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Module 4: Core organic chemistry›Mass spectroscopy (4.2.4)

Mass spectroscopy (4.2.4)

Fundamentals of mass spectroscopy of organic molecules and combining analytical techniques.

2 min

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Organic molecules in a mass spectrometer are vapourised then undergo ionisation, with the loss of an electron from one of the covalent bonds.

This can be represented as:

is the molecular ion, it represents the whole molecule minus one electron.

The singly charged molecular ion peak, , has an m/z equal to the molecule’s relative molecular mass ().

The molecular ion peak has the highest m/z value and is located on the far right of the mass spectrum.

Mass spectra of organic molecules will exhibit a tiny peak at 1 mass unit greater than the molecular ion.

This is called the M+1 peak and is caused by the presence of the carbon-13 isotope which comprises of all carbon atoms.

A mass spectrum graph displaying relative intensity on the vertical axis and mass-to-charge ratio (m/z) on the horizontal axis. The spectrum shows a prominent peak at m/z 58 labeled as M+ and a smaller peak at m/z 59 labeled as M+1. The compound represented is CH3COCH3.

The of propanone, , is 58.

In the spectrum of propanone, the molecular ion peak, , is at 58 and a smaller M+1 peak at 59 shows the proportion of propanone featuring carbon-13.

Molecular ions formed during ionisation are positively charged radicals and are generally unstable.

They split to form a radical and a cation; this is called fragmentation.

A diagram illustrating the mass spectrum fragmentation of a chemical compound. The structure shows a carbon chain with functional groups, and arrows indicate the formation of fragment ions and radicals. Key mass-to-charge ratios (m/z) are labeled, with annotations explaining that radicals do not appear on the mass spectrum while fragment ions provide structural information.

The cationic molecular fragment ions can be seen in the mass spectrum.

All fragment ions will have lower molar mass than the molecular ion, .

Some fragment ions may be formed more frequently.

A table displaying mass-to-charge ratios (m/z) and corresponding fragment ions. The table lists fragment ions for various groups, including methyl, ethyl, aldehyde, acyl, propyl, isopropyl, and phenyl, along with their respective m/z values.

m/z 29 and m/z 43 are commonly used in exams due to the variety of fragments they can be associated with.

Different analytical techniques can provide different details about the structure of a molecule. By combining the different strands of evidence from different techniques a more complete description of the molecule can be obtained.

The NMR spectra gives information about the molecular structure and arrangement of atoms, especially hydrogen () and carbon () atoms.
The IR spectra helps identify functional groups within a molecule based on their characteristic bond vibrations.
The mass spectra provides the molecular weight and details on sections of the molecule through the fragmentation pattern.
Chemical tests involve observed changes and behaviour when molecules undergo chemical reactions. This can often involve colour changes and other observations that are characteristic of different functional groups or component ions.

In an exam you should highlight which analytical evidence links to which conclusion you have made.

A diagram illustrating the relationship between evidence and conclusion. The left side labeled 'Evidence' contains a green box with the text 'The spectrum shows ...', followed by '... therefore ...'. The right side labeled 'Conclusion' features an orange box with the text '... the sample contains ...'.

For example you may write:
“The spectrum shows a broad peak at 3000 cm^-1 indicating an group that is part of a carboxylic acid.”