How do chemists identify organic compounds using modern instruments?
The principles and uses of instrumental methods for identifying organic compounds, including mass spectrometry, infrared spectroscopy and chromatography, and how data from these methods are interpreted to determine structure.
A CCEA Life and Health Sciences answer on instrumental analysis: the principles and uses of mass spectrometry, infrared spectroscopy and chromatography, and how their data are interpreted to identify and determine the structure of organic compounds.
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What this dot point is asking
CCEA wants you to describe the principles and uses of the main instrumental methods for identifying organic compounds, mass spectrometry, infrared spectroscopy and chromatography, and to interpret the data they produce to determine structure. It applies the naming, functional-group and isomerism ideas from the earlier dot points, because these instruments identify functional groups and distinguish isomers, and it connects to analysis in medicine, forensics and quality control.
Mass spectrometry
In outline, the sample is vaporised and ionised (knocking off an electron), the ions are accelerated and separated by their mass-to-charge ratio, and a detector records how many ions of each ratio arrive. The peak at the highest mass-to-charge value (ignoring small isotope peaks) is the molecular ion, and reading its value gives the relative molecular mass of the compound directly. Some molecular ions break apart inside the instrument into fragments; the masses of the fragment peaks, and the differences between peaks, reveal which groups have been lost (a loss of 15 suggests a methyl group, a loss of 17 a hydroxyl group), helping to piece together the structure.
Infrared spectroscopy
To use an IR spectrum, you match the absorption peaks against a table of characteristic frequencies to identify the functional groups present. This is a fast, non-destructive way to confirm what functional groups a molecule contains, and to monitor a reaction (for example watching the O to H absorption of an alcohol disappear as it is converted to something else). The unique fingerprint region also allows an unknown to be matched against a reference spectrum for definitive identification.
Chromatography
Chromatography separates the components of a mixture. There is a stationary phase (such as the paper or a thin solid layer in paper or thin-layer chromatography) and a mobile phase (a solvent that moves through it). As the mobile phase moves, each component is carried along at a rate that depends on how strongly it is attracted to the stationary phase compared with how soluble it is in the mobile phase. Components that are more soluble and less strongly held move further, so the mixture separates into distinct spots or bands. The Rf value (the distance moved by the component divided by the distance moved by the solvent front) is constant for a given substance in a given solvent, so comparing the Rf of an unknown with the Rf values of known reference substances run under the same conditions identifies the component. Gas chromatography works on the same principle for volatile mixtures and is widely used in analysis.
Examples in context
Example 1. Drug testing in sport and medicine. Mass spectrometry and chromatography are combined to detect banned substances or drugs in blood or urine: chromatography separates the mixture, and mass spectrometry identifies each component from its mass spectrum. This is a direct health-science application of the instrumental methods studied here.
Example 2. Confirming a synthesis. A chemist who has made a compound uses infrared spectroscopy to confirm the expected functional groups are present (and unwanted ones absent) and mass spectrometry to confirm the relative molecular mass. Together the methods verify that the right product has been made, showing why instrumental analysis is central to modern chemistry.
Try this
Q1. State what the molecular ion peak in a mass spectrum tells you. [1 mark]
- Cue. The relative molecular mass of the compound.
Q2. Explain how infrared spectroscopy identifies a functional group. [2 marks]
- Cue. Bonds in functional groups absorb infrared radiation at characteristic frequencies, so absorption peaks match a particular bond or group.
Q3. A component moves 2.0 cm and the solvent front moves 8.0 cm. Calculate the Rf value. [2 marks]
- Cue. (no units).
Exam-style practice questions
Practice questions written in the style of CCEA exam questions on this dot point, with worked answer explainers. The year tag is the paper they imitate, not the source.
CCEA A2 26 marksExplain how a mass spectrum is used to determine the relative molecular mass of an organic compound, and explain what the molecular ion peak and fragment peaks tell you.Show worked answer →
The answer should explain the molecular ion peak and how fragments give structural clues.
Principle: in a mass spectrometer the sample is ionised and the ions are separated according to their mass-to-charge ratio. The spectrum plots the abundance of each ion against its mass-to-charge ratio.
Molecular ion peak: the peak with the highest mass-to-charge ratio (other than any small isotope peak above it) is the molecular ion, formed when the whole molecule loses one electron. Its mass-to-charge value gives the relative molecular mass of the compound directly.
Fragment peaks: inside the spectrometer some molecular ions break into smaller fragments. The mass-to-charge values of these fragment peaks, and the mass differences between peaks, indicate which groups have been lost (for example a loss of 15 suggests a methyl group), giving clues to the structure.
Markers reward ionisation and separation by mass-to-charge ratio, the molecular ion peak giving the relative molecular mass, and fragment peaks (or mass differences) giving structural information.
CCEA A2 25 marksDescribe how paper or thin-layer chromatography separates a mixture, and explain how the Rf value is calculated and used to identify a component.Show worked answer →
Describe the separation mechanism, then the Rf calculation and use.
Separation: a spot of the mixture is placed on the stationary phase (paper or a thin layer of solid) near the bottom, which is then dipped in a solvent (the mobile phase). As the solvent rises, the components are carried up at different rates depending on how strongly each is attracted to the stationary phase versus how soluble it is in the mobile phase. Components that are more soluble and less strongly held travel further, so the mixture separates into spots.
Rf value: the Rf value is the distance travelled by the component divided by the distance travelled by the solvent front:
Use: the Rf value is constant for a given substance in a given solvent, so comparing the Rf of an unknown spot with the Rf of known reference substances (run under the same conditions) identifies the component.
Markers reward the stationary and mobile phases and separation by differing attraction or solubility, the correct Rf formula, and comparing Rf values with known references to identify a component.
Related dot points
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A CCEA Life and Health Sciences answer on organic classification: functional groups, homologous series and general formulae, IUPAC nomenclature, the ways of representing organic molecules, and an introduction to structural isomerism.
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- Structural isomerism (chain, position and functional group isomers), stereoisomerism including cis-trans (E-Z) isomerism in alkenes, the conditions needed for each, and why isomers can have different properties.
A CCEA Life and Health Sciences answer on isomerism: structural isomerism (chain, position and functional group), stereoisomerism including cis-trans (E-Z) isomerism in alkenes, the conditions for each, and why isomers differ in properties.
- Addition polymerisation of alkenes and condensation polymerisation, the structures of the polymers formed, the differences between the two types, and the uses and environmental impact of polymers including biodegradability and disposal.
A CCEA Life and Health Sciences answer on polymers: addition polymerisation of alkenes and condensation polymerisation, the structures formed, the differences between the two types, and the uses and environmental impact of polymers.
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Sources & how we know this
- CCEA GCE Life and Health Sciences specification — CCEA (2016)