Mass Spectrometry: Molecular Fragmentation Overview

The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.

One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at various single bonds in the molecule, but the cleavage preferentially occurs at the positions that generate a stable carbocation and a radical. At a specific bond, the unpaired electron can be transferred to either fragment, creating two sets of products. The preferred orientation of electron transfer occurs in such a way as to generate a more stable carbocation rather than a stable radical. Consider the fragmentation pattern of pentane shown in Figure 1.

Figure 1. Fragmentation of the pentane molecular ion.

From the abundance of carbocations in mass spectra, as depicted in Figure 2, it is clear that the cleavage of molecular ions can occur between any two adjacent carbon atoms. However, the cleavage between two inner carbon atoms is preferred to the cleavage between the terminal and its adjacent carbon. The cleavage of inner carbons yields a relatively stable primary carbocation and primary radical. The cleavage of the bond between the terminal and its adjacent carbon yields a primary carbocation and a methyl radical or a primary radical and a methyl carbocation. If this cleavage occurs, it is via the cleavage mode that leads to a butyl carbocation and a methyl radical.

Figure 2. The mass spectrum of pentane.

Another type of cleavage is the dissociation of multiple bonds to yield fragments. This type of fragmentation produces a smaller radical cation and a neutral molecule. For example, alcohols can fragment into a smaller radical cation by expelling a water molecule. Consequently, the mass spectra exhibit an M−18 peak. Figure 3 presents the schematic fragmentation of 1-heptanol.

Figure 3. Fragmentation of 1-heptanol.

The molecular mass of heptanol is 116 u, and a peak at m/z = 98 is visible in its mass spectrum, shown in Figure 4. Similarly, cycloalkenes undergo a retro-Diels–Alder reaction to expel an alkene and a smaller radical cation.

Figure 4. The mass spectrum of heptanol.

The third type of fragmentation is observed in molecules with unshared electrons or π bonds. In molecules with lone pairs, the carbon–carbon bond next to the lone-pair-bearing atom breaks to yield a resonance-stabilized carbocation. Figure 5 depicts the fragmentation of ether as an example.

Figure 5. Fragmentation of ethers.

The π bonds in a molecular ion promote the fragmentation of the molecule to create an allylic carbocation stabilized by resonance. Figure 6 shows the fragmentation pattern of a terminal alkene.

Figure 6. Fragmentation of alkenes.