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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 •+.

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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

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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).
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