Ion formation is achieved by a number of methods; two are discussed for this topic.
Traditionally the most common technique is EI (electron ionisation, aka electron impact), where a vaporised molecule is bombarded with fast-moving electrons and these electrons knock one of the molecule’s electrons away.
Modern setups typically use ESI (electrospray ionisation), where samples are focused through a fine needle with an intense voltage applied. This rips an electron off the molecules as they are sprayed into the detector. The advantage is that the molecule mostly reaches the detector intact rather than breaking apart into smaller fragments.
Unless otherwise informed, you should assume that a sample is run using the traditional EI method, with high degrees of fragmentation.
Detection and output
Numerous detectors are used. Traditionally the most common high-accuracy device is a magnetic sector, where the magnetic field causes the particles to deflect depending on the ratio of mass to charge.
Regardless of the apparatus, the output is a graph of m/z (mass/charge) against intensity, a mass spectrum. Generally most peaks are the result of one electron being lost, therefore m/z = the mass of the molecule analysed, or the mass of a fragment.
The molecular ion [M⁺·] is the peak produced by the original molecule and is located at the right of the spectrum. It is the highest m/z peak with the exception of isotope peaks. Other peaks arise from fragments of the molecule, torn apart by the harsh ionisation process.
The largest peak, be it a fragment or the molecular ion, is the base peak, and has a defined relative intensity of 100.
Worked example The mass spectrum of butane Butane’s spectrum shows peaks including one at 58 and a very tall one at 43. Which is the molecular ion and which is the base peak? Butane is C₄H₁₀, Mr = 4(12) + 10(1) = 58. The 58 peak is the molecular ion. It is the highest m/z peak and sits at the right of the spectrum. The 43 peak is the base peak. It is the tallest, so it is assigned a relative intensity of 100. ✓ The molecular ion is 58; the base peak is 43. They are not the same peak. Never assume the tallest peak gives you the molar mass.
AS91388 data sheet: fragments in a mass spectrum
Relative mass
Molecular ion, M⁺
15
CH₃⁺
17
OH⁺
28
CO⁺
29
CH₃CH₂⁺ or CHO⁺
30
CH₂NH₂⁺
31
CH₃O⁺ or CH₂OH⁺
43
C₃H₇⁺ or CH₃CO⁺
44
CONH₂⁺
45
COOH⁺ or CH₃CHOH⁺ or CH₃CH₂O⁺
57
C₄H₉⁺
Molar masses given on the data sheet: H = 1, C = 12, N = 14, O = 16, Cl = 35.5, Br = 80.
The nitrogen rule
The rule
A molecular ion has an odd numbered mass if and only if it has an odd number of nitrogen atoms present.
Examples: CH₃CH₂CH₃ (M = 44, no nitrogen) · CH₃CH₂CH₂NH₂ (M = 59, one nitrogen) · NH₂CH₂CH₂CH₂NH₂ (M = 74, two nitrogens).
Note the consequence: an even mass means 0, 2 or 4… nitrogens, so you can never say for certain that an even-mass compound contains no nitrogen.
Isotopic analysis
Reading the isotope peaks
Each peak depends on the exact isotopes present in the molecule, and the natural occurrence of each isotope can tell the reader a great deal about the molecule in question.
Carbon is naturally 1.1% ¹³C, so each peak that has carbon in the fragment will be accompanied by a much smaller peak one mass unit higher. This smaller peak is no more than one tenth the size of the main peak and can be freely ignored at this level.
Chlorine has isotopes 35 and 37 in a 3:1 ratio. So a fragment or molecular ion with an M+2 peak that is 1/3 the size of the main peak suggests Cl is present. (Example: chloroethane.)
Bromine has two common isotopes, 79 and 81, which occur in an approximate 1:1 ratio. (Example: bromoethane.)
Iodine does not have multiple isotopes, however its very large mass of 127 is very distinct and often turns up in the mass spectrum, sometimes accompanied by HI⁺ (m/z = 128). In addition there is a large separation between the molecular ion and other fragments.
