Analysing the Structure of Organic Compounds Using Mass Spectrometry



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 Explained

    This video explores how mass spectrometry is used to analyse the structure of organic compounds. It explains how to read a mass spectrum of an organic molecule, at a level suitable for HSC Chemistry students.


    What is Mass Spectrometry?

    • Analytical technique that breaks organic molecules into ionised fragments and sorts them based on their mass-to-charge (m/z) ratio.
    • Mass spectrometry provides information on a molecule’s mass. It can be combined with other techniques to determine the composition of the molecule.

    Components of a Mass Spectrometer

    • Heater: vapourises a small sample of analyte.
    • Electron gun: removes electron(s) from vapourised samples to create positive ions. During ionisation, a molecule can be broken into fragments due to bond breakage and electronic rearrangement of unstable ions.


    • Electric field: accelerates positive molecular ion fragments from rest.
      • The positive plate of the electric field helps to repel positive ions while they are attracted to the negative plate.
    • Magnetic field: deflects ionised fragments.
      • The extent of deflection is inversely proportional to its mass-to-charge ratio
      • Lighter ions and those with higher charges are deflected the more.
    • The detector is able to sort the ion fragments based on their m/z ratio and measure the intensity (number of a particular fragment) at the same time.
    • Negative and neutral molecules are removed from the mass spectrometer before they are detected. These molecules do not reach the detector as only positively charged molecular ions and fragments are accelerated by the electric field. 

    Features of Mass Spectrum

    • The base peak refers to the most abundant ion detected (highest intensity)
    • The molecular ion peak or parent ion peak refers to the signal produced by the original molecule. The m/z of this signal equals the molecular mass of the molecule analysed. The molecular ion peak may not have the greatest intensity.
    • The M+1 peak is produced by a molecule containing a carbon-13 isotope as one of its carbon atoms. This causes the molecule’s m/z to be exactly one unit greater than that of the molecular ion.

     What is the M+2 peak? 


    • Peak in the mass spectrum exactly 2 m/z units higher than parent ion peak (M+)
    • Indicates the presence of an element in the molecule whose isotopes vary in atomic mass of 2. For example, chlorine and bromine as they both have two isotopes of significant relative abundance
    • Isotopes of chlorine:
      • Chlorine-35 makes up 75% of chlorine
      • Chlorine-37 makes up 25% of chlorine
    • Isotopes of bromine:
      • Bromine-79 makes up 51% of bromine
      • Bromine-81 makes up 49% of bromine
    • The relative intensity of parent ion and M+2 peaks reflect relative abundance of the isotopes.
      • Molecules containing chlorine will display M and M+2 peaks with intensities in the approximate ratio of 3:1 (75% : 25%)
      • Molecules containing bromine will display M and M+2 peaks with intensities in the approximate ratio of 1:1 (51% : 49%)


    Mass Spectrum of Chloroethane


    Mass Spectrum of Bromoethane


    A series of preliminary tests on a small, water-soluble organic molecule were conducted. The infrared and mass spectrum of the unknown molecule are shown. Not: Two parent ion peaks are shown. 

    Draw the structural formula for this compound