S3.2.8 Mass spectrometry (Higher Level Only) Notes

Mass Spectrometry (MS) of Organic Compounds

How Does Mass Spectrometry Work?

1. Mass spectrometry operates through three fundamental steps: ionization, separation, and detection.
2. Each step plays a critical role in generating a mass spectrum.
3. Ionization:
   1. The sample is bombarded with high-energy electrons, causing the molecule to lose an electron and form a positively charged ion, known as the molecular ion (M⁺).
   2. This ion may remain intact or fragment into smaller ions.
4. Separation:
   1. The ions are accelerated into a magnetic field, where they are separated based on their mass-to-charge ratio ($m/z$).
   2. Since most ions have a charge of +1, the $m/z$ value typically corresponds to the ion’s mass.
5. Detection:
   1. A detector measures the abundance of ions at each $m/z$ value, producing a mass spectrum, a graph with $m/z$ values on the x-axis and relative abundance on the y-axis.

The Molecular Ion (M⁺): A Key Starting Point

1. The molecular ion (M⁺) is the ionized form of the entire molecule, with no fragmentation.
2. Its $m/z$ value corresponds to the molecular weight of the compound.
3. Identifying the molecular ion peak is often the first step in analyzing a mass spectrum.

Fragmentation Patterns: Clues to Structure

1. When the molecular ion breaks apart, it forms smaller fragments. Each fragment corresponds to a specific part of the molecule, and its $m/z$ value provides clues about its identity.
2. By analyzing these fragmentation patterns, you can deduce structural features of the compound.

Common Fragmentation Patterns

1. Certain bonds in organic molecules are more likely to break during ionization, leading to predictable fragmentation patterns.
2. Here are some common examples:
3. Cleavage of Alkyl Chains:
   1. Straight-chain alkanes often fragment at C-C bonds, producing alkyl cations.
   2. For example, propane ($C_3H_8$) may fragment to form $CH_3^+$ ($m/z = 15$) or $C_2H_5^+$ ($m/z = 29$).
4. Loss of Small Molecules:
   1. Mass spectral fragments lost are outlined in Section 22 of the Data Booklet (e.g., $\cdot CH_3$ or $\cdot OH$).
5. Cleavage at Functional Groups:
   1. Ketones and aldehydes often undergo cleavage near the carbonyl group, forming acylium ions ($RCO^+$).

Interpreting a Mass Spectrum Step-by-Step

Analyzing a mass spectrum involves a systematic approach:

1. Identify the Molecular Ion Peak:
   1. Locate the peak with the highest $m/z$ value.
   2. This represents the molecular ion (M⁺) and provides the molecular weight of the compound.
2. Analyze Fragmentation Peaks:
   1. Compare the $m/z$ values of the fragments to known patterns (e.g., alkyl cations, loss of small molecules).
   2. Use the differences between peaks to deduce which bonds are breaking.
3. Reconstruct the Structure:
   1. Combine the information from the molecular ion and fragments to propose a structure for the compound.