Study Notes: The Interpretation of Mass Spectra

Structural Elucidation
The determination of the structures of organic compounds is a vital part of chemistry in general and analysis in particular. Specialised
instruments are used to provide the chemist with the necessary information for the identification of compounds.

Mass Spectrometry (MS):

The sample is injected (possibly after LC or GLC separation or by hypodermic through a silicone rubber dam) into an ionisation chamber.
A beam of electrons collides with the sample molecules to produce (mainly) single positively charged ions of the molecules (molecular
ions). If the beam energy is high enough, fragments of the molecules will also be produced (fragment ions).

The various ions are linearly accelerated in an electric field then passed through a magnetic field to curve their flight path. The radius of
curvature of the path taken by the ions depends on the mass/charge ratio of the ions. i.e. small radius for low mass and higher charge.

The magnetic field strength is varied so different ions reach the collector (detector) which produces an electric current equivalent to the
masses of the particles. The recorder produces a mass spectrum which registers the relative proportion of molecular and fragment ions
with a particular mass/charge ratio.

The Mass Spectrometer is used to:-

1. measure the masses and abundances of naturally occurring isotopes. This data is used to calculate atomic weights:

(m1 x %1) + (m2 x %2)

Ar =
100

2. Note: %1 means percentage abundance of isotope one.

2. identify molecular formulae based on accurate masses.

eg. 30.0708 = C2H6 30.0268 = H2CO

3. determine molecular structures based on fragmentation of the molecular ion.

eg. For ethanol CH3CH2OH, the following mass peaks may be observed:

17 = OH 14 = CH2 15 = CH3 29 = CH3CH2 46 = CH3CH2OH

Since the masses of C, H, O and N are not integers, and they all differ from each other in their decimal portions, the compound molecular
weight will allow you to look up tables to find the molecular formula. A brief version for some compounds containing only C, H, O, N
follows:
The molecular weight (Mr), if known, can enable the analyst to narrow the choice of possible structures considerably by providing the
molecular formula. However, there may be many isomeric forms for the molecular formula that is obtained.
eg. Mr = 86.1366 corresponds to the molecular formula: C5H10O
Possible structures include:

Ketones CH3COCH2CH2CH3 CH3COCH(CH3)2

CH3CH2COCH2CH3
Aldehydes CH3CH2CH2CH2CHO (CH3)2CHCH2CHO (CH3)3CCHO
Mass spectrum of ethanol: CH3CH2OH

Peak assignments: 46 M+ Parent ion

45 M-H
31 M - CH3, CH2OH+

29 M - OH, CH3CH2+

28 M - H2O

A partial list of fragments follows:

Ion Table / Peak Table

Ion () Intensity () Annotation ()

39.000000 3.100000
50.000000 2.200000
51.000000 22.500000
63.000000 1.300000
76.000000 2.900000
77.000000 55.100000
78.000000 14.100000
105.000000 9.300000
106.000000 99.990000
107.000000 10.300000