Fragmentation Patterns of Hydrocarbons

Mass spectra of the cis- and /ram-isomers of the pyrimido[2,TA [l,3]thiazin-6-ones 294 and 295 were studied. Retro-Diels-Alder fragmentation of the hydrocarbon ring was of medium to low stereospecificity. A number of highly selective processes were discovered allowing differentiation between stereoisomers <1996RCM721>. The mass spectral fragmentation pattern of 296 was studied in detail <1996PS(113)67>. 

McCarthy, E.D., Han, J. and Calvin, M. (1968). Hydrogen atom transfer in mass spectrometric fragmentation patterns of saturated aliphatic hydrocarbons. Anal. Chem., 40, 1475-1480. 

The postulated primary chemical steps can be examined in the light of the mass spectroscopic fragmentation pattern of F-cyclobutane (14), which shows C2F/ as the parent peak (abundance 100 arbitrary units). A 1-3 split is also favorable C3Fr,+ has an intensity of 87 units, and CF3 25 units. These data are consistent with Steps 5b and 5c. Rupture of a C—F bond (Reaction 5a) must be more important in the radiolysis mechanism than indicated by the low abundance of 0.1 unit for the C4F7+ ion in the mass spectrum. However, this anomaly occurs not only in other fluorocarbon systems (1, 5, 10, 11, 22) but in most hydrocarbon systems studied to date. The intensities of CFL>+ and CF+ are also substantial in the mass spectrum, being 13 and 54 units respectively. These results, and the fact that CFL> has often been found under pyrolytic conditions (2,12), suggest the possibility that difluorocarbene plays a role in the mechanism, perhaps leading to a portion of the odd-carbon products. We have no evidence on this point, however. 

The compounds involved and detected by analytical GC-MS workflows like volatiles, PCBs, or pesticides are discussed with representative mass spectra in the following sections. These compounds do not necessarily belong to the same functional compound class with a chemical classification for instance of amines, ester, phenols, hydrocarbons and others. Many standard references cover these characteristic fragmentation patterns of specific functional groups and compound classes in detail (Howe, 1981 McLafferty and Turecek, 1993 Budzikiewicz, 1998). 

A typical SSIMS spectrum of an organic molecule adsorbed on a surface is that of thiophene on ruthenium at 95 K, shown in Eig. 3.14 (from the study of Cocco and Tatarchuk [3.28]). Exposure was 0.5 Langmuir only (i.e. 5 x 10 torr s = 37 Pa s), and the principal positive ion peaks are those from ruthenium, consisting of a series of seven isotopic peaks around 102 amu. Ruthenium-thiophene complex fragments are, however, found at ca. 186 and 160 amu each has the same complicated isotopic pattern, indicating that interaction between the metal and the thiophene occurred even at 95 K. In addition, thiophene and protonated thiophene peaks are observed at 84 and 85 amu, respectively, with the implication that no dissociation of the thiophene had occurred. The smaller masses are those of hydrocarbon fragments of different chain length. 

Because mass-spectral fragmentation patterns are usually complex, it s often difficult to assign structures to fragment ions. Most hydrocarbons fragment in many ways, as the mass spectrum of hexane shown in Figure 12.4 demonstrates. The hexane spectrum shows a moderately abundant molecular ion at m/z = 86... 

A spectacular example of the influence of steric factors on the fragmentation pattern involves the behavior of chloro- and bromoalkanes. If the hydrocarbon chain is unbranched, peaks of C4H8Hal+ ions dominate in the homologous series of fragment ions CnH2nHal+ (Scheme 5.9). Any substitute in the carbon chain sharply decreases the competitiveness of this process. 

The multiple cleavage modes in ketones sometimes make difficult the determination of the carbon chain configuration. Reduction of the carbonyl group to a methylene group yields the corresponding hydrocarbon whose fragmentation pattern leads to the carbon skeleton. 

To establish unambiguously the length of a hydrocarbon chain or the position of double bonds, mass spectral analysis of lipids or their volatile derivatives is invaluable. The chemical properties of similar lipids (for example, two fatty acids of similar length unsaturated at different positions, or two isoprenoids with different numbers of isoprene units) are very much alike, and their positions of elution from the various chromatographic procedures often do not distinguish between them. When the effluent from a chromatography column is sampled by mass spectrometry, however, the components of a lipid mixture can be simultaneously separated and identified by their unique pattern of fragmentation (Fig. 10-24). 

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