How do chemists work out the structure of an unknown compound?
Elemental microanalysis to find the empirical formula, mass spectrometry to find the molecular mass and fragmentation pattern, infrared spectroscopy to identify functional groups, and proton and carbon-13 nuclear magnetic resonance spectroscopy to map the carbon-hydrogen framework.
An SQA Advanced Higher Chemistry answer on the experimental determination of structure, covering elemental microanalysis to find the empirical formula, mass spectrometry for the molecular ion and fragmentation, infrared spectroscopy for functional groups, and proton and carbon-13 NMR spectroscopy for the carbon-hydrogen framework, used together to deduce an unknown structure.
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What this key area is asking
The SQA wants you to use elemental microanalysis to find an empirical formula, mass spectrometry to find the molecular mass and read fragmentation, infrared spectroscopy to identify functional groups, and proton and carbon-13 NMR to map the carbon-hydrogen framework, then combine them to deduce a structure. The empirical-formula calculation and reading each spectrum are reliable exam earners.
Elemental microanalysis
The empirical formula is the first step; the molecular formula is a whole-number multiple of it, found once the molecular mass is known.
Mass spectrometry
In a mass spectrometer the molecule is ionised and may fragment. The molecular ion peak (the highest mass-to-charge peak, ) gives the molecular mass. The smaller fragment peaks correspond to pieces of the molecule, and the mass differences between peaks reveal the groups lost (for example a loss of indicates a methyl group, a loss of a hydroxyl group, and a loss of a CHO or ethyl group). This fragmentation pattern is a fingerprint that confirms the structure.
Infrared spectroscopy
Nuclear magnetic resonance spectroscopy
Nuclear magnetic resonance (NMR) spectroscopy probes the environment of hydrogen and carbon nuclei in a magnetic field.
- Proton (H) NMR shows a peak for each different hydrogen environment. The chemical shift (position) indicates the type of environment, and the relative area under each peak gives the number of hydrogens in that environment.
- Carbon-13 (C) NMR shows a peak for each different carbon environment, mapping the carbon skeleton.
The number and position of the peaks together reveal the arrangement of atoms. A single proton NMR peak, for example, means all the hydrogens are equivalent (a symmetrical molecule).
Examples in context
Combining these techniques is how real structures are solved. A forensic chemist confirming an unknown drug measures its molecular mass by mass spectrometry, checks for key functional groups by infrared, and maps the carbon-hydrogen framework by NMR before declaring a match. Pharmaceutical companies use the same toolkit to prove that a synthesised drug is the intended molecule and is pure. In research, the combination distinguishes isomers that share a molecular formula: ethanol and methoxymethane both are , but their infrared and NMR spectra differ because one has an O-H bond and two hydrogen environments while the other does not. This integrated reasoning, deducing a structure from several spectra at once, is exactly what Advanced Higher questions reward.
Try this
Q1. State what the molecular ion peak in a mass spectrum tells you. [1 mark]
- Cue. The molecular mass of the compound (the highest value).
Q2. State the functional group indicated by a strong infrared absorption near . [1 mark]
- Cue. A carbonyl group ().
Q3. State what the number of peaks in a carbon-13 NMR spectrum tells you. [1 mark]
- Cue. The number of different carbon environments in the molecule.
Exam-style practice questions
Practice questions written in the style of SQA exam questions on this dot point, with worked answer explainers. The year tag is the paper they imitate, not the source.
SQA AH 20194 marksA compound contains carbon, hydrogen and oxygen by mass. (a) Calculate its empirical formula. (b) Its mass spectrum shows a molecular ion peak at . Determine its molecular formula. (Use , , .)Show worked answer →
Markers reward dividing percentages by atomic mass, the simplest ratio, and matching to the molecular mass.
(a) Divide each percentage by the atomic mass:
C: ; H: ; O: .
Divide by the smallest (): C: ; H: ; O: . The empirical formula is .
(b) The empirical formula mass is , which equals the molecular ion mass, so the molecular formula is also (ethanol).
SQA AH specimen3 marksAn unknown compound shows a strong infrared absorption near and a proton NMR spectrum with a single peak. (a) State the functional group indicated by the infrared absorption. (b) State what the single NMR peak tells you about the hydrogen environments. (c) Explain why mass spectrometry is also used.Show worked answer →
The answer must read each technique and explain how they combine.
(a) A strong absorption near indicates a carbonyl group (), as in an aldehyde, ketone, carboxylic acid or ester.
(b) A single proton NMR peak means all the hydrogen atoms are in the same chemical environment (equivalent), so the molecule is symmetrical.
(c) Mass spectrometry gives the molecular mass from the molecular ion peak and fragmentation clues, so it pins down the molecular formula that infrared and NMR alone cannot fully determine. The techniques are used together.
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Sources & how we know this
- SQA Advanced Higher Chemistry Course Specification — SQA (2019)