Example: the spectrum of iodoethane shows [M⁺] = 156, fragments for I and HI (m/z = 127 and 128), as well as a fragment with the loss of I (m/z = 29).
✕
Confusing the ¹³C peak with the molecular ion
One common mistake is to confuse the ¹³C isotope peak with the molecular ion or with other isotope peaks, so be careful during assessment. The workbook illustrates this with cyclobutane: its molecular ion sits at 56, and magnifying the region just above it reveals the small ¹³C peak one mass unit up.
Fragmentation analysis
What fragmentation is, and how far you need to take it
Fragmentation is the process by which an ionised particle dissipates excess energy by breaking covalent bonds. In a traditional mass spectrum (using EI) there are usually many peaks due to fragmentation.
A full discussion of fragmentation is beyond the scope of this course. You can be expected to calculate the difference in mass of the molecular ion and a fragment, and give possible conclusions from this mass loss for simple examples.
You would not be expected to explain the formation of fragments, but could use simple fragmentations as supporting evidence for the assignment of a molecule’s structure.
Due to the complexity of fragmentations, it should not be used as the primary justification for a molecule’s structure without theory beyond the scope of this course.
Simple fragmentation examples
Fragment mass
Fragment
Indicated functionality
1
H
–COOH or –CHO or –NH– or sometimes –OH
15
CH₃
–CH₃
17
OH
–COOH or –OH, but can come from any O containing molecule
18
H₂O
–OH (alcohol)
29
CH₃CH₂ or CHO
–CH₂CH₃ or –CHO
43
CH₃CO
CH₃CO–
Worked fragmentation examples from the workbook
Compound
What its spectrum shows
Ethanamine
[M⁺] = 45; a fragment at m/z 44 (H loss) and one at m/z 30 (CH₃ loss)
Propanoic acid
[M⁺] = 74; m/z 73 (H loss) and m/z 57 (OH loss)
Ethanal
[M⁺] = 44; fragment at 43 (H loss); also loss of 15 (CH₃) to produce m/z 29
Butan-1-ol
very weak [M⁺] = 74; m/z 73 (H loss); base peak m/z 56 from loss of H₂O, typical for alcohols
Pentan-3-one
[M⁺] = 86; base peak m/z 57, due to a loss of 29 (–CH₂CH₃)
Ethanoic acid
molecule ion 60; fragments 45 (loss of 15, CH₃) and 43 (loss of 17, OH), but NO loss of 1
✕
The absence of a fragment proves nothing
Generally, a loss of 1, 15, 17 or 18 is fairly distinct and very useful for analysis, but larger fragmentations become increasingly difficult to make meaningful conclusions from.
It is important to note that the absence of a fragmentation does not mean a functional group is not present. This is in contrast to IR and NMR, where such conclusions can be made.
The workbook’s own example makes the point: ethanoic acid shows no loss of 1, even though a loss of 1 is typical of carboxylic acid groups. ⚠
Sometimes the molecular ion is not there at all
Fragmentation can sometimes be so significant (generally using EI) that the molecular ion does not appear in the mass spectrum. Under these circumstances, examiners will either inform you that you cannot see the molecular ion, or provide the value for it. It is not possible to work this out from the analysis of the spectrum.
Mass spectrometry: what should you take away?
1. The most important piece of information is the molar mass of the molecule, i.e. the molecular ion.
2. The second thing to apply is the nitrogen rule. If the mass is odd then there is an odd number (1, 3, 5…) of nitrogen atoms present.
3. Thirdly, evaluate whether Cl, Br or I are present by considering isotopic analysis.
4. Fourthly, fragmentation may indicate functionality or some structural features. The most important are the loss of 1 (in –COOH, CHO, N–H and less intensely OH), 15 (most likely CH₃ loss), 17 (OH loss, typically COOH but can be alcohol) and 18 (alcohol). Be aware that the absence of a fragment does not tell you anything, as there are often complex reasons why a particular fragment will not form. Fragmentation information should be viewed as less important than IR or NMR information.
5. Lastly, you may revisit the MS data in light of information provided by NMR or IR.