C5H10 mass spectrum of E-pent-2-ene 2-pentene Z-pent-2-ene fragmentation pattern of m/z m/e ions for analysis and identification of cis-pent-2-ene trans-pent-2-ene image diagram doc brown's advanced organic chemistry revision notes

Advanced Organic Chemistry: Mass spectrum of E-pent-2-ene and Z-pent-2-ene CH₃CH=CHCH₂CH₃

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Interpreting the mass spectrum of E-pent-2-ene and Z-pent-2-ene (E/Z geometrical isomers)

[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 spectroscopy analysis of E/Z isomers of pent-2-ene [spectra page updated Mar 25th 2026 *]

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Introductory note on the mass spectrum of E/Z pent-2-ene (cis/trans isomers)

Students and teachers please note my explanation of the mass spectrum of E/Z pent-2-ene (cis/trans isomers) is designed for advanced, but pre-university, chemistry courses.

If M represents the E/Z pent-2-ene (cis/trans isomers) 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 E/Z pent-2-ene (cis/trans isomers) and only the formation of singly charged positive are considered for the mass spectrum of E/Z pent-2-ene (cis/trans isomers).

I've included a stick diagram and table of m/z ions for the mass spectrum of E/Z pent-2-ene (cis/trans isomers) 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 E/Z pent-2-ene (cis/trans isomers).

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 E/Z pent-2-ene (cis/trans isomers), but the mass spectrometer software does!

C5H10 mass spectrum of E-pent-2-ene 2-pentene fragmentation pattern of m/z m/e ions for analysis and identification of trans-pent-2-ene image diagram doc brown's advanced organic chemistry revision notes

The mass spectrum of the stereoisomer E-pent-2-ene (trans-2-pentene)

C5H10 mass spectrum of 2-pentene Z-pent-2-ene fragmentation pattern of m/z m/e ions for analysis and identification of cis-pent-2-ene image diagram doc brown's advanced organic chemistry revision notes

The mass spectrum of the stereoisomer Z-pent-2-ene (cis-2-pentene)

Pent-2-ene C₅H₁₀, has two E/Z isomers E-pent-2-ene and Z-pent-2-ene

Z/cis- alkenes structure and naming (c) doc b , E/trans-

The molecular structure and naming of alkenes

Interpreting the fragmentation pattern of the mass spectrum of E-pent-2-ene and Z-pent-2-ene

The fragmentation patterns are quite similar so the following notes apply to both spectra.

[M]⁺ is the molecular ion peak (M) with an m/z of 70 corresponding to [C₅H₁₀]⁺, the original E-pent-2-ene and Z-pent-2-ene molecule minus an electron, [CH₃CH₂CH=CHCH₃]⁺

The small M+1 peak at m/z 71, corresponds to an ionised E-pent-2-ene and Z-pent-2-ene molecule with one ¹³C atom in it i.e. an ionised E-pent-2-ene and Z-pent-2-ene molecule of formula ¹³C¹²C₄H₁₀

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.

Pent-2-ene has 5 carbon atoms, so on average, ~1 in 20 molecules will contain a ¹³C atom.

The most abundant ion of the molecule under mass spectrometry investigation (E/Z isomers of pent-2-ene) 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 ion peak for the mass spectrum of both E/Z isomers of pent-2-ene is the m/z 55 ion [C₄H₇]⁺

Some of the possible positive ions, [molecular fragment]⁺, formed in the mass spectrometry of E/Z isomers of pent-2-ene based on parent molecular ion, m/z 70 [C₅H₁₀]⁺ or [CH₃CH₂CH=CHCH₃]⁺

Identifying the species giving the most prominent peaks (apart from M) in the fragmentation pattern of E-pent-2-ene and Z-pent-2-ene.

m/z value of [fragment]⁺	69	67	56	56	55	53
[molecular fragment]⁺	[C₅H₉]⁺	[C₅H₇]⁺	[¹³C¹²C₃H₈]⁺	[C₄H₈]⁺	[C₄H₇]⁺	[C₄H₅]⁺

m/z value of [fragment]⁺	43	43	42	41	40	39	29	27
[molecular fragment]⁺	[C₃H₇]⁺	[¹³C¹²C₂H₆]⁺	[C₃H₆]⁺	[C₃H₅]⁺	[C₃H₄]⁺	[C₃H₃]⁺	[C₂H₅]⁺	[C₂H₃]⁺

Analysing and explaining the principal ions in the fragmentation pattern of the mass spectrum of E-pent-2-ene and Z-pent-2-ene

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.

