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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.Skip flash movie

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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

    Note: %1 means percentage abundance of isotope one.
  1. identify molecular formulae based on accurate masses.
  2. 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:

Table of compounds containing only C, H, O and N

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

A typical mass spectrum is shown below:
Mass spectrum of n-octane: CH3CH2CH2CH2CH2CH2CH2CH3

Mass spectrum of n-octane

At high energies, the ionising electron beam can fragment the molecule by cleaving particular bonds. The molecular fragmentation peaks in the mass spectrum can give clues as to the sub-structure of the molecule.

The peak height is the relative abundance of each species. The most intense peak (called the Base peak) is assigned a relative abundance of 100. The parent ion peak (i.e. the singly charged ion of the test molecule denoted by M+ located at m/e of 114 in the spectrum above) is often too weak to be seen in the high energy spectra that are necessary to produce a fragmentation pattern.

Peak assignments: 114 arrow right M+ Parent ion
  99 arrow right M - CH3 (cleavage of methyl group)
  85 arrow right M - CH2CH3 (cleavage of ethyl group)
  71 arrow right M - CH2CH2CH3 (cleavage of propyl group)
  57 arrow right M - CH2CH2CH2CH3  
  43 arrow right CH3CH2CH2+ Base peak
  29 arrow right CH3CH2+  

Straight chain alkanes and alkyl groups produce a typical series of peaks:
29 (CH3CH2+), 43 (CH3CH2CH2+), 57 (CH3CH2CH2CH2+), 71 (CH3CH2CH2CH2CH2+), etc.

Cleavage is more likely to occur at carbons exhibiting a greater degree of branching and the largest substituent is cleaved most easily.

Mass spectrum of 3,3-dimethyl hexane: CH3CH2C(CH3)2CH2CH2CH3

Mass spectrum of dimethyl hexane

Peak assignments: Parent ion too weak for highly branched alkane
  99 arrow right M - CH3  
  85 arrow right M - CH2CH3  
  71 arrow right M - CH2CH2CH3  
  57 arrow right M - CH2CH2CH2CH3  
  43 arrow right CH3CH2CH2+  
  29 arrow right CH3CH2+  

Rearrangement can also occur. This is when a small stable molecule (eg. H2O from alcohol) is eliminated or, as in the case of a carbonyl grouping, a terminal H attaches to O during fragmentation of the hydrocarbon substituent.

The identities of a number of fragments may be deduced from the spectrum but the assignment of functional groups and branched substituents is usually used as a confirmation of information obtained from IR and NMR analyses.

Mass spectrum of ethanol: CH3CH2OH

Mass spectrum of ethanol

Peak assignments: 46 arrow right M+ Parent ion  
  45 arrow right M - H  
  31 arrow right M - CH3, CH2OH+  
  29 arrow right M - OH, CH3CH2+
  28 arrow right M - H2O

A partial list of fragments follows:

Table showing a partial list of fragments

Mass spectrum of ethyl ether: CH3CH2OCH2CH3

Mass spectrum of ethyl ether

Peak assignments: 74 arrow right M+ Parent ion
  59 arrow right M - CH3
  45 arrow right M - CH2CH3
  29 arrow right CH3CH2+


Mass spectrum of octanal: CH3(CH2)6CHO

Mass spectrum of octanal

Peak assignments: 128 arrow right M+ Parent ion  
  127 arrow right M - H    
  112 arrow right M - H2O  
  100 arrow right CH2CH2  
  85 arrow right M - CH2CO  
  84 arrow right M - CH2CHOH  
  57 arrow right C4H9+  
  43 arrow right C3H7+  
  29 arrow right C2H5+, CHO+  

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