Mass Spectrometry: Reading Fragmentation Patterns

What the spectrum shows

The sample is ionised, and the resulting ions are separated by mass-to-charge ratio. The peak at the highest mass corresponding to the intact molecule is the molecular ion, and it gives the molecular mass directly. The base peak is the most intense peak, which is the most stable fragment and is not necessarily the molecular ion.

Isotope patterns — the fastest structural clue

Sulphur gives a smaller but detectable M+2. Carbon's minor isotope gives an M+1 peak whose height is roughly proportional to the number of carbon atoms, which is occasionally used to estimate carbon count.

The nitrogen rule

A compound containing only carbon, hydrogen, oxygen and the halogens has an even molecular mass. An odd molecular mass indicates an odd number of nitrogen atoms.

The rule follows from nitrogen being the only common element whose most abundant isotope has an even mass but an odd valency. It is a quick check that is asked directly and is also useful for validating a proposed structure.

Common losses and what they indicate

Reading the difference between the molecular ion and a strong fragment, then matching it against this list, is the fastest route into an unknown structure.

Why molecules fragment where they do

Fragmentation is governed by cation stability. The bond that breaks is the one giving the more stable carbocation, so the same stability order that governs ionic organic chemistry applies here.

• Alpha cleavage next to a heteroatom, because the resulting cation is stabilised by the lone pair.
• Benzylic and allylic cleavage, giving resonance-stabilised cations. The benzylic fragment is often the base peak in aromatic compounds.
• Cleavage at branch points, since that yields the more substituted, more stable cation.

The McLafferty rearrangement

A carbonyl compound with a hydrogen on the carbon three positions along can transfer that hydrogen through a six-membered cyclic transition state, with cleavage giving a characteristic fragment. The requirement for that specific hydrogen makes its presence or absence structurally informative.

Seeing a McLafferty fragment tells you both that a carbonyl is present and that the chain is long enough to supply the hydrogen — two structural facts from one peak, which is why it is so heavily examined.

A working order for an unknown

1. Identify the molecular ion and note the molecular mass.
2. Check the isotope pattern for chlorine, bromine or sulphur.
3. Apply the nitrogen rule.
4. Compute the differences between the molecular ion and major fragments, and match against common losses.
5. Assemble a structure consistent with all of it, then check that structure would produce the observed base peak.

Step five matters. A structure that explains most peaks but not the base peak is usually wrong, because the base peak corresponds to the most favourable cleavage available.

Frequently asked questions

Why is the molecular ion sometimes absent?

Because some molecules fragment completely under the ionisation conditions used. Softer ionisation methods preserve the molecular ion and are chosen for exactly that reason.

How do I tell chlorine from bromine?

By the relative height of the M+2 peak — roughly one third of M for chlorine, nearly equal to M for bromine. The difference is large enough to be unambiguous.

What does the base peak tell me?

That it corresponds to the most stable fragment cation, so it identifies the most favourable cleavage. It is often the single most informative peak in the spectrum.

Why does the nitrogen rule work?

Because nitrogen alone among the common elements has an even isotopic mass with an odd valency, so each nitrogen shifts the molecular mass parity.