Fragment ions, list

Assign possible structures to all abundant fragment ions from the tabulated ions listed in the structurally significant tables of Part III. Two or more ions together may define the type of compound. For example, the presence of the following ions suggest specific compounds ... 

The first step in the application of mass spectra is obviously to obtain a list of fragment ions formed by electron bombardment of the molecule under study and their relative amounts by appropriate techniques. The goal from this point will necessarily be to relate the positive ions to the molecular structure whether it be an unknown structure to be identified, or a known structure of which a knowledge of fragmentation is desired. The fragment ions observed indicate the pieces of which the molecule is composed... 

In Table IV some physical data and spectral characteristics of 6,7-secoberbines are listed. Only methyl corydalate (55) is optically active. Formula 55 presents the spatial structure of this compound, deduced by Nonaka et al. (65) and confirmed by Cushman et al. by both correlation with (+)-mesotetrahydrocorysamine (72) (<5S) and total synthesis (69). It is difficult to find common characteristic features in both the mass and H-NMR spectra of these alkaloids because they differ significantly from each other in their structures. On one hand, corydalic acid methyl ester (55) incorporates a saturated nitrogen heterocycle, while the three aromatic bases (56-58) differ in the character of the side chain nitrogen. For example, in mass fragmentation, ions of the following structures may be ascribed to the most intensive bands in the spectrum of 55 ... 

The appearance potential (AP) of an ion refers to the experimentally determined minimum energy required to produce that specific ion from the ground state of the neutral atom. The appearance potentials of ions of specific types, such as the fragment ions, have been listed by Franklin et al. (1969). Some common appearance potentials of ions are given in Table 4.2. 

Extensive molecular ion and fragment ion abundances are listed for positive ion El mass spectra of carotenoids. 

The appearance potentials for molecular ions (ionization potentials) and for fragment ions formed in the mass spectra of metallocenes and related compounds are listed in Table XIII. These appearance potentials have been used to calculate bond dissociation energies and heats of formation of organometallic compounds, but the results obtained must be treated cautiously because the appearance potentials of fragment ions include excess energy due to excited species. The values obtained for the heats of formation are best considered as upper limits, rather than precise determinations. The extent to which energy due to excited states can contribute... 

Hard ionisation techniques commonly fragment molecular ions, leading to the loss of neutral species and the formation of fragmentation ions. Some common species lost in mass spectra, and possible chemical inferences that can be drawn from this information, are shown in Table 13.10. In contrast, examples of common fragment ions that are formed are listed in Table 13.11. 

It is important to report the conditions under which the spectrum was run together with a list of the main peaks. It is also useful to work out the structures of the fragment ions. 

While the above classifications and lists probably do not exhaust all possibilities, it may be hoped that the omissions do not overlook any obviously promising stable ions. For example, we have not considered ions based on linked polyhedra or linked fragments of polyhedra. We have not tried to list completely the results of applying the processes of classes (c), (d), and (e) to all ions listed above. Also, we have not... 

Definitive confirmation of pesticide residues was obtained by comparison of parent and fragment ion intensities and mass numbers of eluted pesticides and reference pesticides. Table I lists the residues encountered and the mass numbers and intensities of the characteristic fragments employed for identification in the adipose tissue sample. The mass spectral fragmentation patterns for all the compounds included in Table I with the exception of -HCH have been adequately discussed by other investigators (7). 

Li et al. [162] reported the use of on-line LC-ESI-FT-ICR-MS for the identification of intact proteins in mixtures by alternating seans a short list of candidate proteins is generated from a database search by accmate-mass determination ( 0.1 Da at 10 kDa), and IRMPD is applied to generate fragment ions and sequence tags for each protein, enabling further protein identifieation from the short list. Typical results are shown in Figure 17.4. 

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