Mass Spectrometry (OCR A-Level Chemistry A): Revision Notes

Mass Spectrometry

Introduction to mass spectrometry

Mass spectrometry is a powerful analytical technique used to identify organic compounds by determining their molecular mass and providing information about their structure. When an organic sample is analysed using a mass spectrometer, the instrument produces a mass spectrum - a graph showing the different masses of particles detected and their relative abundances.

The technique works by converting molecules into ions, separating them according to their mass-to-charge ratio, and detecting them. The resulting spectrum provides a unique "fingerprint" for each compound, making mass spectrometry invaluable for identifying unknown substances in chemistry, medicine, and forensic science.

Molecular ions and the ionisation process

When an organic compound enters the mass spectrometer, it undergoes ionisation. During this process, the molecule loses one electron and becomes a positively charged ion called the molecular ion, represented as $\text{M}^+$. This ionisation can be shown in an equation. For example, propan-1-ol is ionised as follows:

$\text{CH}_3\text{CH}_2\text{CH}_2\text{OH} \rightarrow \text{CH}_3\text{CH}_2\text{CH}_2\text{OH}^+ + e^-$

For propan-1-ol, the molecular ion appears at $m/z = 60$, indicating a molecular mass of 60.

Reading and interpreting mass spectra

A mass spectrum displays relative intensity (or relative abundance) on the y-axis and the mass-to-charge ratio ($m/z$) on the x-axis. Understanding how to read this spectrum is essential for identifying compounds.

The molecular ion peak (M⁺ peak)

The molecular ion peak, often called the M⁺ peak, is the most important feature of a mass spectrum. It appears as a clear peak at the highest $m/z$ value on the right-hand side of the spectrum. This peak directly reveals the molecular mass of the compound being analysed.

The M+1 peak and carbon-13

Just beyond the molecular ion peak, you will often observe a very small peak at one mass unit higher than the M⁺ peak. This is called the M+1 peak. This peak exists because approximately 1.1% of naturally occurring carbon atoms are the carbon-13 isotope ($^{13}\text{C}$) rather than the more common carbon-12 ($^{12}\text{C}$).

For propan-1-ol with a molecular mass of 60, a small proportion of molecules will contain one atom of $^{13}\text{C}$, giving them a molecular mass of 61. This creates the small M+1 peak.

Fragmentation in mass spectrometry

Not all molecular ions remain intact in the mass spectrometer. Many break apart in a process called fragmentation. Understanding fragmentation is key to using mass spectrometry for structural determination.

How fragmentation occurs

Inside the mass spectrometer, some molecular ions break down into smaller pieces called fragments. The simplest fragmentation process splits a molecular ion into two species: a positively charged fragment ion and an uncharged radical.

For propan-1-ol, one possible fragmentation pathway is:

$\text{CH}_3\text{CH}_2\text{CH}_2\text{OH}^+ \rightarrow \text{CH}_3\text{OH}^+ + \text{CH}_3\text{CH}_2\bullet$

In this example, the molecular ion breaks to form a fragment ion ($\text{CH}_3\text{OH}^+$) at $m/z = 31$ and a radical ($\text{CH}_3\text{CH}_2\bullet$). The fragment ion appears as a peak in the mass spectrum (often the base peak - the tallest peak in the spectrum), while the radical is not detected.

Fragment ion patterns

The fragment ions produced create additional peaks in the mass spectrum at various $m/z$ values lower than the molecular ion peak. These fragmentation peaks provide valuable information about the structure of the original molecule.

Using fragmentation patterns for identification

The uniqueness of fragmentation patterns makes mass spectrometry extremely useful for identifying unknown compounds and distinguishing between isomers.

Distinguishing between isomers

Even when two molecules are isomers with identical molecular masses, they will produce different fragmentation patterns. This is because their different structures lead to different fragmentation pathways.

The mass spectra above compare hexane and 2-methylpentane, which are both isomers with the molecular formula $\text{C}_6\text{H}_{14}$. Both compounds show the molecular ion peak at $m/z = 86$, confirming they have the same molecular mass. However, their fragmentation patterns are distinctly different, allowing us to distinguish between them. The varying heights and positions of the fragment peaks reflect the different ways these molecules break apart due to their structural differences.

Common fragment ions

Certain fragment ions appear frequently in mass spectra of organic compounds. Recognising these common fragments can help you piece together the structure of an unknown molecule.

Fragment ion	$m/z$
$\text{CH}_3^+$	15
$\text{C}_2\text{H}_5^+$	29
$\text{C}_3\text{H}_7^+$	43
$\text{C}_4\text{H}_9^+$	57

Interpreting a complete spectrum

Let's examine the mass spectrum of ethanol to see how we can use both the molecular ion peak and fragment peaks to understand a molecule's structure.

The main features of the ethanol spectrum are:

• Molecular ion peak at $m/z = 46$, confirming the molecular mass
• M+1 peak at $m/z = 47$, indicating the presence of carbon-13
• Several fragment ion peaks at lower $m/z$ values

By analysing the fragment peaks, we can identify pieces of the ethanol molecule:

• Peak at $m/z = 15$ corresponds to $\text{CH}_3^+$ (methyl cation)
• Peak at $m/z = 29$ corresponds to $\text{CH}_3\text{CH}_2^+$ or $\text{C}_2\text{H}_5^+$ (ethyl cation)
• Peak at $m/z = 31$ corresponds to $\text{CH}_3\text{O}^+$ or $\text{CH}_2\text{OH}^+$
• Peak at $m/z = 45$ corresponds to $\text{CH}_3\text{CH}_2\text{O}^+$

Practical application: drug testing in sport

Mass spectrometry has important real-world applications beyond the chemistry laboratory. One significant use is in drug testing for athletic competitions. During major sporting events like the Olympics, mass spectrometry is used to analyse urine samples and detect banned performance-enhancing substances.