Mass spectrometry

Molecular ions and fragment ions

  • When an organic compound is placed in the mass spectrometer, it loses an electron and forms a positive ion, the molecular ion.
  • The mass spectrometer detects the mass-to-charge ratio (m/z) of the molecular ion which gives the molecular mass of the compound. 
  • The molecular ion M+ is the positive ion formed when a molecule loses an electron. 
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Molecular mass from a mass spectrum

  • To find the molecular mass, the molecular ion peak (M+) has to be located. 
  • The molecular ion peak is the peak on the far right with the highest m/z value. 
  • The small peak after the M+ peak is the M+1 peak. It exists because 1.1% of the carbon atoms present is the carbon-13 isotope. 
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Fragmentation

  • Some molecular ions break down into smaller pieces known as fragments in a process fragmentation.
  • The other peaks are caused by fragment ions, formed from the breakdown of the molecular ion. 
  • The simplest fgragmentation breaks a molecular ion down into two species - a positively charged fragment ion and a radical.
  • Any positive ions formed will be detected by the mass spectrometer but the uncharged radicals are not detected. 
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Using fragmentation peaks to identify a molecule

  • The mass spectrum of each compound is unique, as molecules will all fragment in slightly different ways depending on their structures. 
  • Mass spectra can therefore be used to help identify molecules.
  • Although two mat have the same molecular mass and the same molecular ion peak, the fragment ions may be different. 
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Common fragment ions

  • CH3+  = 15
  • C2H5+ = 29
  • C3H7+ = 43
  • C4H9+ = 57 
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