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Interpreting the mass
spectrum of 3-methylhexane
[Author
©
Dr WP 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: Mass
spectrometry - analysing the
mass spectrum of
3-methyl hexane
[updated
Nov 4th 2025]
email doc
brown
Re-edit
mass spectrum of
CH3CH2CH(CH3)CH2CH2CH3
Links associated
with
3-methylhexane
The chemistry of ALKANES and the petrochemical
industry
This is a BIG
website, PLEASE take time to explore it
Mass spectrometry - spectra index
See also
comparing the
1H NMR and 13C NMR spectra of the nine alkane structural isomers of C7H16
Introductory note on the mass spectrum of 3-methylhexane
Students and teachers please note
my explanation of the mass spectrum of 3-methylhexane is designed for
advanced, but pre-university, chemistry courses.
If M represents the
3-methylhexane 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 3-methylhexane and only the formation of singly charged
positive are considered for the mass spectrum of 3-methylhexane.
I've included a stick diagram and table of m/z ions for the mass spectrum of
3-methylhexane
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
3-methylhexane.
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
3-methylhexane,
but the mass spectrometer software does!
3-methylhexane
C7H16
The molecular structure and
naming of alkanes
Interpreting the fragmentation pattern of the mass spectrum of
3-methylhexane
[M]+ is the molecular ion peak (M) with an m/z of
100 corresponding to [C7H16]+, the original 3-methylhexane molecule minus an electron,
[CH3CH2CH(CH3)CH2CH2CH3]+
The very tiny M+1 peak at m/z 105, corresponds to an ionised
3-methylhexane
molecule with one 13C atom in it i.e. an ionised 3-methylhexane molecule of
formula
[13C12C6H16]+
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.
3-methylhexane has 7 carbon atoms, so, on average,
~1 in every 14 molecules will contain a 13C atom.
This sort of argument also applies to fragment ions
from the parent molecular ion of 3-methylhexane - though the ratio will be
greater: e.g.
m/z 44 ion could be [13C12C2H7]+, m/z 58 ion [13C12C3H9]+, m/z 72 ion [13C12C4H11]+
These ions might be more likely than those containing
only 12C isotope atoms
i.e.
more likely than [C3H8]+,
[C4H10]+ and
[C5H12]+
respectively.
Either way, for identification
purposes, all these peaks add uniqueness to the fragmentation pattern of the mass spectrum of
3-methylhexane.
The most abundant ion of the molecule under mass
spectrometry investigation (3-methylhexane) 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 3-methylhexane is m/z ion 43
[C3H7]+
Identifying the species giving the most prominent peaks
(apart from M) in the fragmentation pattern of 3-methylhexane.
Unless otherwise indicated, assume the carbon atoms in
heptane are the 12C isotope.
Some of the possible positive ions, [molecular fragment]+,
formed in the mass spectrometry of
3-methylhexane.
The parent molecular ion of 3-methylhexane m/z
100:
[C7H16]+
Identifying the species giving the most prominent peaks
(apart from M) in the fragmentation pattern of
3-methylhexane.
|
m/z value of
[fragment]+ |
85 |
71 |
70 |
57 |
56 |
55 |
|
[molecular fragment]+ |
[C6H13]+ |
[C5H11]+ |
[C5H10]+ |
[C4H9]+ |
[C4H8]+ |
[C4H7]+ |
|
m/z value of
[fragment]+ |
43 |
42 |
41 |
39 |
29 |
27 |
|
[molecular fragment]+ |
[C3H7]+ |
[C3H6]+ |
[C3H5]+ |
[C3H3]+ |
[C2H5]+ |
[C2H3]+ |
Analysing and explaining the principal ions in the
fragmentation pattern of the mass spectrum of 3-methylhexane
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.
Examples of equations to explain some of the most abundant ion peaks
in the mass spectrum of 3-methylhexane
Atomic masses: H = 1; C = 12 (13 for ~1
in 100)
Bond enthalpies = kJ/mol: C-C = 348;
C-H = 412
Formation of m/z 85 ion:
[CH3CH2CH(CH3)CH2CH2CH3]+
===> [C6H13]+
+ CH3
Most fragmentation in alkanes arises from C-C bond
scission (C-C bond weaker than C-H).
In this case and end methyl group is broken off,
mass change = 100 - 15 = 85 (M-15 ion)
Note in the equations below that both fragments are
capable of being ionised, but only one at a time.
Many other fragments are formed by
hydrogen atm loss so
you get sequences like:
71 => 70, 57 => 56 => 55, 43 => 42 => 41 => 40 => 39 and 29 =>
28 =>
27 etc.
