Interpreting Mass Spectrum Fragmentation Patterns


This is part of the HSC Chemistry course under Module 8 Section 2: Analysis of Organic Substances

HSC Chemistry Syllabus

  • Investigate the processes used to analyse the structure of simple organic compounds addressed in the course, including but not limited to:
– proton and carbon-13 NMR
– mass spectrometry
– infrared spectroscopy (ACSCH130)

      Mass Spectrometry Fragmentation Patterns

      This video explores how mass fragmentation patterns in the mass spectrum can be utilised to help us confirm the identity of a compound. 

      Understanding Mass Spectrometry

      Mass spectrometry is a spectroscopic technique which measure the mass-to-charge ratio of molecules. The process involves a heater vaporising a sample molecule which is then ionised by an electron gun. This ionisation typically fragments the molecule.

      You can learn about the basics of mass spectrometry here

      The Role of Fragmentation

      The fragments which are formed as a result of ionisation each produce unique signals in the mass spectrum. By analysing these fragmentation patterns, we can deduce and confirm the structure of a suspected compound. Analysis involves looking at the mass-to-charge (m/z) ratio, which directly indicates the molecular mass of the fragment. 

      It is important to understand that both mass and charge are conserved during fragmentation. This means the total number of atom of each element before and after fragmentation are equal; so is the total charge of molecules and fragments.

      The molecule that undergoes fragmentation should always be positively charged due to the removal of electrons. Although uncharged molecules and fragments are present and produced, they are not accelerated in the electric field of mass spectrometers, and therefore do not possess the required velocity to be deflected by the subsequent magnetic field. These uncharged molecular species are generally not detected, and thus not reflected in the fragmentation equations.

      Example Fragmentation Patterns (Watch Video for Full Analysis)

      • Pentane:

        $$C_5H_{12}^+ \rightarrow C_2H_5 + C_3H_7^+$$
        $$C_5H_{12}^+ \rightarrow C_3H_7 + C_2H_5^+$$

        This molecule's molecular ion peak at a mass-to-charge ratio of 72 matches its molar mass. The peak at 29 in the mass spectrum aligns with the `C_2H_5^+` fragment. 

      • Ethanol:
        $$C_2H_6O^+ \rightarrow CH_2OH^+ + CH_3$$
        $$C_2H_6O^+ \rightarrow C_2H_5O^+ + H$$
        Here, the base peak at 31 correlates with the `CH_2OH^+` fragment. Additionally, a peak at 45 signifies the loss of a hydrogen atom, likely from the alcohol group. 

      • Propane:
        $$C_3H_6O^+ \rightarrow CH_3^+ + C_2H_3O$$
        $$C_3H_6O^+ \rightarrow C_2H_3O^+ + CH_3$$

        A peak at 15 in its spectrum often indicates a methyl group (`CH_3^+`), resulting from cleavage between specific carbon atoms. 

      • Propanoic Acid:
        $$C_3H_6O_2^+ \rightarrow CHO_2^+ + C_2H_5$$
        $$C_3H_6O_2^+ \rightarrow C_3H_5O^+ + OH$$
        $$C_3H_6O_2^+ \rightarrow CO^+ + OH + C_2H_5$$

        Signals at 45 and 57 in this acid's spectrum are indicative of the carboxylic acid group and the cleavage of a hydroxyl group.

        Esters and Amines (Watch Video for Full Analysis)

        • Esters:

          Ester molecules can have multiple different fragmentation patterns. 

          $$C_4H_8O_2^+ \rightarrow C_3H_5O^+ + CH_3O$$
          $$C_4H_8O_2^+ \rightarrow CH_3O^+ + C_3H_5O$$

          The C–O bond of methyl propanoate can cleave, or the C–C bond next to the ester functional group can cleave. 

          $$C_4H_8O_2^+ \rightarrow C_2H_5^+ + C_2H_3O_2$$
          $$C_4H_8O_2^+ \rightarrow C_2H_3O_2^+ + C_2H_5$$

        • Ethanamine:
          $$C_2H_7N^+ \rightarrow CH_2NH_2^+ + CH_3$$

          The m/z ratio difference of 15 between the two ion peaks of interest are indicative of methyl group cleavage. The peak at 45 corresponds with the molecular ion peak, therefore the peak at 30 is likely indicative of the fragment formed when a methyl group has been cleaved – `CH_2NH_2^+`.