Mass Spectrometry

The Mass Spectrometer is a useful machine to have in chemistry, as it allows much of the “wet” chemistry to be replaced by more accurate methods of analysis.
It is important that a low pressure is maintained in the spectrometer so that the ions can pass through unhindered by molecules in the air.

Fragmentation

The molecular ion peak corresponds to the molecular mass of the compound being analysed. It is the peak furthest to the right on the spectrum.
From the mass spectrum above, it is clearly evident that the ions which correspond to the molecular ion (X⁺) are not the only ones reaching the detector.
This is because the other lines on the spectrum correspond to lighter ions that are the result of fragmentation (breakdown of X⁺).
The strongest signal detected is set to 100% on the spectrum, and this is referred to as the base peak.
The other peaks are expressed as a percentage fraction of the base peak's value.
In some cases, the molecular ion peak can be unnoticeable as it is very small compared to the base peak.
All of the peaks in 2-ethoxybutane spectrum can be identified. The mass of 2-ethoxybutane is 102, so if we look at the 87 peak for example, it has a mass 15 less than 2-ethoxybutane, and so it must have lost a CH₃ group (CH₃ has an Mr of 15).
This process can be repeated with all of the peaks, for example:
It is important to note that it is the positively charged fragments that are being measured by the mass spectrometer.
Eventually the masses that have been lost from a compound become familiar. For example, 28 is the loss of a C=O group, 77 for the loss of a C₆H₅ (benzene ring) etc.

Some elements have more than one naturally-occurring isotope. For example natural chlorine consists of 75% ³⁵Cl and 25% ³⁷Cl.
So, what happens when a molecule containing chlorine is fragmented in the mass spectrometer? Well, there are two sorts of ions, one containing ³⁵Cl and the other containing³⁷Cl.
³⁵Cl will give a mass reading at M, and ³⁷Cl will give a mass reading at M+2. The heights of the two peaks will be in ratio to the abundance of the isotopes, i.e. 3:1. A pair of peaks like this indicates that chlorine is present in the compound.
Another example of a useful isotope is Bromine. Bromine has an almost equal percentage of ⁷⁹Br and ⁸¹Br isotopes; and so peaks that are the same height and 2 apart from each other indicate that Bromine is present in the molecule.
¹³C can be very useful for interpreting more complicated mass spectra. ¹³C accounts for around 1.1% of a sample of carbon atoms; however when there are many carbon atoms in a compound, the abundance of ions containing ¹³C will become more significant; the more carbon atoms in a molecule, the greater the chance of one of them being ¹³C.
For example, decan-1-ol contains 10 carbon atoms, and so there will be an 11% chance (1.1% x 10) of at least one carbon atom being ¹³C, and so the molecular ion peak at 158 will be followed at 159 by a peak which is 11% as intense. This can be used to establish the number of carbon atoms in a compound.