Put a sample of butan-2-one into a mass spectrometer and the spectrum gives you two useful numbers at once. A peak at 72 is the mass of the whole molecule. A taller peak at 43 is the mass of the piece left behind when the molecule breaks at one particular bond.
Mass spectrometry (MS) turns molecules into ions, sorts the ions by mass and counts them. IR finds functional groups. NMR, later in the course, maps carbon and hydrogen environments. Neither gives the molecular weight. MS does, and often the molecular formula too. The pieces a molecule breaks into show which bonds break most easily, and that follows the cation-stability rules from How Reactions Happen.
Ionization and the molecular ion
The instrument first turns the sample into a gas. A beam of fast electrons then hits the molecules, and a collision can knock one electron out of a molecule. This is electron ionization. The electron that leaves most easily is a lone-pair electron, so in butan-2-one it comes from the oxygen.
Having lost one electron, the molecule carries a charge of +1 and has one unpaired electron. A species with an unpaired electron is a radical, so this ion is a radical cation, written M⁺•. It is still the whole molecule, so it is called the molecular ion.
The spectrometer sorts ions by m/z, the mass of an ion divided by its charge. The molecular ion has a charge of 1, so its m/z equals its mass: 72 for butan-2-one. That is the molecular weight. The molecular ion is usually the highest-mass peak in the spectrum, apart from isotope peaks just above it.
The mass is counted with the most common isotope of each element (¹²C, ¹H, ¹⁶O and so on), not with the averaged atomic masses on a periodic table. That is why the molecular ion of bromobenzene, C₆H₅Br, appears at 156, even though its molecular weight from the periodic table is 157.
The height of each peak tells you how many ions reached the detector at that m/z. The tallest peak in the spectrum is the base peak. Its height is set to 100%, and every other peak is given as a percentage of it. The base peak is often a fragment rather than the molecular ion. In butan-2-one it is the peak at 43.
Two quick reads from the molecular ion
The nitrogen rule. Methylamine, CH₃NH₂, has a mass of 12 + 5 + 14 = 31. Methanol, CH₃OH, has a mass of 12 + 4 + 16 = 32. The odd mass belongs to the compound with a nitrogen. In general, a molecule with an odd molecular weight contains an odd number of nitrogens, and a molecule with an even molecular weight contains none or an even number.
The rule comes from counting atoms. Carbon and oxygen have even masses. Hydrogen and the halogens have odd masses and form one bond each. Carbon forms four bonds and oxygen two, so in a molecule without nitrogen the one-bond atoms always come in an even number, and the mass is even. Nitrogen has an even mass but forms three bonds, so each nitrogen changes the number of hydrogens by one and switches the total between even and odd. One number from the spectrum gives you this for free.
The M+1 peak. Butan-2-one shows a small peak at 73, one mass unit above the molecular ion and about 4% as tall. It comes from molecules that contain one ¹³C atom in place of a ¹²C. About 1.1% of all carbon atoms are ¹³C, so each carbon in a molecule adds roughly 1.1% to the M+1 peak. Four carbons give about 4.4%, which matches, and ten carbons would give about 11%. Divide the height of the M+1 peak (as a percentage of M) by 1.1 and you have an estimate of the number of carbons.
Fragmentation
In butan-2-one, the base peak at 43 sits 29 mass units below the molecular ion. The missing 29 is an ethyl radical, CH₃CH₂•, and the ion at 43 is CH₃CO⁺. The molecular ion has split in two.
This happens because the collision leaves the molecular ion with a lot of extra energy, and many molecular ions break apart before they reach the detector. Each break gives one piece that keeps the positive charge and one that is neutral. The detector records only ions, so the neutral piece never appears as a peak. Its mass shows up only as the gap between M and the fragment.
One pattern is worth knowing before the details. A molecule with no nitrogen has an even mass, and a radical with no nitrogen has an odd mass, such as CH₃• (15) or CH₃CH₂• (29). So when the molecular ion loses a radical, the cation left behind has an odd mass: 72 − 29 = 43. Most fragment peaks of a nitrogen-free compound sit at odd m/z for this reason. An even-mass fragment means the molecular ion lost a whole neutral molecule instead, such as water or an alkene.
