Mass spectrometry - introduction and mass spectra index

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

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

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

I've included a stick diagram and table of m/z ions for the mass spectrum of E/Z but-2-ene (cis/trans 2-butene 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 but-2-ene (cis/trans 2-butene 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 but-2-ene (cis/trans 2-butene isomers), but the mass spectrometer software does!

(other names: E-2-butene & Z-2-butene, trans-but-2-ene & cis-but-2-ene, trans-2-butene & cis-2-butene)

, structural formula of but-2-ene , but doesn't show the two different spatial arrangements possible due to a high energy barrier to rotation about the double bond, known as the E/Z stereoisomers  (trans-but-2-ene and cis-but-2-ene isomers).

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

[M]⁺ is the parent molecular ion peak (M) with an m/z of 56 corresponding to [C₄H₈]⁺, the original E-but-2-ene and Z-but-2-ene molecules minus an electron, [CH₃CH=CHCH₃]⁺

The small M+1 peak at m/z 57, corresponds to an ionised E-but-2-ene or Z-but-2-ene molecule with one ¹³C atom in it i.e. an ionised E-but-2-ene and Z-but-2-ene molecule of formula [¹³C¹²C₃H₈]⁺

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.

E-but-2-ene and Z-but-2-ene have 4 carbon atoms, so on average, ~1 in 25 molecules will contain a ¹³C atom.

The most abundant ion of the molecule under mass spectrometry investigation (E-but-2-ene and Z-but-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.

For both but-2-ene E/Z isomers, the base ion peak is for m/z ion 41 [C₃H₅]⁺

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

Unless otherwise indicated, assume the carbon atoms in E-but-2-ene and Z-but-2-ene are the ¹²C isotope.

The molecular structure and naming of alkenes

Some of the possible positive ions, [molecular fragment]⁺, formed in the mass spectrometry of but-2-ene.

(fragmentation data table applies to both E/Z isomers of but-2-ene)

The parent molecular ion peak is from the m/z 56 ion: [H₃CCH=CHCH₃]⁺  or  [C₄H₈]⁺

The mass spectra of E/Z but-2-ene isomers are quite similar, their common ions are tabulated below, though they do NOT have detailed identical fingerprint patterns of ion intensities.

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

Atomic masses: H = 1;  C = 12

Bond enthalpies = kJ/mol: C-C = 348;  C-H = 412;  C=C = 612

The fragmentation patterns are very similar for both E/Z isomers of but-2-ene (2-butene).

I can't see any particular characteristic ion peak that readily distinguishes these two E/Z (cis/trans) isomers?

Possible equations to explain some of the most abundant ion peaks in the mass spectrum of E-but-2-ene and Z-but-2-ene (tabulated above)

Formation of m/z 55 ion:

[CH₃CH=CHCH₃]⁺  ===>  [C₄H₇]⁺  +  H

C-H bond scission of the parent molecular ion with loss of a hydrogen atom,

mass change 56 - 1 = 55 (M-1 ion peak)

Further loss of hydrogen atom/molecule creates m/z ions of 55 down to 50 (see table of ions).

Formation of m/z 41 ion:

[CH₃CH=CHCH₃]⁺  ===>  [C₃H₅]⁺  +  CH₃

C-H bond scission of the parent molecular ion with loss of a methyl group,

mass change 56 - 15 = 41 (M-15 ion peak)

The m/z 41 ion gives the base ion peak, the most abundant 'stable' ion formed from the but-ene isomeric molecules.

Further loss of hydrogen atom/molecule creates m/z ions of 40 down to 37 (see table of ions).

The m/z 42 ion is probably formed in the same way, but contains a ¹³C isotope?

Note that an accurate mass spectrometer can sort out 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, from which you can calculate (predict) that the accurate relative ion masses are:

For m/z 42: [C₃H₆]⁺  = 42.0468  and  [¹³C¹²C₂H₅]⁺ =  42.0424, a difference of 0.0044 in relative ion mass.

Formation of m/z 29 ion:

[C₄H₇]⁺  ===>  [C₂H₅]⁺  +  C₂H₂

e.g. C-C bond scission in a larger fragment and proton rearrangement, mass change 55 - 26 = 29.

Further loss of hydrogen atom/molecule creates m/z ions of 28 down to 25 (see table of ions).

Formation of m/z 15 ion:

[CH₃CH=CHCH₃]⁺  ===>  [CH₃]⁺  +  C₃H₅

C-H bond scission of the parent molecular ion with loss of a C₃H₅ group,

mass change 56 - 41 = 15 (M-15 ion peak),

but much less likely than the formation of the m/z 41 ion.

The m/z 15 ion can also be formed from other fragments containing at least two carbon atoms.

The chemistry of ALKENES revision notes INDEX

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

The H-1 NMR spectrum of E/Z but-2-ene (cis/trans isomers of 2-butene)

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

 Mass spectrometry - introduction and mass spectra index

All Advanced Organic Chemistry Notes

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