[Author ©  Dr Phl 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 & AP honors chemistry courses: Mass spectrometry - analysing mass spectrum of 3,3-dimethylpentane [spectra updated Mar 19th 2026 *]

 email doc brown  Re-edit mass spectrum of CH₃CH₂C(CH₃)₂CH₂CH₃

 3,3-dimethylpentane C₇H₁₆  

Interpreting the fragmentation pattern of the mass spectrum of 3,3-dimethylpentane

[M]⁺ is the molecular ion peak (M) with an m/z of 100 corresponding to [C₇H₁₆]⁺, the original 3,3-dimethylpentane molecule minus an electron, [CH₃CH₂C(CH₃)₂CH₂CH₃]⁺.

It must be very unstable as it is a very tiny peak!

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 from  [¹³C¹²C₆H₁₆]⁺.

3,3-dimethylpentane has 7 carbon atoms, so on average, ~1 in 14 molecules will contain a ¹³C atom.

This sort of argument also applies to fragment ions from the parent molecular ion of 3,3-dimethylpentane - though the ratio will be greater (in fact here the M peak is almost absent, so even less chance of observing the M+1 peak).

e.g. m/z 44 ion could be [¹³C¹²C₂H₇]⁺, m/z 72 ion [¹³C¹²C₄H₁₁]⁺, and m/z 86 ion [¹³C¹²C₅H₁₃]⁺

These ions might be more likely than those containing only ¹²C isotope atoms

i.e. [C₃H₈]⁺, [C₅H₁₂]⁺ and [C₆H₁₄]⁺

Either way, for identification purposes, all these peaks add uniqueness to the fragmentation pattern of the mass spectrum of 3,3-dimethylpentane.

The most abundant ion of the molecule under mass spectrometry investigation (3,3-dimethylpentane) 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 3,3-dimethylpenttane is the m/z ion 43 [C₃H₇]⁺

Identifying the species giving the most prominent peaks (apart from M) in the fragmentation pattern of 3,3-dimethylpentane.

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 3,3-dimethylpentane.

The parent molecular ion of heptane m/z 100: [C₇H₁₆]⁺

Identifying the species giving the most prominent peaks (apart from M) in the fragmentation pattern of 3,3-dimethylpentane.

Identifying the species giving the most prominent peaks (apart from M) in the fragmentation pattern of 3,3-dimethylpentane.

Analysing and explaining the principal ions in the fragmentation pattern of the mass spectrum of 3,3-dimethylpentane

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 possible equations to explain some of the most abundant ion peaks in the mass spectrum of 3,3-dimethylpentane

Atomic masses: H = 1;  C = 12 (13 for ~1 in 100)

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

Most fragmentation in alkanes arises from C-C bond scission (C-C bond weaker than C-H bond).

Ethene is often eliminated to give a smaller fragment

e.g. the m/z 71 ion gives the m/z ion 43

[C₅H₁₁]⁺  ===>  [C₃H₇]⁺  +  C₂H₄

Mass change = 71 - 28 = 43

The m/z 57 ion can be formed by loss of a ethene from the m/z 85 ion.

[C₆H₁₃]⁺  ===>  [C₄H₉]⁺  +  C₂H₄

Mass change = 85 - 28 = 57

Many other fragments are formed by hydrogen atom/molecule loss, so you get m/z ion sequences like 71 ==>70, 57 ==> 56 ==> 55, 43 ==> 39 and 29 ==> 27 etc. (see examples below).

Formation of m/z 85 ion:

[CH₃CH₂C(CH₃)₂CH₂CH₃]⁺  ===>  [C₆H₁₃]⁺  +  CH₃

C-C bond fission in the parent molecular ion of 3,3-dimethylpentane.

Here a methyl group is broken off,

mass change = 100 - 15 = 85 (M-15 ion peak)

The m/z 86 ion is probably formed in the same way but containing a ¹³C atom rather than the alternative ion [C₆H₁₄]⁺

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:

m/z 86: [C₆H₁₄]⁺ = 86.1092  and  [¹³C¹²C₅H₁₃]⁺ = 86.1048, a relative ion mass difference of 0.0044

Formation of m/z 71 ion:

[CH₃CH₂C(CH₃)₂CH₂CH₃]⁺  ===>  [(CH₃)₂CHCHCH₃]⁺  +  CH₂CH₃

C-C bond fission in the molecular ion of 3,3-dimethylpentane.

Here an end ethyl group is broken off,

mass change = 100 - 29 = 71 (M-29 ion peak)

The m/z 72 ion is probably formed in the same way but containing a ¹³C atom rather than the alternative ion [C₅H₁₂]⁺

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 72: [C₅H₁₂]⁺ = 72.0936 *  [¹³C¹²C₄H₁₁]⁺ = 72.0892, a difference of 0.0044 in relative ion mass.

Formation of m/z 70 ion:

[C₆H₁₃]⁺]⁺  ===>  [C₅H₁₀]⁺  +  CH₃

A methyl group is broken off from the m/z 85 ion,

mass change = 85 - 15 = 70

Formation of m/z 57 ion:

[C₇H₁₆]⁺  ===>  [C₄H₉]⁺  +  C₃H₇

C-C bond fission in the molecular ion of 3,3-dimethylpentane.

Loss of a C₃H₇ group,

mass change = 100 - 43 = 57 (M-43 ion peak)

Formation of m/z 43 ion:

[(CH₃)₂CHCH(CH₃)CH₂CH₃]⁺  ===>  [C₃H₇]⁺  +  C₄H₉

Loss of a C₄H₉ group,

mass change = 100 - 57 = 43 (M-57 ion peak)

The m/z 43 ion intensity is the base peak ion.

The m/z 44 ion is probably formed in the same way but containing a ¹³C atom rather than the alternative ion [C₃H₈]⁺

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 44: [C₃H₈]⁺ = 44.0624  and [¹³C¹²C₂H₇]⁺ = 44.0580, a difference of 0.0044 in relative ion mass.

The m/z 43 ion can lose hydrogen atoms to give the m/z 42, 41 and then 39 ions (see ion data table).

Formation of m/z 29 ion:

[(CH₃)₂CHCH(CH₃)CH₂CH₃]⁺  ===>  [CH₂CH₃]⁺  +  C₅H₁₁

C-C bond fission in the molecular ion of 3,3-dimethylpentane.

Here an end ethyl group is broken off,

mass change = 100 - 71 = 29 (M-71 ion peak)

The m/z 29 ion can lose hydrogen atoms to give the m/z 28 and then 27 ions (see ion data table).

Structural Overview: 3,3-Dimethylpentane

Molecular formula: C₇H₁₆
Molecular ion (M⁺): m/z = 100

This is a branched alkane with a quaternary carbon at position 3, which influences fragmentation patterns.

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Prominent m/z Ions and Their Origins

m/z Value	Fragment Ion Formula	Origin of Fragmentation	Notes
100	C7H16⁺	Molecular ion (M⁺)	Often weak or absent in alkanes
85	C6H13⁺	Loss of CH3 (15)	Common alkyl loss
71	C5H11⁺	Loss of C2H5 (29)	Ethyl cleavage
57	C4H9⁺	Loss of C3H7 (43)	Propyl cleavage
43	C3H7⁺ base peak ion	Isopropyl or propyl ion	Very stable carbocation
41	C3H5⁺	Allylic-like fragment	Less common in saturated alkanes
29	C2H5⁺	Ethyl ion	Common in alkane spectra
15	CH3⁺	Methyl ion	Small but diagnostic peak

Common Misconceptions

Misconception	Clarification
The base peak is always the molecular ion	Not true—alkanes often fragment extensively, and the base peak is usually a stable carbocation.
All fragments are neutral	No—only charged fragments are detected.
Mass spectrum shows all atoms	It only shows ions, not neutral species.
Fragmentation is random	It follows carbocation stability and bond strength rules.
Quaternary carbons don’t affect fragmentation	They do—they often lead to branched alkyl ion formation.

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Exam Revision Tips

• Know the molecular ion (M⁺) and its m/z value.
• Know common alkyl fragment ions: m/z 15 (CH₃⁺), 29 (C₂H₅⁺), 43 (C₃H₇⁺), 57 (C₄H₉⁺),  are frequently tested, but not always diagnostic.
• Base peak is often the most stable carbocation, not the largest fragment.
• Use the structure to predict likely cleavage points.
• Quaternary carbons often lead to branched fragment ions.
• Only charged fragments appear in the spectrum.
• Practice with branched alkanes—they produce distinctive fragmentation patterns.

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Practice Question (Exam Style)

Question:
The mass spectrum of 3,3-dimethylpentane shows a molecular ion peak at m/z = 100.
(a) Identify two prominent fragment ions and their m/z values.
(b) Explain why the base peak is not the molecular ion.
(c) Suggest a fragment ion that results from loss of a methyl group.
(d) Why are only certain fragments detected in the spectrum?

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Model Answer

(a)

• m/z = 43 (C₃H₇⁺)
• m/z = 57 (C₄H₉⁺)

(b)
The molecular ion is often unstable in alkanes and fragments quickly. The base peak corresponds to the most stable carbocation, not necessarily the parent ion.

(c)
Loss of CH₃ (15) from M⁺ gives m/z = 85 (C₆H₁₃⁺)

(d)
Only positively charged fragments are detected by the mass spectrometer. Neutral species are not recorded.

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

The infrared spectrum of 3,3-dimethylpentane

The H-1 NMR spectrum of 3,3-dimethylpentane

The C-13 NMR spectrum of 3,3-dimethylpentane

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