Alpha cleavage
Look again at the molecular ion of butan-2-one. The carbonyl carbon has two carbon neighbors: the CH₃ on one side and the CH₂ on the other. A carbon bonded directly to a carbonyl carbon is called an α (alpha) carbon, so each of these neighbors is one, and the bond joining it to the carbonyl carbon is an α bond. Breaking one of these bonds is called alpha cleavage.
Break the bond to the ethyl group, and the ethyl radical leaves with one of the bond’s two electrons. (Each one-electron move is drawn as a single-barbed fishhook arrow, as in How Reactions Happen.) The other electron pairs with oxygen’s unpaired electron to make a third bond between the carbon and the oxygen. The cation left behind is CH₃–C≡O⁺, an acylium ion, at m/z 43. Break the bond to the methyl group instead, and the methyl radical leaves. That gives the acylium ion CH₃CH₂–C≡O⁺ at m/z 57.
An acylium ion can be drawn two ways: R–C⁺=O and R–C≡O⁺. In the second form every atom has an octet, because the oxygen’s lone pair has moved in to share the positive charge. That stability is why bonds next to a carbonyl break so readily. (The same ion comes back in Aromatic Chemistry, where it puts a C=O group onto a benzene ring.)
Both routes give an acylium ion, so the cation does not decide between them. The radical does. An ethyl radical is more stable than a methyl radical, following the same order as carbocations, so the ethyl group leaves more easily. In general, alpha cleavage favors losing the larger alkyl group as the radical. That is why m/z 43 is the base peak of butan-2-one, while m/z 57 is a small peak.
Alcohols, ethers and amines undergo alpha cleavage too. In these, a C–C bond next to the carbon that carries the O or N breaks, and the lone pair on the O or N shares the positive charge of the cation left behind. For an alcohol or ether, that cation is an oxocarbenium ion (a carbon double-bonded to a positively charged oxygen). For an amine it is an iminium ion (C=N⁺). Both ions come back in Carbonyl Chemistry, as intermediates of reactions at a C=O. Either ion is often the base peak.
The McLafferty rearrangement
Hexan-2-one (M = 100) shows a strong peak at m/z 58. That is an even mass, so the molecular ion has lost a neutral molecule of mass 42, not a radical. The molecule lost is propene, and it leaves through a rearrangement.
To follow it, label the carbons along the chain from the C=O. The first is the α carbon, the next is β and the third is γ (gamma). In hexan-2-one the γ carbon carries hydrogens. The molecular ion curls around so that one of those γ hydrogens comes close to the carbonyl oxygen. That makes a ring of six atoms: the oxygen, the carbonyl carbon, the α, β and γ carbons, and the hydrogen.
Three changes then happen together. The γ hydrogen moves to the oxygen, the bond between the α and β carbons breaks, and the β and γ carbons become the C=C of propene, which leaves as a neutral molecule. What remains is the radical cation of an enol (a C=C with an OH on one of its carbons): CH₂=C(OH)CH₃, the enol of acetone, at m/z 58. This is the McLafferty rearrangement.
The rearrangement needs a hydrogen on the γ carbon. With no γ hydrogen there is no McLafferty peak, so the peak’s presence or absence tells you whether the chain has a γ hydrogen.
Many carbonyl compounds with a long enough chain show it. Butanal, butanoic acid and methyl butanoate each lose ethene (28) this way, giving peaks at m/z 44, 60 and 74. In a carbonyl compound with no nitrogen, a strong even-mass fragment is most likely a McLafferty fragment.
Common losses worth recognizing
The gap between M and a fragment peak names the piece that left. Some gaps come up again and again, such as 15 for a methyl group or 18 for water from an alcohol.
| Loss | Mass | Suggests |
|---|---|---|
| CH₃ | 15 | methyl branch |
| H₂O | 18 | alcohol |
| C₂H₅ | 29 | ethyl group |
| CO or C₂H₄ | 28 | phenol (CO), or a McLafferty alkene (C₂H₄) |
| COOH | 45 | carboxylic acid |
| CHO | 29 | aldehyde |
| Cl | 35 | chloride |
| C₃H₇ | 43 | propyl |
| CH₃CO | 43 | methyl ketone |
| Br | 79 | bromide |
Two fragment masses are worth knowing by sight. The first is m/z 91. Toluene, a benzene ring carrying a CH₃ (M = 92), shows it as its base peak. Its molecular ion loses a hydrogen atom from the CH₃, which gives the benzyl cation, C₆H₅CH₂⁺. The ring shares the positive charge, as it does in any benzylic cation.
