3-methylpentane C₆H₁₄,  ,  ,

For more see The molecular structure, classification and naming of alkanes

Interpreting the fragmentation pattern of the mass spectrum of 3-methylpentane

[M]⁺ is the molecular ion peak (M) with an m/z of 86 corresponding to [C₆H₁₄]⁺, the original 3-methylpentane molecule minus an electron, [(CH₃CH₂)₂CHCH₃]⁺

The very tiny M+1 peak at m/z 87, corresponds to an ionised 3-methylpentane molecule with one ¹³C atom in it i.e. an ionised 3-methylpentane molecule of formula ¹³C¹²C₅H₁₄

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

A similar argument applies to fragment ions from the breakdown of the parent molecular ion of 3-methylpentane - though the ratio will be greater e.g. the m/z 58 ion [¹³C¹²C₃H₉]⁺

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

The most abundant ion of the molecule under mass spectrometry investigation 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 of the mass spectrum of 3-methypentane is m/z ion 57 [C₄H₉]⁺

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

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 (13 for ~1 in 100)

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

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

Formation of m/z 71 ion:

[(CH₃CH₂)₂CHCH₃]⁺  ===>  [(CH₃CH₂)₂CH]⁺  +  CH₃

C-C bond scission in the parent molecular ion, leading to loss of a methyl group from the parent molecular ion via C-C bond fission.

Mass change: 86 - 15 = 71 (M-15 ion peak), to give a secondary carbocation.

I've quoted a possible structure of the [C₅H₁₁]⁺ ion.

The m/z 72 ion can be formed by the same process i.e. [¹³C¹²C₄H₁₁]⁺ rather than the [C₅H₁₂]⁺ ion.

A modern accurate mass spectrometer can sort out ions of the same integer m/z value, by measuring relative fragment ion masses to four decimal places e.g. using very accurate relative isotopic masses,

¹²C = 12.0000  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  and  [¹³C¹²C₄H₁₁]⁺ = 72.0892, a difference of 0.0044 in relative ion mass.

Formation of m/z 57 ion:

[(CH₃CH₂)₂CHCH₃]⁺  ===>  [CH₃CH₂CHCH₃]⁺  +  CH₃CH₂

C-C bond scission of the parent molecular ion, leading to loss of an ethyl group from the parent molecular ion.

Mass change = 86 - 29 = 57 (M-29 ion), to give a secondary carbocation.

The m/z 57 ion is the base peak ion, the most abundant and 'stable' ion fragment.

The m/z 58 ion can be formed by the same process i.e. [¹³C¹²C₃H₉]⁺ rather than the [C₄H₁₀]⁺ ion.

A modern accurate mass spectrometer can sort out ions of the same integer m/z value, by measuring relative fragment ion masses to four decimal places e.g. using very accurate relative isotopic masses,

¹²C = 12.0000  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 29 ion:

[(CH₃CH₂)₂CHCH₃]⁺  ===>  [CH₃CH₂]⁺  +  CH₃CH₂CHCH₃

or from: [CH₃CH₂CHCH₃]⁺  ===>  [CH₃CH₂]⁺  +  CH₃CH

C-C bond scission of the parent molecular ion or larger fragment ion.

Mass change = 86 - 57 = 29 (M-57 ion) or 57 - 28 = 29

Sequences, including m/z values of 42, 41, 40, 39 or 28, 28, 27, 26, indicate successive hydrogen atom/molecule loss from the m/z 43 or 29 ions.

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Key points about the mass spectrum of 3-methylpentane

The mass spectrum of 3-methylpentane features a molecular ion peak at m/z = 86 and a base peak at m/z = 57, arising from stable alkyl fragmentations.

It’s a classic example of branched alkane fragmentation.

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Key Fragmentation Peaks of 3-Methylpentane

3-Methylpentane (C₆H₁₆) undergoes electron ionization, producing a molecular ion and several alkyl fragments.

Here's a breakdown of the most prominent peaks:

m/z	Fragment Ion	Origin	Notes
86	C6H14⁺•	Molecular ion (M⁺•)	Often weak due to alkane instability
71	C5H11⁺	Loss of CH3 (15)	Secondary carbocation
57	C4H9⁺	Loss of C2H5 (29)	Base peak – most stable
43	C3H7⁺	Loss of C3H7 (43)	Common in alkanes
29	C2H5⁺	Ethyl fragment	Often seen in branched alkanes

Sources: NIST Chemistry WebBook, Pearson Chemistry Prep, Transtutors analysis.

