This page looks at how fragmentation patterns are formed when organic molecules are fed into a mass spectrometer, and how you can get information from the mass spectrum.
Fragmentation
The molecular ions are energetically unstable, and some of them will break up into smaller pieces. The simplest case is that a molecular ion breaks into two parts - one of which is another positive ion, and the other is an uncharged free radical.
\[M^{\cdot +} \rightarrow X^+ + Y^{\cdot}\]
The uncharged free radical won't produce a line on the mass spectrum. Only charged particles will be accelerated, deflected and detected by the mass spectrometer. These uncharged particles will simply get lost in the machine - eventually, they get removed by the vacuum pump. The ion, X+, will travel through the mass spectrometer just like any other positive ion - and will produce a line on the stick diagram. All sorts of fragmentations of the original molecular ion are possible - and that means that you will get a whole host of lines in the mass spectrum. For example, the mass spectrum of pentane looks like this:
It's important to realize that the pattern of lines in the mass spectrum of an organic compound tells you something quite different from the pattern of lines in the mass spectrum of an element. With an element, each line represents a different isotope of that element. With a compound, each line represents a different fragment produced when the molecular ion breaks up.
In the stick diagram showing the mass spectrum of pentane, the line produced by the heaviest ion passing through the machine (at m/z = 72) is due to the molecular ion. The tallest line in the stick diagram (in this case at m/z = 43) is called the base peak. This is usually given an arbitrary height of 100, and the height of everything else is measured relative to this. The base peak is the tallest peak because it represents the commonest fragment ion to be formed - either because there are several ways in which it could be produced during fragmentation of the parent ion, or because it is a particularly stable ion.
Examples involving carbocations (carbonium ions)
Summarizing the most important conclusion from the page on carbocations:
Order of stability of carbocations
primary < secondary < tertiary
Applying the logic of this to fragmentation patterns, it means that a split which produces a secondary carbocation is going to be more successful than one producing a primary one. A split producing a tertiary carbocation will be more successful still. Let's look at the mass spectrum of 2-methylbutane. 2-methylbutane is an isomer of pentane - isomers are molecules with the same molecular formula, but a different spatial arrangement of the atoms.
Look first at the very strong peak at m/z = 43. This is caused by a different ion than the corresponding peak in the pentane mass spectrum. This peak in 2-methylbutane is caused by:
The ion formed is a secondary carbocation - it has two alkyl groups attached to the carbon with the positive charge. As such, it is relatively stable. The peak at m/z = 57 is much taller than the corresponding line in pentane. Again a secondary carbocation is formed - this time, by:
You would get the same ion, of course, if the left-hand CH3 group broke off instead of the bottom one as we've drawn it. In these two spectra, this is probably the most dramatic example of the extra stability of a secondary carbocation.
Examples involving acylium ions, [RCO]+
Ions with the positive charge on the carbon of a carbonyl group, C=O, are also relatively stable. This is fairly clearly seen in the mass spectra of ketones like pentan-3-one.
The base peak, at m/z=57, is due to the [CH3CH2CO]+ ion. We've already discussed the fragmentation that produces this.
Using mass spectra to distinguish between compounds
Suppose you had to suggest a way of distinguishing between pentan-2-one and pentan-3-one using their mass spectra.
pentan-2-one |
|
CH3COCH2CH2CH3 |
pentan-3-one |
|
CH3CH2COCH2CH3 |
Each of these is likely to split to produce ions with a positive charge on the CO group. In the pentan-2-one case, there are two different ions like this:
That would give you strong lines at m/z = 43 and 71.
With pentan-3-one, you would only get one ion of this kind:
In that case, you would get a strong line at 57. You don't need to worry about the other lines in the spectra - the 43, 57 and 71 lines give you plenty of difference between the two. The 43 and 71 lines are missing from the pentan-3-one spectrum, and the 57 line is missing from the pentan-2-one one.
The two mass spectra look like this: