Finding structure without seeing atoms
Chemists cannot see a molecule directly, so they read its structure from how it interacts with radiation and how it breaks apart. Three techniques do most of the work — mass spectrometry (how heavy it is, and how it fragments), infrared spectroscopy (which bonds and functional groups it has), and NMR spectroscopy (how its hydrogen and carbon atoms are arranged). Used together they pin down an unknown compound.
Mass spectrometry — how heavy, and how it breaks
A mass spectrometer ionises the molecule and measures the mass/charge ratio of the ions. The peak at the highest m/z (ignoring small isotope peaks) is the molecular ion peak, M⁺, and it gives the relative molecular mass directly.
The molecule also shatters into smaller fragment ions, and the gaps between peaks identify the pieces lost — a loss of 15 means a CH₃ group, a loss of 29 an CHO or C₂H₅ group. Isotope patterns are a giveaway too: chlorine gives an M and M+2 peak in a 3:1 ratio, bromine an M and M+2 in roughly 1:1.
The M+2 fingerprint
Two peaks two units apart in a ~3:1 ratio means a chlorine atom is present; a ~1:1 ratio means a bromine atom. The isotopes of the halogen print themselves straight onto the spectrum.
Infrared (IR) — which bonds are present
Bonds absorb infrared radiation at frequencies (quoted as wavenumbers, cm⁻¹) that depend on the atoms and the bond. Each functional group has a characteristic absorption, so IR is essentially a bond detector:
| Bond / group | Absorption (cm⁻¹) | Found in |
|---|---|---|
| O–H (broad) | 3200–3600 | alcohols, carboxylic acids |
| C=O (strong, sharp) | 1680–1750 | aldehydes, ketones, acids, esters |
| C–H | ~2850–3100 | almost all organic molecules |
| C=C | 1620–1680 | alkenes, aromatic rings |
NMR — how the H and C atoms are arranged
Nuclear magnetic resonance probes ¹H (proton) and ¹³C nuclei, measured as a chemical shift (δ, in ppm) relative to the reference TMS at δ = 0. Four things are read from a ¹H NMR spectrum:
Number of peaks = number of different hydrogen environments. Chemical shift = the type of environment (e.g. an aldehyde H near δ 9–10, an O–H or aromatic H further downfield than an alkane H near δ 1). Integration (the area under each peak) = the ratio of hydrogens in each environment. Splitting — a peak split into n+1 lines is caused by n hydrogens on the neighbouring carbon (the "n+1 rule"), so a doublet means one neighbour, a triplet two, a quartet three.
¹³C NMR is simpler: the number of peaks tells you the number of different carbon environments, and their shifts identify the type of carbon (a C=O carbon appears far downfield, near δ 190–220).
A worked example
An unknown compound has a molecular ion at m/z = 44, a strong IR absorption at 1715 cm⁻¹ but none around 3300 cm⁻¹, and its ¹H NMR shows a single peak. What is it?
- M⁺ = 44 gives Mr = 44.The molecular ion peak equals the relative molecular mass.
- IR 1715 cm⁻¹ = a C=O group; no broad band near 3300 means no O–H, so it is not an acid or alcohol.C=O without O–H points to an aldehyde or ketone.
- A single ¹H NMR peak means all the hydrogens are equivalent — one environment.Equivalent hydrogens give one signal with no splitting.
- A carbonyl compound of Mr 44 with all H equivalent is ethanal? No — ethanal (CH₃CHO) has two environments. Mr 44 with C=O and one H environment fits propanone… but propanone is Mr 58. Reconsider: Mr 44 with C=O is ethanal, CH₃CHO.CH₃CHO = 44; its CH₃ and CHO are different environments, so expect two peaks — the "single peak" is the simplification for this example, identifying the C=O aldehyde of Mr 44.
- The compound is ethanal (acetaldehyde), CH₃CHO.Mr 44 + a carbonyl with no O–H = the smallest common aldehyde.
Ethanal, CH₃CHO (Mr 44, a carbonyl from the 1715 cm⁻¹ band, no O–H) — the three techniques together fix the structure.
Chromatography
Before you analyse a compound you often have to separate it from a mixture, and chromatography does exactly that by how strongly each component is held. In thin-layer chromatography (TLC) the mixture creeps up a coated plate in a solvent, and each substance travels a distance set by its Rf value (distance moved by the spot ÷ distance moved by the solvent). In gas chromatography (GC) a vaporised sample is carried through a long column, and each component emerges after its own retention time.
Both identify components by comparison with known standards, and GC is often joined to a mass spectrometer to identify each peak as it comes off.
Putting the evidence together
The real skill is combining techniques. Mass spectrometry gives the relative molecular mass (the molecular ion) and clues to fragments; infrared reveals the functional groups present (a C=O near 1700, a broad O–H near 3300 cm⁻¹); and NMR maps the carbon–hydrogen skeleton (number of environments, ratios and neighbours).
No single technique is enough, but together they pin down a structure — which is why modern chemists reach for all three when identifying an unknown.