Organic molecules fragmentation patterns

Qualitative analysis MS can be used to identify the molecular weight of organic and inorganic compounds, from very small molecules to large polymers and biological molecules (> 100,000 Da). MS is a powerful tool in the determination of the structure of organic compounds. Fragmentation patterns can reveal the presence of substructure units within the molecule. 

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. 

Molecular orbital calculations indicate that cyclo C-18 carbyne should be relatively stable and experimental evidence for cyclocarbynes has been found [25], Fig. 3B. Diederich et al [25] synthesised a precursor of cyclo C-18 and showed by laser flash heating and time-of flight mass spectrometry that a series of retro Diels-Alder reactions occurred leading to cyclo C-18 as the predominant fragmentation pattern. Diederich has also presented a fascinating review of possible cyclic all-carbon molecules and other carbon-rich nanometre-sized carbon networks that may be susceptible to synthesis using organic chemical techniques [26]. 

In addition to forming molecular ions, organic molecules decompose into fragment ions in a mass spectrometer. As a result, a host of ions form that have a m/z less than that of the molecular ion. These ions give rise to the characteristic mass spectrum of the molecule. The fragmentation pattern of a molecule is characteristic of the molecule, and an unknown compound may be identified by comparison with a catalog of standard spectra. 

Mass spectrometry of organic molecules has become well established in recent years and both the recording of spectra and the fragmentation patterns of functional groups have been comprehensively discussed (14, 19, 33, 126, 142). In the last 2 3 years the study of the behavior of organometallic compounds in the mass spectrometer, previously a neglected... 

The decay-induced fragmentation pattern of a number of representative organic molecules has been determined with appropriate mass spectrometric techniques (7), showing that, in most cases, the daughter organic cation escapes further dissociation, for example, the methyl cation from Equation 1 is obtained with a 82% yield, being formed in its ground electronic state with little or no vibrational excitation. 

As mentioned before, MS is a useful technique to analyze unknown organic molecules by studying their fragmentation pattern. However, since there are several requirements for samples to be analyzed, when an organic molecule is unsuitable to be studied by gas chromatography, another suitable analytical technique can be chosen, for example, liquid chromatography (EC), direct injection probe (DIP), and direct exposure probe (DEP). 

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