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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 radicals: Only the molecular ion is a radical cation; fragments are typically carbocations.

• Overlooking branching effects: Branched alkanes like 3-methylpentane favour fragmentation that forms more stable secondary or tertiary carbocations.

• Expecting functional group fragments: Alkanes lack functional groups, so no peaks for acylium ions, benzyl ions, etc.

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Exam Revision Tips for Mass Spectrometry

Applicable across AQA, Edexcel, OCR, WJEC, CCEA, CIE, IB HL/SL, and US AP Chemistry:

• Learn common alkyl fragment m/z values: CH₃⁺ = 15, C₂H₅⁺ = 29, C₃H₇⁺ = 43, C₄H₉⁺ = 57, etc.

• Understand fragmentation logic: Stable carbocations form preferentially—secondary > primary.

• Use molecular ion to determine M_r: The M⁺• peak gives the relative molecular mass (Mr = 86 for 3-methylpentane).

• Practice deducing structures from m/z: Work backwards from fragment ions to possible parent structures.

• Compare spectra of isomers: 3-methylpentane versus hexane versus 2-methylpentane—same M⁺•, different fragmentation patterns.

• Watch for isotope patterns: Not relevant for hydrocarbons, but crucial for halogenated compounds.

Comparing the infrared, mass, 1H NMR and 13C NMR spectra of the five structural alkane isomers of C6H14 NOTE: The images are linked to their original detailed spectral analysis pages AND can be doubled in size with touch screens to increase the definition to the original hexane, 2-methylpentane, 3-methylpentane, 2,2-dimethylbutane and 2,3-dimethylbutane image sizes.  These five molecules are structural isomers of saturated alkanes of molecular formula C6H14 and exemplify the infrared, mass, 1H NMR and 13C NMR spectra of lower aliphatic alkanes (non-cyclic alkanes).
Infrared spectra below.
	INFRARED SPECTRA: Apart from the significant differences in the fingerprint region at wavenumbers 1500 to 400 cm-1, there are no other great striking differences, but each could be identified from its infrared spectrum. All the absorption bands are typical of molecules containing saturated alkyl structure and there are no characteristic infrared absorptions due to a specific functional group.
Infrared spectra above, mass spectra below.
	MASS SPECTRA: Base ion peaks plus m/z comments. Hexane: m/z 57, 42 and 56 prominent 2-methylpentane: m/z 43, 42 and 71 prominent 3-methylpentane: m/z 57, 41 and 56 prominent 2,2-dimethylbutane: m/z 43, 41, 57 and 71 prominent 2,3-dimethylbutane: m/z 43, 41, 42 and 71 prominent
Mass spectra above, 1H NMR spectra below.
	1H NMR SPECTRA: They can all be distinguished by their different integrated proton ratios - need very high resolution. Hexane: 3 1H δ shifts, H ratio 3:2:2 (6:4:4 in formula) 2-methylpentane: 5 1H δ shifts, H ratio 6:3:2:2:1 3-methylpentane: 4 1H δ shifts, H ratio 6:4:3:1 2,2-dimethylbutane: 3 1H δ shifts, H ratio 9:3:2 2,3-dimethylbutane: 2 1H δ shifts, H ratio 6:1 (12:2 in formula)
1H NMR spectra above, 13C NMR spectra below.
	13C NMR SPECTRA: From the number of shifts, you can't distinguish (iii) and (iv) but you can distinguish them from (i), (ii) and (v). (i) Hexane: 3 13C δ shifts (ii) 2-methylpentane: 5 13C δ shifts (iii) 3-methylpentane: 4 13C δ shifts (iv) 2,2-dimethylbutane: 4 13C δ shifts (v) 2,3-dimethylbutane: 2 13C δ shifts
13C NMR spectra above.

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The chemistry of ALKANES revision notes INDEX

The infrared spectrum of 3-methylpentane

The H-1 NMR spectrum of 3-methylpentane

The C-13 NMR spectrum of 3-methylpentane

Mass spectroscopy index

ALL SPECTROSCOPY INDEXES

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