Mass Spectrometry

EI-MassSpectra of Assorted Organic Compounds

The mass apectra of three different saturated hydrocarbons are displayed below. Two are isomeric hexanes and the third is cyclohexane. Comments regarding the fragmentation patterns are presented in the box to the right of each spectrum. Ions are sometimes characterized by loss of a specific neutral fragment from the molecular ion. For example, a M-15 ion is identified as loss of a methyl group. Odd-electron ions, including the molecular ion, are colored orange when marked. Even-electron ions are colored magenta. The "Toggle Examples" button at the bottom will display a different set of spectra in which the influence of a particular functional group may be examined. Repeated clicking of this button will cycle through fifteeen spectra. In each example the molecular ion is designated by M •⁺.

End of this supplementary topic

Common Fragment Ions and Neutral Fragments

Common Small Ions
m/z	composition
15 Da	CH₃
17	OH
18	H₂O
19	H₃O, F
26	C₂H₂, CN
27	C₂H₃
28	C₂H₄, CO, H₂CN
29	C₂H₅, CHO
30	CH₂NH₂
31	CH₃O
33	SH, CH₂F
34	H₂S
35(37)	Cl
36(38)	HCl
39	C₃H₃
41	C₃H₅, C₂H₃N
42	C₃H₆, C₂H₂O, C₂H₄N
43	C₃H₇, CH₃CO
44	C₂H₄O
46	NO₂
56	C₄H₈
57	C₄H₉
60	CH₄CO₂
79(81)	Br
80(82)	HBr
91	C₇H₇
127	I
128	HI

Common Neutral Fragments
mass loss	composition
1 Da	H
15	CH₃
17	OH
18	H₂O
19	F
20	HF
27	C₂H₃, HCN
28	C₂H₄, CO
30	CH₂O
31	CH₃O
32	CH₄O, S
33	CH₃ + H₂O, HS
33	H₂S
35(37)	Cl
36(38)	HCl
42	C₃H₆, C₂H₂O, C₂H₄N
43	C₃H₇, CH₃CO
44	CO₂O, CONH₂
45	C₂H₅O
55	C₄H₇
57	C₄H₉
59	C₂H₃O₂
60	C₂H₄O₂
64	SO₂
79(81)	Br
80(82)	HBr
127	I
128	HI

End of this supplementary topic

Rearangement Mechanisms in Fragmentation

4-nonanone

The odd-electron fragment ions at m/z = 86 and 58 are the result of a McLafferty rearrangement, involving the larger alkyl chain, and a subsequent loss of ethene (the "double-McLafferty" rearrangement).
Alpha-cleavage leads to the m/z = 99, 71 and 43 ions. The charge is apparently distributed over both fragments.

butylpentanoate

Alpha-cleavage gives ions at m/z=57 & 85 Da. The McLafferty rearrangement on the acid side generates a m/z=116 ion. Subsequent rearrangement on the alcohol side generates m/z=60 and 56 ions. The m/z=103 ion is probably C₄H₉CO₂H₂⁽⁺⁾.

5-methyl-5-hexen-3-ol

The molecular ion (m/z=114 Da) is not observed under electron impact ionization conditions. The highest mass ion (m/z=85) is due to an alpha-cleavage of ethyl; the other alpha-cleavage generates m/z=59. The rearrangement cleavage shown here generates the m/z=56 ion.

4,4-dimethylcyclohexene

The loss of a methyl radical generates the base peak at m/z=95 Da. The m/z=81 & 67 ions are smaller homologues of this ion (14 mass units less). Cyclohexene compounds undergo a retro-Diel-Alder rearrangement to give diene and alkene fragments. The charge may reside on either fragment, with the larger usually predominating. In this case both ions are relatively strong (m/z=54 & 56).

4-nonanone	The odd-electron fragment ions at m/z = 86 and 58 are the result of a McLafferty rearrangement, involving the larger alkyl chain, and a subsequent loss of ethene (the "double-McLafferty" rearrangement). Alpha-cleavage leads to the m/z = 99, 71 and 43 ions. The charge is apparently distributed over both fragments.
butylpentanoate	Alpha-cleavage gives ions at m/z=57 & 85 Da. The McLafferty rearrangement on the acid side generates a m/z=116 ion. Subsequent rearrangement on the alcohol side generates m/z=60 and 56 ions. The m/z=103 ion is probably C₄H₉CO₂H₂⁽⁺⁾.
5-methyl-5-hexen-3-ol	The molecular ion (m/z=114 Da) is not observed under electron impact ionization conditions. The highest mass ion (m/z=85) is due to an alpha-cleavage of ethyl; the other alpha-cleavage generates m/z=59. The rearrangement cleavage shown here generates the m/z=56 ion.
4,4-dimethylcyclohexene	The loss of a methyl radical generates the base peak at m/z=95 Da. The m/z=81 & 67 ions are smaller homologues of this ion (14 mass units less). Cyclohexene compounds undergo a retro-Diel-Alder rearrangement to give diene and alkene fragments. The charge may reside on either fragment, with the larger usually predominating. In this case both ions are relatively strong (m/z=54 & 56).