The ion at 91 is largely the tropylium ion, a seven-membered ring cation with the same formula, C₇H₇⁺. It is unusually stable because it is aromatic, an idea Aromatic Chemistry, two chapters on, explains. It forms when the ring takes the side-chain carbon into itself, before or after the hydrogen is lost. Either way, the charge ends up spread over seven carbons.
Toluene is not the only source. Any otherwise unsubstituted benzene ring carrying a CH₃ or CH₂ group can give this ion. That carbon is the benzylic carbon, the one joined directly to the ring. Ethylbenzene, for example, loses a methyl radical from the end of its chain, and its base peak is also 91. So a strong peak at m/z 91 is a sign of a benzylic CH₃ or CH₂.
The second is m/z 77, the phenyl cation, C₆H₅⁺: the ring left when a monosubstituted benzene loses its substituent. It points to a C₆H₅– group.
Isotope patterns: chlorine and bromine leave a fingerprint
The molecular ion of bromobenzene, C₆H₅Br, is not one peak but two, at 156 and 158, of almost equal height. The reason is bromine itself. Natural bromine is a nearly even mix of two isotopes, ⁷⁹Br and ⁸¹Br. About half the molecules carry the lighter isotope and weigh 156, and the other half carry the heavier one and weigh 158.
Most elements in organic molecules have one isotope that far outnumbers the rest, so they give no such pair. Chlorine and bromine are the exceptions. Chlorine is about 3 parts ³⁵Cl to 1 part ³⁷Cl. For each halogen, the heavier isotope gives a peak two mass units above M, called the M+2 peak. One chlorine gives M and M+2 in a ratio of about 3:1, and one bromine gives about 1:1.
Two halogens give three peaks, at M, M+2 and M+4, and the ratios come from multiplying. Each chlorine is 3 parts light to 1 part heavy. In a molecule with two chlorines, both are light in 3 × 3 = 9 parts, one of each is present in 3 × 1 + 1 × 3 = 6 parts, and both are heavy in 1 × 1 = 1 part. The pattern is 9:6:1.
The same multiplication gives 1:2:1 for two bromines and 3:4:1 for one chlorine and one bromine. So three peaks two units apart mean two halogens, and the ratio says which ones.
Iodine has only one natural isotope, ¹²⁷I, so it gives no M+2 peak. Its sign is a large gap of 127 between M and a fragment.
Two peaks of nearly equal height, two mass units apart: one bromine. Counting it as ⁷⁹Br, the rest of the molecule weighs 108 − 79 = 29.
Even molecular weight: no nitrogen, or an even number of them.
What is 29? It could be C₂H₅ or CHO. No C=O stretch in the IR rules out CHO, so the 29 is an ethyl group.
Structure: CH₃CH₂Br, bromoethane. The isotope pattern did most of the work.
High-resolution mass spectrometry
C₃H₈O, C₂H₄O₂ and C₂H₈N₂ all have a mass of 60 when you count in whole numbers, so an ordinary spectrometer cannot tell them apart. Their exact masses differ, though, because atomic masses are not whole numbers. ¹²C is exactly 12 by definition, but ¹H is 1.007825, ¹⁴N is 14.003074 and ¹⁶O is 15.994915.
Added up, the three formulas come to 60.0575, 60.0211 and 60.0687. A high-resolution mass spectrometer (HRMS) measures m/z to four decimal places, which is precise enough to pick out the molecular formula from a single measurement. That is why a paper reporting a new compound usually gives its HRMS value.
Putting the four techniques together
Given an unknown sample, each technique answers its own question. MS gives the molecular weight, and HRMS gives the formula. IR names the functional groups. Two more methods come later in the course, in NMR Spectroscopy: ¹³C NMR counts the carbon environments, and ¹H NMR shows how the pieces connect. Together they let you work out a structure.
Chemists characterize every new compound this way, in research and in industry. The first thing you do with a new product is prove that it is the molecule you meant to make.
Gather independent lines of evidence and check that they agree. When they agree, you have your structure.