ion structural studies by ion kinetic energy spectrometry [CtHtJ + j [C7Hg]+, C7H70CH3] +. Organic Mass Spectrometry 7 1303-12. 

Background. As an analytical technique, tandem mass spectrometry is just entering its second decade of development. The variety of reported applications belies its relative youth. Tandem mass spectrometry (MS/MS) grew out of early work which used metastable ion transitions in order to establish ion structures and interrelationships. After extensive applications to ion structural studies, its usefulness in direct catplex mixture analysis became apparent with the early work of Cooks (1-3). Its successes in problem solving are summarized in a recent book edited by McLafferty (4). New, with several ccnmercial instruments available, MS/MS is being evaluated for application in several new areas, including biochemical analysis, forensic chemistry, and food and flavor analyses. The principles of MS/MS will be surmarized in the first part of this chapter. The second part of the chapter will deal with the reported applications of MS/MS to flavor analysis. 

The hammerhead ribozyme is a small RNA that catalyzes specific RNA cleavage in the sugar-phosphate backbone. The function of this RNA strongly relies on Mg placement to maintain structural integrity. Aminoglycoside action in inhibition of hammerhead ribozyme function has been shown to involve displacement of these necessary Mg ions. Structural studies of the hammerhead ribozyme bound by neomycin have indicated that the charged ammo-... 

The evidence discussed to this point, both for and against the nonclassical structure, rests on indirect evidence derived from interpretation of kinetic results and stereochemical features of the substitution reactions. With the development of the techniques for directly observing carbonium ions, structural studies on the ion became possible. The norbornyl cation was subjected to intense scrutiny by George Olah at Case Western Reserve University. These spectroscopic investigations constituted a new approach to the problem. 

In this section, the wide diversity of teclmiques used to explore ion chemistry and ion structure will be outlined and a sampling of the applications of ion chemistry will be given in studies of lamps, lasers, plasma processing, ionospheres and interstellar clouds. 

Nonclassical ions, a term first used by John Roberts (an outstanding Caltech chemist and pioneer in the field), were defined by Paul Bartlett of Harvard as containing too few electrons to allow a pair for each bond i.e., they must contain delocalized (T-electrons. This is where the question stood in the early 1960s. The structure of the intermediate 2-norbornyl ion could only be suggested indirectly from rate (kinetic) data and observation of stereochemistry no direct observation or structural study was possible at the time. 

The alkyl-bridged structures can also be described as comer-protonated cyclopropanes, since if the bridging C—C bonds are considered to be fully formed, there is an extra proton on the bridging carbon. In another possible type of structure, called edge-protonated cyclopropanes, the carbon-carbon bonds are depicted as fully formed, with the extra proton associated with one of the bent bonds. MO calculations, structural studies under stable-ion conditions, and product and mechanistic studies of reactions in solution have all been applied to understanding the nature of the intermediates involved in carbocation rearrangements. 

Nitrogen-containing fulvalenes have not been systematically studied by mass spectroscopy. Only isolated data for several examples of compounds have been reported. Most of the data consist of electron impact (El) mass spectra recorded for analytical purposes. Only a minor fraction dealt with the characterization of ion structures or focused on the effects of substituents, the ring size of fulvalenes, or the number and arrangement of nitrogen atoms and the fragmentation pathways. 

The mass spectra of free carbohydrates and their glycosides, obtained by ionization upon electron impact, are limited in their usefulness for structural studies. Peaks corresponding to molecular ions are generally not observed due to extensive fragmentation to ions of low m/e (4,9,11, 24, 26). In contrast, positive ions produced by field ionization do not give fragment spectra as characteristic as do those produced by electron impact, but the molecular ion peaks are intense, often the most intense in the spectra (3). 

In practice, the valne depends on the type of analysis being attempted. Structural studies may require the extent of fragmentation to be maximized, while quantification may require the opposite, i.e. the efficient prodnction of a small number of ions of different m/z ratios, in order to maximize sensitivity. Selectivity may be obtained simply by monitoring of the molecular ions formed. On occasions, when significant background is observed, this may not be adequate and fragmentation of the molecnlar species may be necessary to provide a number of ions to be monitored. Some componnds may be ionized very effectively under positive-ionization conditions, while others may require the formation of negative ions to allow analysis. 

The initial work in this field appeared as a communication in 1969 8), and this work was later expanded to a full paper (9). Badley et al. described the synthesis of m-Pt(PEt3)(CNCjH5)Cl2 from Pt2(PEt3)2Cl4 and the isocyanide the bromide complex could be obtained from this complex by addition of bromide ion. These complexes were then observed to react with various substances [Eq. (16)]. A crystal structure study on the complex... 

Bond length differences between HS and LS isomers have been determined for a number of iron(II), iron(III) and cobalt(II) complexes on the basis of multiple temperature X-ray diffraction structure studies [6]. The available results have been collected in Table 17. Average values for the bond length changes characteristic for a particular transition-metal ion have been extracted from these data and are obtained as AR 0.17 A for iron(II) complexes, AR 0.13 A for iron(III) complexes, and AR = 0.06 A for cobalt(II) complexes. These values may be compared with the differences of ionic radii between the HS and LS forms of iron(II), iron(III) and cobalt(II) which were estimated some time ago [184] as 0.16, 0.095, and 0.085 A, respectively. 

The chemistry of the heavy carbenium ion analogs has been the subject of several preceding reviews, of which the latest one by Miiller P is the most comprehensive. In this section we will deal briefly with the most essential achievements made in the 1990s, and will emphasize the latest progress in the field, particularly concerning the synthesis and structural studies of the stable noncoordinated ( free ) cations of the type RR R"E+. 

The group at Aarhus have reported carbon-induced structures at Ni(lll) and Ni(110) surfaces resulting from the dissociation of ethylene at high temperatures.27 Between 400 and 500 K, the Ni(l 10) surface is seen to form two carbidic structures with (4 x 3) and (4 x 5) domains present arising from surface reconstruction with substantial transport of nickel taking place. At higher temperatures (560 K), the surface becomes dominated by the (4 x 5) structure, which is well ordered and can be observed clearly by LEED. Ion scattering studies provide additional information which enables models to be constructed for both the (4 x 3) and (4 x 5) phases. 

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