[Author © Dr Phil Brown PhD: Doc Brown's advanced level organic chemistry exam revision notes suitable for students of UK A level chemistry courses & US K12 grade 11, grade 12 and AP honors chemistry courses: Molecular spectrometry analysis of cyclohexane [spectra page updated Mar 22nd 2026 *]

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Introductory note on the mass spectrum of cyclohexane

Students and teachers please note my explanation of the mass spectrum of cyclohexane is designed for advanced, but pre-university, chemistry courses.

If M represents the cyclohexane molecule, the initial ionisation to give the molecular ion is:

M_(g) + high KE e^-  ==> [M•]⁺_(g) + 2e^- and for fragmentation equations assume [M]⁺ is the start of the processes and all species are in a gaseous state.

I've not usually shown an unpaired electron on e.g. an ion or a non-ionised alkyl radical R e.g.

[M•]⁺ ==> [X]⁺  +  R•, but you should be aware this is a more accurate depiction of some processes.

I've used simplified equations to show how some of the ions that might be formed in the fragmentation pattern for the mass spectrum of cyclohexane and only the formation of singly charged positive are considered for the mass spectrum of cyclohexane.

I've included a stick diagram and table of m/z ions for the mass spectrum of cyclohexane and doing the mass spectrum analysis under standard conditions, databases can be compiled based on complex fingerprint patterns, often involving the relative intensities of many fragment ions, and used to identify compounds including cyclohexane.

In selected cases, where two different fragment ions have the same integer m/z value, I've pointed out that modern mass spectrometers can measure relative ion mass to four decimal places. So, using accurate isotopic masses, I've calculated the accurate ion masses, BUT strictly speaking, 0.0005 should be deducted for singly charged ions to account for the loss of the electron in their formation. I have NOT done this for cyclohexane, but the mass spectrometer software does!

Cyclohexane, C₆H₁₂ , , , all bond angles ~109^o

Interpreting the fragmentation pattern of the mass spectrum of cyclohexane

[M]⁺ is the molecular ion peak (M) with an m/z of 84 corresponding to [C₆H₁₂]⁺, the original cyclohexane molecule minus an electron.

The small M+1 peak at m/z 85, corresponds to an ionised cyclohexane molecule with one ¹³C atom in it i.e. an ionised cyclohexane molecule of formula ¹³C¹²C₅H₁₂

Carbon-13 only accounts for ~1% of all carbon atoms (¹²C ~99%), but the more carbon atoms in the molecule, the greater the probability of observing this ¹³C M+1 peak.

Cyclohexane has 6 carbon atoms, so on average, ~1 in 17 molecules will contain a ¹³C atom.

The most abundant ion of the molecule under mass spectrometry investigation (cyclohexane) is usually given an arbitrary abundance value of 100, called the base ion peak, and all other abundances ('intensities') are measured against it.

The base peak ion for the mass spectrum of cyclobutane is the m/z 56 ion [C₄H₈]⁺

Identifying the species giving the most prominent peaks (apart from M) in the fragmentation pattern of cyclohexane.

The parent molecular ion of cyclohexane is m/z 84: [C₆H₁₂]⁺

Analysing and explaining the principal ions in the fragmentation pattern of the mass spectrum of cyclohexane

PLEASE NOTE I have found it difficult to find 'authentic' equations to explain mass spectra fragmentation patterns and it is complex chemistry! I've identified the formulae of the ionised fragments on the mass spectrum diagram, but the equations are from the internet or my conjecture as to how the ions might be formed - please take care in using the information, especially for assignments at university or pre-university level.

Atomic masses: H = 1;  C = 12 (~1% 13)

Bond enthalpies = kJ/mol: C-C = 348;  C-H = 412

Possible equations to explain the most abundant ion peaks of cyclohexane

Formation of m/z 69 ion:

[C₆H₁₂]⁺  ===>  [C₅H₉]⁺  +  CH₃

_{C-C bond scission of the parent molecular ion and proton rearrangement}

_{mass change 84 - 15 = 69 (M-15 ion peak)}

Formation of m/z 57 ion:

[C₆H₁₂]⁺  ===>  [C₄H₉]⁺  +  C₂H₃

[C₆H₁₁]⁺  ===>  [C₄H₉]⁺  +  C₂H₂

Formation of m/z 56 ion:

[C₆H₁₂]⁺  ===>  [C₄H₈]⁺  +  C₂H₄

It is formed by the elimination of ethene from the cyclohexane molecular ion.

mass change 84 - 28 = 56, from the molecular ion (M-28 ion peak)

The m/z 56 ion is the base peak ion, the most abundant and 'stable' ion fragment.

The m/z values of 83, 69, 55 and 41 are related by the loss of a mass unit of 14 (CH₂) from one fragment ion to the next e.g

Formation of m/z 43 ion:

[C₅H₉]⁺  ===>  [C₃H₇]⁺  +  CH₂

Formation of m/z 41 ion from the m/z 55 ion:

[C₄H₇]⁺  ===>  [C₃H₅]⁺  +  CH₂

_{mass change 55 - 14 = 41}

_{and you can construct lots of other possibilities!}

_{Formation of ions in varies series e.g. < m/z 56, < m/z 43 and < m/z 29}

_{All of these can lose hydrogen atoms to give m/z values down to 50, m/z down to 38 and m/z down to 26, respectively.}