Fragmentation Processes

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Chapter: Organic Chemistry : Structure Determination of Organic Compounds

Besides the molecular ion, fragmentation processes can be used to infer groups present in the molecule and the connectivity of those groups.


Besides the molecular ion, fragmentation processes can be used to infer groups present in the molecule and the connectivity of those groups. The requirement of spin and charge conservation in any fragmentation means that both cations and radical cations can be produced as ions by fragmentation. Because of the great amount of energy deposited in the molecular ion, there is sufficient energy to break any of the bonds in the molecule. It has been found, however, that fragmentations tend not to be random but occur in such a way that the most stable ions are produced. Normally the most stable ion is the most abundant ion in the mass spectrum. The most abundant ion is called the base peak of the spectrum and is arbitrarily scaled at 100%, and the abundances of other ions are given as percentage relative to the base peak. Several examples of very stable ions are as follows:

Fragmentations often occur from the molecular ion by loss of neutrals or rad-icals to give more stable ions or radical ions. The differences in mass correspond to the mass of the uncharged fragment that has been expelled. The mass spectrum of ethane has a molecular ion at m/e = 30 and a major peak at m/e = 15. This corresponds to the loss of a fragment of 15 amu from the molecular ion. Thus the ethane molecular ion undergoes fragmentation of the C–C bond to give a methyl cation which is detected at m/e = 15 and a methyl radical which is not detected as it is uncharged. This very simple example is indicative of the process.

Ethyl benzoate (Figure 11.49) has a molecular ion at m/e = 150 and a base peak at m/e = 105 (M 45) and a smaller peak at m/e = 77. The base peak at m/e = 105 corresponds to loss of the ethoxy radical from the molecular ion to give the very stable phenylacylium ion. 

Loss of CO from the phenylacylium ion gives the phenyl cation, but due to the instability of the phenyl cation, this pathway is minor. Also observed is a peak at m/e = 122 due to the benzoic acid radical cation resulting from loss of the neutral ethylene molecule from the molecular ion by a different fragmentation process.

1,3-Diphenylpropanone has a molecular ion at m/e = 210 and significant frag-ment ions of m/e = 119 (M 15) and m/e = 65. The base peak is m/e = 91. In this example, loss of a benzyl radical from the molecular ion produces an acylium ion (m/e = 119) which rapidly loses CO because the resulting benzyl cation is extremely stable — one of the most stable ions normally encountered. Examination of the mass spectrum (Figure 11.50) shows that there are many additional small peaks present other than those just discussed. Their presence is indicative of the high energy deposited in the molecular ion upon ionization which permits a large number of fragmentations to occur. Nevertheless the frag-mentations which occur most often and lead to the most intense peaks are those that follow common ideas about reactivity and ion stability.

Both ethers and alcohols readily undergo loss of groups next to the oxygen so as to produce an oxonium ion. Thus tert-butyl ethyl ether m/e = 102 has a very large M 15 peak due to loss of a methyl radical.

The methyl group could be lost from either the t -butyl group (path a) or the ethyl group (path b) to give two different oxonium ions with the same m/e value. The base peak at m/e = 57 is the t -butyl cation and indicates that at least part of the time the methyl group is lost from the ethyl group (path b) because subsequent loss of formaldehyde from the oxonium ion gives the t -butyl cation. The t -butyl cation can also be produced by a single fragmentation of the molecular ion by loss of the ethoxy radical. The stability of the t -butyl cation makes it the base peak and ensures its production by a variety of routes. This is not to say that all of the M 15 peak comes from path b, and most likely there is some contribution to the m/e = 87 peak from path a; however, the oxonium ion thus produced is unlikely to fragment into the very unstable ethyl cation.

By working with mass spectral fragmentation patterns, it is possible to develop very keen insight into the ways that molecules disintegrate under high-energy conditions. This permits identification of the structure from the pieces and insight into how they were produced. In conjunction with other structural tools, MS provides invaluable insight into molecular formula and connectivity issues in a molecule and is thus an important tool in structure elucidation.

The foregoing discussion has been a very elementary introduction into MS as a tool for structure identification. Advances in sample introduction, methods of ionization, and ion collection and detection have been remarkable, and today the mass spectra of peptides, nucleic acids, proteins, and other biopolymers are routinely obtained. Using known cracking patterns, MS is the method of choice for identifying drugs and drug testing since it requires only minute quantities (micrograms). It has been sent on the Mars probe to look for amino acids as an indication of life forms on Mars. One goal of current research efforts is to use MS as a method for sequencing peptides and oligonucleotides by their fragmentation patterns. Mass spectrometry is thus an important analytical and structural tool whose evolution continues at a rapid pace. It remains an important component of structural investigation.

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