Mass Spectrometry and Determining Organic Structures

Mass Spectrometry gives information about the molecular mass of a compound and can also give important
structural information if used with other spectroscopic techniques like IR and NMR.
When organic molecules are put into the mass spec electrons cause the molecule to ioni!e forming a molecular
ion. "nlike atoms though those whi!!ing electrons also cause the molecules to break down into smaller pieces.
#hese pieces can give us structural information about the molecule which can be very useful.
$ mass spectra for a molecule like pentane% &'(&')&')&')&'( might look like%
*rom the spectra you can figure out that the molecular mass is about +) g,mol since this is the largest
fragment formed. -#his isn.t always true. If the molecular ion is unstable than this could be /ust a
fragment.0
#he other peaks in the spectra are fragments.
Relative Mass of Common Fragments
#he relative molecular weight of common fragments -Mr120
3
are%
-Mr1450
3
which is methyl group -&'(0
o #he mass of one carbon and ( hydrogen atoms add up to 45 amu
o If two peaks differ by 45 units this is often an indication that the fragments only differ by a methyl
group
-Mr1)60
3
which is either &)'5 or &'7
o If you add up the mass of ) carbons and 5 hydrogens you get )6 or
o If you add up the mass of 4 carbon one 'ydrogen and one o8ygen you get )6
o If you have a peak at )6 you can.t know for sure if it.s &)'5 or &'7 unless you.ve also done an
Infrared spectra and identified the presence -or lack0 of a carbonyl group -&970
-Mr1(40
3
&'(7
-Mr1:50
3
&77'
*ragments that differ by only 4 or ) mass unit differ by a hydrogen atom or ).
Since we know the molecule is pentane which doesn.t have a carbonyl group the peak at )6 represents
a &)'5
3
fragment.
#he peak at 5+ differs from +) by 45 mass units so probably the fragment at 5+ has lost a methyl group
and is the fragment &'(&')&')&')
3
#he peak at :( we kind of have to infer;it has to have less than : carbons since the mass of : carbons
is :< mass units. If it.s ( carbons it must have + 'ydrogen atoms to add up to :( mass units.
#herefore the fragment is probably &'(&')&')
3
Relative
number of
Ions
4==
5=
m,!
-m 9 mass ! 9 charge0
:=
)5
(=
>
5=
)5
?=
)5
+=
)5
)= 4=
)6
:(
5+
+)
#he smaller peaks that are only 4 or ) different from the larger peaks are the same fragments that have
lost one or ) hydrogen atoms.
Distinguishing between two possible structures:
@et say you figured out that you have a pentanone molecule but you don.t know on which carbon the carbonyl
group is located. Aou can use the fragmentation patter from a mass spec to figure it out.
@et.s say that the spectra gave peaks at )6 5+ and <?
If the carbonyl was on the )
nd
carbon% &'(1&71&')&')&'(
&ommon fragments would be%
4. &'(&7 9 Mr1:(
). &'(&')&')&7 9 Mr1+4
If the carbonyl was on the (
rd
carbon% &'(&')1&71&')&'(
#he most common fragment would be%
4. &'(&')&'7 9 Mr15+
Since the peak at 5+ matches the peak e8pected for pentan1(1one this carbonyl must be on the third carbon.
What does the height of the pea tell you!
#he height of the peak tells you which fragment is the most stable.
#his is useful for determining the presence of branched structures. *or e8ample a tertiary molecular ion
would be more stable than a primary ion.