Mass spectrum, fragmentation mechanisms

The interpretation of an unknown mass spectrum, to a point where a structural assignment is possible, is in many cases difficult without a considerable background knowledge of the mass spectral fragmentation mechanisms and pathways of many classes of compounds. 

Figure 4.2 Mass spectrum of palmitic acid and main fragmentation mechanisms. This spec trum was obtained by DE MS with a Polaris Q ion trap external ionisation mass spectrometer. Reproduced from Talanta, 74, Ribechini et al., 2008a, Copyright 2008 with permission from Elsevier...

The mass spectrum of cyclohexanone has been examined by deuterium-labeling to reveal the mechanism effective for propyl loss, [M-43], m/z 55, from the molecular ion, = 98. [38,39] The corresponding signal represents the base peak of the spectrum (Fig. 6.11). Obviously, one deuterium atom is incorporated in the fragment ion that is shifted to m/z 56 in case of the [2,2,6,6-D4]isotopomer. These findings are consistent with a three-step mechanism for propyl loss, i.e., with a double a-cleavage and an intermediate 1,5-H shift. 

The results of elctron-impact studies of phosphine by Halmann et al. are given in Table 3a. The authors used the appearance potentials, in conjunction with thermochemical data, to choose the probable reaction processes. In many simple cases the observed appearance potential A (Z) for an ion fragment Z from a molecule RZ is related to its ionisation potential 7(Z) and to the energy of dissociation 7)(R—Z) of the bond by the expression A (Z) = /(Z) + D (R—Z). This assumes that the dissociation products are formed with little, if any, excitation energy, and that /(Z) < /(R). The most abundant ion species in the usual mass spectrum of phosphine is PH, which is probably formed according to the following mechanism... 

Exercise 9-47 The mass spectrum of propylbenzene has a prominent peak at mass number 92. With (3,3,3-trideuteriopropyl)benzene, this peak shifts to 93. Write a likely mechanism for breakdown of propylbenzene to give a fragment of mass number 92. 

In neutralization-reionization mass spectrometric experiments on CH2Si+ formed by electron-impact dissociative ionization of ClCH2SiH3, Srinivas, Stilzle and Schwarz found evidence for the formation of a viable neutral molecule whose fragmentation pattern and collisional activation mass spectrum were in accord with a H2C=Si structure422. These authors suggested that their experiments supported electron-capture by CH2Si+" as a mechanism for the formation of H2C=Si in interstellar space. Various models have predicted that H2C=Si is one of the most abundant forms of silicon in dense interstellar clouds423. 

The mass spectrum of cyclohexene shows a peak at mlz 54. Show a structure for this fragment and suggest a mechanism for its formation. 

DBT, 2-DBT (2-methyldibenzo[3]thiophene), and 4,6-DBT (4,6-dimethyldibenzo[3]thiophene) in ESI tandem mass spectra have a a consistent 32 Da neutral loss, which is believed to be sulfur. Based on the tandem mass spectrum of the PASH compounds, the mechanism of fragmentation is considered to be a charge site-initiated reaction followed by a radical site-initiated fragmentation. Taking the example of DBT, Scheme 4 shows a possible mechanism. 

Finally, the combined voltammetric and on-line differential electrochemical mass spectrometry measnrements allow a quantitative approach of the ethanol oxidation reaction, giving the partial current efficiency for each product, the total number of exchanged electrons and the global product yields of the reaction. But, it is first necessary to elucidate the reaction mechanism in order to propose a coherent analysis of the DBMS results. In the example exposed previously, it is necessary to state on the reaction products in order to evaluate the data relative to acetic acid production which cannot be directly detected by DBMS measurements. However, experiments carried out at high ethanol concentration (0.5 mol L" ) confirmed the presence of the ethyl acetate ester characterized by the presence of fragments at m/z = 61, 73 and 88 at ratios typical of the ethyl acetate mass spectrum. " This ethyl acetate ester is formed by the following chemical reaction between the electrochemically formed acetic acid and ethanol (Bq. 29) and confirms the formation of acetic acid. 

A further important aspect of the abundances of ions is their relationship to the initial structure of the sample molecule. It is often possible to deduce this structure, or elements of it, by comparison of the MS fragmentation reactions of related compounds. Examples of mass spectra are shown in Figures 1.6, 1.12 and 1.13. The reasoning used in the interpretation of a mass spectrum is based on the accumulated knowledge from the rationalisation of fragmentation mechanisms of known compounds and supported by labelling studies and the accurate mass measurement of ions. Detailed information of such mechanisms can be found in specific textbooks [14] and throughout the literature. 

The formation of the mass spectra fragments can be explained by a variety of mechanisms. For example, the formation of the ion m/z 163 for the trisaccharide with the spectrum shown in Figure 3.6,2 can be explained as follows ... 

Figure 6 The phosphopantetheinyl ejection assay (PEA), (a) McLafferty-type ejection mechanism, (b) Oxazoline ejection mechanism. McLafferty-type ejection (c) and oxazoline ejection (d) on phosphopantetheinylated protein yield charge-reduced protein minus water and phospho-PPant ejection ion. (e) Iminolactone PPant ejection on phosphopantetheinylated protein yields charge-reduced phospho-apo protein and PPant ion. PEA on CouN5 fragment in broadband FT mass spectrum (t), MS2 spectrum (g) shows PPant ion (261.16m/z) and phospho-PPant ion (359.12m/z).

The manual interpretation of a mass spectrum - nature and origin of the fragmentation peaks - is a difficult but interesting exercise. Organic chemists are usually familiar with these methods of interpretation since they retrieve different types of transient ions considered to explain reaction mechanisms in condensed phases. The difference here is that these ions move in a vacuum and do not collide. The very short period of time between ion formation and ion detection (a few pis), allows to observe the existence of very unstable species that are unstable under normal conditions. 

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