Mass Spectrometry for Organic Compounds

Mass spectrometry (MS) is the second great analytical technique of A-Level organic chemistry. Where infrared spectroscopy tells you which functional groups are present, mass spectrometry tells you the molecular mass of the compound and gives structural clues from how the molecule fragments inside the instrument. When you combine IR and MS on the same unknown, you can usually determine its structure with very few assumptions. This lesson develops MS from the introductory ideas you met at AS (the mass spectrum of an element and of a simple molecule) to the full A2-level interpretation of fragmentation patterns for organic compounds.

This lesson covers the OCR A-Level Chemistry A (H432) specification point 4.2.4 (c): interpretation of mass spectra of organic compounds, including identification of the molecular ion peak (M+) and fragmentation patterns, and the combined use of MS and IR to determine structures.

1. Recap: How the Mass Spectrometer Works

We met this at AS but it is worth a quick reminder:

Ionisation — the sample is vaporised and bombarded with high-energy electrons (in electron impact MS) or ionised more softly in electrospray MS. One electron is knocked off, giving a positive molecular ion, M⁺.
Fragmentation — the molecular ion has too much internal energy and breaks apart into smaller charged fragments and neutral pieces.
Acceleration and deflection — the charged fragments are accelerated by an electric field and deflected by a magnetic field by an amount that depends on their mass-to-charge ratio (m/z).
Detection — a detector records the abundance of ions at each m/z value.
Spectrum — a vertical bar-chart of abundance against m/z is produced.

In an A-Level spectrum, the y-axis is abundance as a percentage of the tallest peak (the "base peak"), and the x-axis is m/z (almost always equal to mass, because z = 1 for most ions).

2. The Molecular Ion (M⁺) Peak

The molecular ion, M⁺, is formed by the loss of a single electron from the parent molecule:

$M + e^- \rightarrow M^+ + 2\,e^-$

It has the same mass as the parent molecule (to within one electron mass, which is negligible). Its m/z value therefore tells you the molecular mass of your unknown — a massively useful piece of data.

2.1 Finding M⁺ in a Spectrum

The molecular ion is (almost always) the peak with the highest m/z in the spectrum — because it has not lost any pieces, it is the heaviest ion present.
It may be small compared to fragment peaks, because many molecular ions break apart before reaching the detector.
Small isotope peaks at M+1 and M+2 appear to the right of M⁺ due to ¹³C, ³⁷Cl, ⁸¹Br etc. — these are discussed in section 5.

2.2 Worked Example — Reading M⁺

The mass spectrum of an unknown compound shows its highest-m/z peak at 60. Deduce the molecular mass.

Answer: Mᵣ = 60. Possible formulas with mass 60 include C₃H₈O (propan-1-ol or propan-2-ol), CH₃COOH (ethanoic acid), C₂H₄O₂ (methanoate), C₂H₈N₂, and so on. The next step is to use IR and the fragment pattern to narrow this down.

3. Fragmentation — How and Why

When the molecular ion breaks apart, it does so by breaking a weak bond to give two pieces. One piece carries the positive charge and is detected; the other is neutral and is invisible to the detector.

General equation:

$M^+ \rightarrow F^+ + R\bullet$

Where F⁺ is the detected fragment and R• is a neutral radical.

3.1 Typical Mass Losses (Neutral Fragments)

When you go from M⁺ to a smaller peak, the difference in m/z tells you the mass of the neutral fragment that was lost. Common losses to recognise:

Mass lost	Neutral fragment	Common source
1	H•	C–H cleavage
15	•CH₃ (methyl)	Alkane, methyl branch
17	•OH	Alcohol, acid
18	H₂O	Alcohol dehydration in MS
28	CO or C₂H₄ or N₂	Aldehyde, ketone, alkene
29	•CHO or •C₂H₅	Aldehyde, ethyl branch
31	•OCH₃	Ester (methyl ester)
43	•C₃H₇ (propyl) or •CH₃CO (acetyl)	Propyl branch, methyl ketone
45	•COOH	Carboxylic acid

So if you see a peak 15 units below M⁺, you almost certainly have a methyl group being lost.

3.2 Common Fragment Ions

Conversely, some fragment cations are so stable they appear in many spectra. Learn to recognise them:

m/z	Fragment cation	Meaning
15	CH₃⁺	Methyl cation — methyl group present
17	OH⁺	Alcohol or acid
29	CHO⁺ or C₂H₅⁺	Aldehyde or ethyl branch
43	CH₃CO⁺ (acylium) or C₃H₇⁺	Methyl ketone or propyl
45	COOH⁺ or C₂H₅O⁺	Carboxylic acid or ether/alcohol
57	C₄H₉⁺ (tert-butyl) or CH₃CH₂CO⁺	Tert-butyl or ethyl ketone
77	C₆H₅⁺ (phenyl)	Benzene ring
91	C₇H₇⁺ (benzyl / tropylium)	Methylbenzene and derivatives
105	C₆H₅CO⁺ (benzoyl)	Benzoic acid and derivatives

3.3 Why Do These Fragments Dominate?

Cations are more stable when the positive charge can be stabilised:

Methyl, ethyl, propyl cations — stabilised by alkyl hyperconjugation.
Tert-butyl cation — very stable, 3° carbocation.
Acylium (RCO⁺) — stabilised by resonance between C and O.
Tropylium (C₇H₇⁺) — aromatic, very stable.
Phenyl and benzoyl — aromatic ring stabilisation.

Fragmentation always prefers pathways that lead to the most stable cation.

graph TD
  A[Molecular ion M+] --> B{Weakest bond?}
  B --> C[C-H next to branch -<br/>loss of H, minor]
  B --> D[C-C alpha to C=O -<br/>loss of R as radical,<br/>gives acylium]
  B --> E[C-C at branch -<br/>gives stable branched cation]
  B --> F[Alcohol -<br/>loss of OH or H2O]

4. Worked Example — Full Interpretation

The mass spectrum of an organic compound shows the following major peaks:

m/z = 72: medium abundance (M⁺)
m/z = 57: very strong
m/z = 43: strong
m/z = 29: medium
m/z = 15: weak

The IR spectrum shows a strong sharp peak at 1715 cm⁻¹, a C–H peak around 2900, and no O–H or N–H peaks. Identify the compound.

Step 1: Molecular mass. M⁺ = 72 ⇒ Mᵣ = 72.

Step 2: IR.

1715 cm⁻¹ → C=O (aldehyde, ketone, acid, ester, amide).
No O–H → rules out acid, alcohol.
No N–H → rules out primary amine, amide.
So this is a ketone or aldehyde or ester.

Step 3: Molecular formula.

Mᵣ = 72 and contains C=O. Possible formulas: C₄H₈O (Mᵣ = 72, butanone or butanal) or C₃H₄O₂ (Mᵣ = 72, methyl methanoate) or C₃H₈N₂.
Given no N–H and a simple spectrum, C₄H₈O is the strong candidate.

Lesson 10: Mass Spectrometry for Organic Compounds