Mass spectrometry organic compounds
● If you run a mass spectrum of an organic compound, it is able to tell you
the Mr of the molecule, and what it is made up of
● Once the organic molecule is in the mass spectrometer, it is bombarded
with electrons form an electron gun in order to knock out an electron and
give the molecule a positive charge so that it can be detected by the
mass spectrometer, which will measure the mass to charge ratio
● The mass of the electron is negligible, so the mass to charge ratio given for the ion will
be the same as for the atom
★ On the mass spectrum graph for the organic molecule, there would be a peak at the M/Z
representing the Mr of the molecule (i.e for oxygen this would be at 18 as the Mr for
oxygen is 1+1+16= 18, and this is the furthest right peak)
● Don’t forget to put a ‘+’ after the name of the molecule on the graph, as everything
measured by the mass spectrometer must have a positive charge
● This furthest right peak on the graph is called the molecular ion peak
Fragmentation
● When doing fragmentation, always start with the molecular ion
(positively charged ion of the original molecule)
● When an organic molecule is in the mass spectrometer, it is
being bombarded with high energy electrons, which could
cause bonds to break
★ Mass spectrometers can only measure positively charged species, so in this example
only the positive methyl group would be detected
★ It is common to have an M/Z peak at 15 as many molecules contain methyl groups
★ So peaks other than the furthest right peak are a result of fragments breaking off
● Using these fragment peaks, we can build up a picture of what the molecule is made up
of
★ If we put structural isomers into a mass spectrometer, they would both
peak at the same point as they both have the same mass
★ We would distinguish between them by looking at their fragment peaks,
as different fragment peaks would be possible for each, though some
fragments would still be the same
● Mass spectrometers are linked to computers, so the computer would have a huge
database of spectra in its memory, and as the fragmentation is unique to each molecule,
the computer would rule the molecule through its database until it found a match
Infrared spectroscopy
● Infrared spectroscopy allows us to identify bonds and functional groups in organic
molecule
● Infrared radiation is a form of energy, and is part of electromagnetic spectrum at the low
frequency end
★ If you apply several slightly different frequency waves of infrared radiation to an organic
molecule, it will absorb some of the infrared radiation (the rest will pass on through),
causing the bonds in the molecule to vibrate
★ If the bonds are all the same type in the molecule, they will absorb the same amount of
energy
★ If we have something at the other end to detect the radiation, we can
measure the radiation that is absorbed by the molecule by looking at
what percentage of each frequency of energy get to the detector, and
working out what’s missing
● The units of measurement for infrared radiation is wave numbers (cm^-
1)
★ To graph what is detected by the detector, we would have the
wavenumber on the x axis, and the transmittance in percent on the y
axis
★ So as only a particular frequency of infrared radiation would be
absorbed, meaning that there will be about 100% transmittance for all other frequencies,
making there be a line constant line at about 100% (so at the top of
the graph) spanning across all frequencies, with a steep dip to show
where the energy isn’t getting through/is being absorbed
● If an organic molecule has multiple different kinds of bond, then each
kind of bond will absorb a different section of radiation
● This means there will be multiple dips on the graph to represent each bond
type
★ Don’t talk about C-H bonds when attempting to identify molecules from
these graphs as all organic molecules have them
★ Don’t talk about dips that can’t be identified on the data sheet
★ The OH absorption region tends to be quite wide
★ Dips may not be clean, they may combine so that one irregular dip my represent two
dips
● Anything reading below 1500 is the fingerprint region and is unique to that molecule, so
won’t tell you anything
● You get a section in your data sheet telling you which region is which
● Can’t identify which is which by elimination as certain dips have to be there to identify
the presence of correct functional groups (so say what it has and hasn’t got, and based
on that, what it has)