There are striking similarities in the mass spectra of the E/Z isomers of pent-2-ene.

e.g. (i) they have the same base ion peak of m/z 55.

(ii) m/z ions 53 and 56, small intensities, and in the same ratio.

(iii) Similarly, m/z ions 67, 69 and 71, small intensities, and in the same ratio.

(iv) Both spectra show a similar ratio pattern for the more intense peaks of m/z ions 39 to 42.

Suggested equations to the most abundant ion peaks of E-pent-2-ene and Z-pent-2-ene

Formation of m/z 67 and 69 ions

[C₅H₁₀]⁺ ===> [C₅H₉]⁺ + H

Proton loss from the parent molecular ion.

mass change 70 - 1 = 69 (M-1 ion peak)

The m/z 69 ion can lose a hydrogen molecule to give the m/z 67 ion

[C₅H₉]⁺ ===> [C₅H₇]⁺ + H₂

mass change 69 - 2 = 67 (M-3 ion peak)

Formation of m/z 55 ion

[CH₃CH₂CH=CHCH₃]⁺ ===> [CH₃CH₂CH=CH]⁺ + CH₃

via C-C bond chain scission of the parent molecular ion,

mass change 70 - 15 = 55 (M-15 ion peak)

similarly, a possible different structure, but still [C₅H₁₀]⁺

[CH₃CH₂CH=CHCH₃]⁺ ===> [CH₂CH=CHCH₃]⁺ + CH₃

The m/z 55 ion is the base peak ion, the most abundant and 'stable' ion fragment.

The m/z 56 ion is probably formed in the same way i.e the [¹³C¹²C₃H₈]⁺ ion rather than the [C₄H₈]⁺

Note that an accurate mass spectrometer can sort out (resolve) pairs of ions with the same integer m/z value because they can measure relative fragment ion masses to four decimal places,

e.g. using accurate relative isotopic masses:

¹H = 1.0078 ¹²C = 12.0000 ¹³C = 13.0034: you can then calculate (predict) that the accurate relative ion masses are:

For m/z 56: [¹³C¹²C₃H₇]⁺ = 56.0580, [C₄H₈]⁺ = 56.0624, a difference of 0.0044 in relative ion mass.

Formation of m/z 42 ion

[C₅H₁₀]⁺ ===> [C₃H₆]⁺ + C₂H₄

via C-C bond chain scission of the parent molecular ion, and loss of ethene molecule

mass change 70 - 28 = 42 (M-28 ion peak)

The m/z 43 ion is probably formed in the same way but contains a ¹³C atom i.e. it has the formula [¹³C¹²C₂H₆]⁺ rather than [C₃H₇]⁺

So again, using accurate relative isotopic masses:

¹H = 1.0078 ¹²C = 12.0000 ¹³C = 13.0034: you can then calculate (predict) that the accurate relative ion masses are:

For m/z 43: [C₃H₇]⁺ = 43.0546 and [¹³C¹²C₂H₆]⁺ = 43.0502 relative ion mass difference of 0.0044.

Formation of m/z 39, 40 and 41 ions

e.g. loss of protons from the m/z 41 and 42 ions

m/z 41 ion: [C₃H₆]⁺ ===> [C₃H₅]⁺ + H

m/z 40 ion: [C₃H₆]⁺ ===> [C₃H₄]⁺ + H₂

m/z 39 ion: [C₃H₅]⁺ ===> [C₃H₃]⁺ + H₂

Formation of m/z 29 ion

[CH₃CH₂CH=CHCH₃]⁺ ===> [CH₃CH₂]⁺ + CH=CHCH₃

via C-C bond chain scission of the parent molecular ion,

mass change 70 - 41 = 29 (M-41 ion peak)

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Links associated with E-pent-2-ene and Z-pent-2-ene

The chemistry of ALKENES revision notes INDEX

Mass spectroscopy index

The infrared spectra of the E/Z isomers of pent-2-ene (cis/trans isomers of 2-pentene)

The H-1 NMR spectra of the E/Z isomers of pent-2-ene (cis/trans isomers of 2-pentene)

The C-13 NMR spectra of the E/Z isomers of pent-2-ene (cis/trans isomers of 2-pentene)

ALL SPECTROSCOPY INDEXES

STEREOISOMERISM general definition, E/Z (geometric/geometrical cis/trans) isomerism
All Advanced Organic Chemistry Notes

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