Ethene is often eliminated to give a smaller
fragment e.g. the m/z ion 85 gives the m/z ion 57
[C6H13]+ ===>
[C4H7]+
+ C2H4
Mass change 85 - 28 = 57
Formation of m/z 71 ion:
[CH3CH2CH(CH3)CH2CH2CH3]+
===> [C5H11]+
+ CH2CH3
C-C bond scission of the parent molecular ion of
3-methylhexane.
Here an end ethyl group is broken off, mass change =
100 - 29 = 71 (M-29 ion)
The m/z 72 ion can be
formed by the same process but containing a 13C carbon isotope ion
i.e.
[13C12C4H11]+
rather than the [C5H12]+ ion.
An accurate mass
spectrometer sorts this out, measuring relative fragment ion
masses to four decimal places e.g. using v ery accurate relative isotopic masses,
12C
= 12.0000 and 13C = 13.0034, 1H = 1.0078, you can then calculate
(predict) that the accurate relative ion masses are:
For m/z 72:
[C5H12]+
= 72.0936 *
[13C12C4H11]+
= 72.0892,
a difference of 0.0044 in relative ion mass.
Formation of m/z 57 ion:
[CH3CH2CH(CH3)CH2CH2CH3]+
===> [CH3CH2CHCH3]+
+ CH2CH2CH3
Loss of propyl group, mass change = 100 - 43 = 57
(M-43 ion peak)
The m/z 58 ion can be
formed by the same process but containing a 13C carbon isotope ion
i.e. [13C12C3H9]+
rather than the [C4H10]+ ion.
An accurate mass
spectrometer sorts this out, measuring relative fragment ion
masses to four decimal places e.g. using v ery accurate relative isotopic masses,
12C
= 12.0000 and 13C = 13.0034, 1H = 1.0078, you can then calculate
(predict) that the accurate relative ion masses are:
For m/z 58:
[13C12C3H9]+
= 58.0736,
[C4H10]+
= 58.0780,
a difference of 0.0044 in relative ion mass.
Formation of m/z 43 ion:
[CH3CH2CH(CH3)CH2CH2CH3]+ ===> [CH2CH2CH3]+
+ C4H9
Loss of a C4H9 group, mass
change = 100 - 57 = 43 (M-57 ion peak)
The m/z 43 ion is the base peak ion, the most
abundant and 'stable' ion fragment.
Loss of a C4H9 group, mass
change = 100 - 57 = 43 (M-57 ion peak)
The m/z 44 ion can be
formed by the same process but containing a 13C carbon isotope ion
i.e. [13C12C2H7]+
rather than the [C3H8]+ ion.
An accurate mass
spectrometer sorts this out, measuring relative fragment ion
masses to four decimal places e.g. using v ery accurate relative isotopic masses,
12C
= 12.0000 and 13C = 13.0034, 1H = 1.0078, you can then calculate
(predict) that the accurate relative ion masses are:
For m/z 44: [C3H8]+
= 44.0624 and
[13C12C2H7]+ = 44.058,
a difference of 0.0044 in relative ion mass .
Formation of m/z 29 ion:
[CH3CH2CH(CH3)CH2CH2CH3]+ ===> [CH2CH3]+
+ C5H11
Here an end ethyl group is broken off
from either end of the parent molecular ion via C-C bond fission.
mass change =
100 - 71 = 29 (M-71 ion)
Key points about the mass spectrum of 3-methylhexane
The mass
spectrum of 3-methylhexane features a molecular ion peak at m/z = 100 and
prominent fragment ions from alkyl cleavage, notably at m/z = 57 and 85.
These
reflect stable carbocations formed during fragmentation.
Key Mass Spectrum
Features of 3-Methylhexane
3-Methylhexane (C7H16)
is a branched alkane, and its mass spectrum reflects typical alkane
fragmentation patterns under electron ionization (EI). Here's a breakdown of
the most significant peaks:
| m/z |
Fragment
Ion |
Origin /
Fragmentation Pathway |
Notes |
| 100 |
Molecular ion (M⁺) |
Entire molecule C7H16⁺ |
Often weak due to alkane
instability |
| 99 |
[M–H]⁺ |
Loss of H from molecular ion |
Minor peak |
| 85 |
C6H13⁺ |
Loss of CH3
(methyl group) |
Common in branched alkanes |
| 71 |
C5H11⁺ |
Loss of C2H5
(ethyl group) |
Indicates chain cleavage |
| 57 |
C4H9⁺ |
Loss of C3H7
(propyl group) |
Often base peak (most intense) |
| 43 |
C3H7⁺ |
Smaller alkyl fragment, base
ion |
Common in many hydrocarbons |
| 29 |
C2H5⁺ |
Ethyl cation |
Low intensity |
Sources: NIST Chemistry WebBook, MassBank
Europe
Common
Misconceptions in Mass Spectrometry
- Confusing base peak with molecular
ion: The base peak is the most
intense, not necessarily the molecular ion.
