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16.9: Organic Compounds Containing Halogen Atoms

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    This page explains how the M+2 peak in a mass spectrum arises from the presence of chlorine or bromine atoms in an organic compound. It also deals briefly with the origin of the M+4 peak in compounds containing two chlorine atoms.

    One chlorine atom in a compound


    The molecular ion peaks (M+ and M+2) each contain one chlorine atom - but the chlorine can be either of the two chlorine isotopes, 35Cl and 37Cl.

    The molecular ion containing the 35Cl isotope has a relative formula mass of 78. The one containing 37Cl has a relative formula mass of 80 - hence the two lines at m/z = 78 and m/z = 80.

    Notice that the peak heights are in the ratio of 3 : 1. That reflects the fact that chlorine contains 3 times as much of the 35Cl isotope as the 37Cl one. That means that there will be 3 times more molecules containing the lighter isotope than the heavier one.

    So . . . if you look at the molecular ion region, and find two peaks separated by 2 m/z units and with a ratio of 3 : 1 in the peak heights, that tells you that the molecule contains 1 chlorine atom.

    You might also have noticed the same pattern at m/z = 63 and m/z = 65 in the mass spectrum above. That pattern is due to fragment ions also containing one chlorine atom - which could either be 35Cl or 37Cl. The fragmentation that produced those ions was:


    Two chlorine atoms in a compound


    The lines in the molecular ion region (at m/z values of 98, 100 ands 102) arise because of the various combinations of chlorine isotopes that are possible. The carbons and hydrogens add up to 28 - so the various possible molecular ions could be:

    28 + 35 + 35 = 98

    28 + 35 + 37 = 100

    28 + 37 + 37 = 102

    If you have the necessary math, you could show that the chances of these arrangements occurring are in the ratio of 9:6:1 - and this is the ratio of the peak heights. If you don't know the right bit of math, just learn this ratio! So . . . if you have 3 lines in the molecular ion region (M+, M+2 and M+4) with gaps of 2 m/z units between them, and with peak heights in the ratio of 9:6:1, the compound contains 2 chlorine atoms.

    Compounds containing bromine atoms

    Bromine has two isotopes, 79Br and 81Br in an approximately 1:1 ratio (50.5 : 49.5 if you want to be fussy!). That means that a compound containing 1 bromine atom will have two peaks in the molecular ion region, depending on which bromine isotope the molecular ion contains. Unlike compounds containing chlorine, though, the two peaks will be very similar in height.


    The carbons and hydrogens add up to 29. The M+ and M+2 peaks are therefore at m/z values given by:

    29 + 79 = 108

    29 + 81 = 110

    Hence, if two lines in the molecular ion region are observed with a gap of 2 m/z units between them and with almost equal heights, this suggests the presence of a bromine atom in the molecule.

    Contributors and Attributions

    This page titled 16.9: Organic Compounds Containing Halogen Atoms is shared under a CC BY-NC 4.0 license and was authored, remixed, and/or curated by Jim Clark.

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