Mass Spectroscopy

What is the molecular ion (M⁺) and what does the molecular ion peak tell you?

When a sample enters a mass spectrometer, it gets hit by high-energy electrons. This makes the molecule lose an electron, resulting in a molecular ion (M⁺), which is the molecule with a positive charge. The mass of this ion is similar to the molecule's relative molecular mass (Mr). The molecular ion peak is the highest point in the mass spectrum (not counting the M+1 peak), and the m/z value here shows the relative molecular mass of the compound.

What does m/z stand for, and why is it almost always equal to the mass of the ion for organic compounds at AS level?

m/z stands for mass-to-charge ratio, where m is the mass of the ion and z is the charge. At AS level, ions are limited to single charges (z = 1), so m/z = m/1 = m. The m/z value of a peak therefore directly equals the mass of the ion producing it.This relationship simplifies the interpretation of mass spectra, allowing for easier determination of molecular weights.

What is the M+1 peak and what causes it?

The M+1 peak is a small peak at m/z one unit higher than the molecular ion peak. It is caused by the presence of carbon-13 (¹³C) — a naturally occurring stable isotope of carbon with a relative atomic mass of 13 rather than 12. Molecules containing one or more ¹³C atoms have a mass one unit higher than those containing only ¹²C, giving a small M+1 peak. The larger the molecule (the more carbon atoms it contains), the larger the M+1 peak relative to the M⁺ peak.

What is fragmentation in mass spectrometry, and why does it occur?

After the molecular ion is formed, it often has enough energy to break apart — this is called fragmentation. Covalent bonds in the molecular ion break, producing smaller fragment ions (positively charged) and neutral radicals (which are not detected). The fragment ions are detected and appear as peaks at lower m/z values than the molecular ion peak. The pattern of fragmentation peaks is characteristic of the molecule's structure.

How do you interpret fragmentation peaks to identify parts of a molecule's structure?

Each fragmentation peak corresponds to a fragment ion with a particular m/z value. You can work out what fragment has been lost by subtracting the fragment ion's m/z from the molecular ion's m/z:

• Loss of 15 (mass 15) suggests a CH₃ group has been lost

• Loss of 17 suggests loss of OH

• Loss of 29 suggests loss of CHO (or C₂H₅)

• Loss of 31 suggests loss of CH₂OH (from a primary alcohol)

• Loss of 45 suggests loss of COOH (from a carboxylic acid) or OC₂H₅

By identifying what has been lost from the molecular ion to give each fragment peak, you can piece together the structure of the molecule.

Walk through an example: the mass spectrum of ethanol (Mr = 46) shows peaks at m/z = 46, 45, 31, and 29. What does each peak represent?

Ethanol is CH₃CH₂OH (Mr = 46):

• m/z = 46: the molecular ion M⁺ — the whole ethanol molecule minus one electron. This confirms Mr = 46.

• m/z = 45: loss of 1 (a H atom) → [CH₃CH₂O]⁺ or [CH₃CHOH]⁺

• m/z = 31: loss of 15 (a CH₃ group) from M⁺ → [CH₂OH]⁺, which is a fragment containing the –OH group. This peak strongly suggests the presence of an –OH group.

• m/z = 29: loss of 17 (OH) from M⁺ → [CH₃CH₂]⁺, the ethyl cation. This peak suggests a C₂H₅ fragment.

How do you use both IR and mass spectrometry together to identify an unknown organic compound?

Use mass spectrometry first to establish the relative molecular mass from the M⁺ peak, and use fragmentation peaks to identify groups present. Then use IR spectroscopy to confirm the functional groups — for example, a broad O–H peak and a C=O peak would suggest a carboxylic acid, which you could cross-check against the Mr from the mass spectrum. Combining both techniques gives far more certainty than either technique alone. For example: if the mass spectrum gives Mr = 46 and the IR shows a broad O–H around 3300 cm⁻¹ but no C=O peak, you can identify the compound as ethanol (C₂H₅OH, Mr = 46).