- Assuming all fragments are neutral:
Only ions are detected; neutral fragments are invisible.
- Overinterpreting low m/z peaks:
Peaks like m/z = 15 (CH₃⁺) are common but not always diagnostic.
- Ignoring isomer effects:
Branching alters fragmentation pathways—3-methylhexane fragments differently
than n-heptane.
Exam Revision Tips
(A Level, IB, AP Chemistry)
- Learn common alkyl fragment ions:
CH3⁺ (15), C2H5⁺ (29), C3H7⁺
(43), C4H9⁺ (57), etc.
- Use molecular ion to find Mr:
The highest m/z peak (if present) gives the molecular mass.
- Practice with isomers:
Compare spectra of 3-methylhexane vs. 2-methylhexane or n-heptane.
- Annotate spectra:
Label key peaks with fragment identities and origins.
- Understand fragmentation logic:
Electron ionization favours formation of stable carbocations.
- Use base peak for structure clues:
It often reflects the most stable fragment.
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Comparing the
1H NMR and 13C NMR spectra of the nine alkane structural isomers of C7H16
You can distinguish all 9 isomers from a data combination of their number of
1H NMR
chemical shifts,
and their resulting integrated 1H proton ratios, plus, their number of
13C
chemical shifts. |
|
Name of the alkane structural isomer of molecular
formula C7H16 |
Abbreviated structural formulae
of the nine isomers of molecular formula C7H16 (interpretation complications with 3-methylhexane and
2,3-dimethylpentane because they exhibit R/S isomerism due to a
chiral carbon) |
Skeletal formula of the
nine
alkane isomers of
molecular formula C7H16 |
Number of 1H NMR chemical shifts (δ) and
proton ratio (links
to spectrum) |
Number of 13C chemical shifts (δ)
(links
to spectrum) |
|
heptane |
 |
 |
4 δ: proton ratio: 3:2:2:1 (6:4:4:2 in the molecule) |
4 δ shifts |
|
2-methylhexane |
 |
 |
6 δ: proton ratio :
6:3:2:2:2:1 |
6 δ shifts |
|
3-methylhexane |
|
|
7 δ: proton ratio:
3:3:3:2:2:2:1 (simplification) ! |
7
δ shifts |
|
3-ethylpentane |
 |
 |
3 δ: proton ratio:
9:6:1 |
3 δ
shifts |
|
2,2-dimethylpentane |
 |
 |
4 δ: proton ratio:
9:3:2:2 |
5 δ shifts |
|
2,3-dimethylpentane |
 |
 |
6 δ: proton ratio:
6:3:3:2:1:1 (simplification) ! |
6 δ
shifts (simplification) !!! |
|
2,4-dimethylpentane |
 |
 |
3 δ: proton ratio:
12:2:2 |
3 δ
shifts |
|
3,3-dimethylpentane |
 |
 |
3 δ: proton ratio:
3:3:2 (6:4:4 in the molecule) |
4 δ
shifts |
|
2,2,3-trimethylbutane |
 |
 |
3 δ: proton ratio:
9:6:1 |
4 δ shifts |
Key words & phrases: C7H16 image diagram on how to interpret and explain the mass spectrum of
3-methylhexane m/z m/e base peaks, image and diagram of the mass spectrum of
3-methylhexane, details of the mass spectroscopy of 3-methylhexane, low and high resolution mass
spectrum of 3-methylhexane, prominent m/z peaks in the mass spectrum of
3-methylhexane, comparative
mass spectra of 3-methylhexane, the molecular ion peak in the mass spectrum of
3-methylhexane,
analysing and understanding the fragmentation pattern of the mass spectrum
of 3-methylhexane, characteristic pattern of peaks in the mass spectrum of
3-methylhexane, relative
abundance of mass ion peaks in the mass spectrum of 3-methylhexane, revising the mass
spectrum of 3-methylhexane, revision of mass spectroscopy of 3-methylhexane, most abundant ions in the
mass spectrum of 3-methylhexane, how to construct the mass spectrum diagram for abundance
of fragmentation ions in the mass spectrum of 3-methylhexane, how to analyse the mass
spectrum of 3-methylhexane, how to describe explain the formation of fragmented ions in the
mass spectra of 3-methylhexane equations for explaining the formation of the positive ions
in the fragmentation of the ionised molecule of 3-methylhexane recognising the
base ion peak of 3-methylhexane interpreting
interpretation the mass spectrum of 3-methylhexane CH3CH2CH(CH3)CH2CH2CH3
Stick diagram of the relative abundance
of ionised fragments in the fingerprint pattern of the mass spectrum of
3-methylhexane. Table of the m/e m/z values and formula of the ionised fragments in the
mass spectrum of 3-methylhexane. The m/e m/z value of the molecular ion peak in the
mass spectrum of 3-methylhexane. The m/e m/z value of the base ion peak in the
mass spectrum of 3-methylhexane. Possible examples of equations showing the formation
of the ionised fragments in 3-methylhexane. Revision notes on the mass spectrum of
3-methylhexane.
Matching and deducing the structure of the 3-methylhexane molecule from its mass
spectrum. Mass spectroscopy of
aliphatic alkanes,
mass spectra of 3-methylhexane, a structural isomer of molecular formula
C7H16
How do you interpret the mass spectrum of
3-methylhexane How to interpret
the mass spectrum of 3-methylhexane Explanatory diagram of the mass spectrum of the
3-methylhexane molecule in
terms of its molecular structure.
Listing data of the prominent main peaks in the mass spectrum of
3-methylhexane. How to explain the mass spectrum of 3-methylhexane. The m/z value of the
molecular ion peak in the mass spectrum of 3-methylhexane. Identifying
3-methylhexane from
its mass spectrum pattern. The m/z m/e peak analysis interpretation
diagram of the mass
spectrum of the 3-methylhexane molecule. The uses of the mass spectrum of the
3-methylhexane molecule. The distinctive features of the mass spectrum of
the 3-methylhexane molecule explained. explaining the fragmentation pattern of the mass spectrum of
3-methylhexane equations showing the
formation of the ionised fragments in the mass spectrum of
3-methylhexane
what does the mass spectrum tell you about the structure and
properties of the 3-methylhexane molecule? Data table of ionised fragments in
the mass spectrum of 3-methylhexane and equations for their formation in the
fragmentation of 3-methylhexane molecules
Links associated
with
3-methylhexane
The
infrared spectrum of 3-methylhexane
The
H-1 NMR spectrum of 3-methylhexane
The
C-13 NMR spectrum of 3-methylhexane
The chemistry of ALKANES
revision notes INDEX
Mass spectrometry index
ALL SPECTROSCOPY INDEXES
All Advanced Organic
Chemistry Notes
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Infrared spectra of the isomers of C7H16
The infrared
spectrum of heptane
The
infrared spectrum of 2-methylhexane
The
infrared spectrum of 3-methylhexane
The
infrared spectrum of 3-ethylpentane
The infrared spectrum of
2,2-dimethylpentane
The infrared spectrum of
2,3-dimethylpentane
The infrared spectrum of
2,4-dimethylpentane
The infrared spectrum of
3,3-dimethylpentane
The infrared spectrum
of 2,2,3-trimethylbutane
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Mass spectra of the isomers of C7H16
The mass
spectrum of heptane
The mass
spectrum of 2-methylhexane
The mass
spectrum of 3-methylhexane
The
mass spectrum of 3-ethylpentane
The mass spectrum of
2,2-dimethylpentane
The mass spectrum of
2,3-dimethylpentane
The mass spectrum of
2,4-dimethylpentane
The mass spectrum of
3,3-dimethylpentane
The mass
spectrum of 2,2,3-trimethylbutane
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H-1 proton NMR spectra of ALKANES
1H NMR spectra of the isomers of C7H16
The H-1 NMR
spectrum of heptane
The
H-1 NMR spectrum of 2-methylhexane
The
H-1 NMR spectrum of 3-methylhexane
The
H-1 NMR spectrum of 3-ethylpentane
The H-1 NMR spectrum of
2,2-dimethylpentane
The H-1 NMR spectrum of
2,3-dimethylpentane
The H-1 NMR spectrum of
2,4-dimethylpentane
The H-1 NMR spectrum of
3,3-dimethylpentane
The H-1
NMR spectrum of 2,2,3-trimethylbutane
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C-13 carbon-13 NMR spectra
of ALKANES
13C NMR spectra of the isomers of C7H16
The C-13 NMR
spectrum of heptane
The
C-13 NMR spectrum of 2-methylhexane
The
C-13 NMR spectrum of 3-methylhexane
The
C-13 NMR spectrum of 3-ethylpentane
The C-13 NMR spectrum of
2,2-dimethylpentane
The C-13 NMR spectrum of
2,3-dimethylpentane
The C-13 NMR spectrum of
2,4-dimethylpentane
The C-13 NMR spectrum of
3,3-dimethylpentane
The
C-13 NMR spectrum of 2,2,3-trimethylbutane
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