Great thinkers have often suggested that our entire universe
could be nothing more than an atom in another even more colossally gigantic
universe. Let’s imagine that’s true. In this other, larger universe there are
scientists who are investigating our smaller universe, which is just an atom in
their world.
Look around you and what can you see? I can see my notepad,
a television, the floor, a plate and a plant. But the giant scientist
investigating our universe can’t see any of those things. With his most
powerful microscope, he can just see a dot that represents our entire planet.
But he has this idea that there are some really interesting things on our
planet, and he needs to figure out a way to find out about these things, these things
that are too small to see even with his most powerful microscope.
In particular, this scientist is interested in vehicles. We
can readily distinguish the difference between small cars, big cars, lorries
and coaches. But this giant scientist can’t see them. So he invests a machine.
This machine has a laser beam that can zap things into pieces. Also, it has a
weighing scale that, astonishingly, can weigh things. (Strictly speaking, we
should say it’s a balance that measures the mass of objects.)
So the giant scientist has been saying to his giant
scientist friends that there are these tiny little things called vehicles and
he thinks they come in different types. His friends say: “Prove it!” as any
good scientist would. This is what he comes up with.
Using the laser, he blasts different vehicles to bits and
weighs the pieces. Doing this he learns some interesting things. He finds that
a certain kind of piece always has roughly the same mass, no matter which
vehicle you blast it off. He calls this piece a wheel. He finds another piece
which also has a similar mass no matter which vehicle it comes from. This piece
is a seat.
Using his data, he makes some interesting deductions. One
thing that he notices is that there are two kinds of four-wheeled vehicle. Once
he’s blasted all 4 wheels off each of these vehicles, he notices a big
difference – one is much, much heavier than the other. He also notices that if
he blasts the heavier one, about 50 seats come out of it, whereas only 4 seats
come out of the other one. He calls the smaller one a car and the bigger one a
coach. Another vehicle has 12 wheels that can be blasted. He calls this kind of
vehicle a lorry. And that’s how he proves to his friends that there are these
different kinds of vehicles on this teeny, tiny atom he’s been investigating,
which is actually our universe.
Back in our world we have a similar issue. How can we work
out the character of different molecules when they are too small to see?
Funnily enough, we can use a machine very much like the laser machine with the
weighing balance. It’s called a mass spectrometer.
The laser is actually an electron gun that can fire a beam
of electrons. The weighing scale is still a weighing scale (that actually isn’t
a weighing scale because it measures mass).
What this machine does is blast molecules to bits and then measures the mass of
the bits. It also counts how many of each different bit is produced.
Some language. First of all, rather than calling the pieces
of molecules “bits”, they get called fragments.
Secondly, the word used to describe the number of each fragment that gets
produced, is relative abundance.
What that means is how many there are of one kind of fragment compared to the
other kinds. If you had 5 lemons and 10 oranges, you could express the relative
abundance as follows: there are twice as many oranges as lemons. In fact, the
way you would express it on a mass spectrometry chart, would be that there were
100 oranges for every 50 lemons.
Figure
1: A mass spec machine
So,
what happens when you put your sample in the machine? First of all, keep in
mind the relationship between compounds and molecules. A compound is a type of
molecule. Water is the kind of molecule that has one oxygen atom bonded to two
hydrogen atoms. In a droplet of pure water, there are trillions and trillions
of molecules and they are all made according to that recipe. Back to the mass
spec machine, when we add our mystery sample that we want to identify, each
droplet will contain trillions and trillions of molecules of the compound we
want to identify. Figure 1 shows the machine. We add the sample and it passes
through the beam of electrons. What happens when you blast a molecule with a
beam of electrons is that it knocks an electron off each molecule. That’s a bit
odd when you think about it. It’s like drying something off by spraying it with
a hose. Never mind, science can be that way sometimes.
When
a molecule loses an electron, it becomes an ion and we call it the molecular
ion. Since it now has one more protons than electrons, it has a positive
charge. As it flies down the tube towards the sensor, it passes through a
magnetic field. The point of this is to deflect the ion towards the sensor. How
you work out the mass of the ion is by measuring the size of the magnetic force
necessary to deflect it so that it hits the sensor. Notice in figure 1 that
there are three dashed lines. If the magnetic field is not strong enough, the
fragment will hit the top of the tube, as shown by the yellow line, because it
doesn’t curve around enough. If the magnetic field is too strong, the fragment
will hit the bottom of the tube, as shown by the purple line. This is how the molecular ion peak is generated. It is
the peak on the right hand side of the mass spec reading and it tells you the relative molecular mass of the
compound. Figure 2 shows a reading for the compound 2-ethoxybutane,
while figure 3 shows a diagram of 2-ethoxybutane. The molecular ion peak is at
102, telling us that 2-ethoxybutane has a relative molecular mass of 102. For any students who are doing GCSE
additional science with AQA, this is all you need to know about the mass spec chart.
But if you are interested about what the rest of it means, read on.
Figure 2: A mass spec chart for the compound 2-ethoxybutane
Figure
3: 2-ethoxybutane
You may have noticed that the molecular ion peak is rather short, indicating a low relative abundance. That’s because not many of the molecular ions stay the same. Having had electrons knocked off them, the molecular ions feel a bit awkward and it causes them to sort of disintegrate into smaller pieces – the fragments. Each molecular ion tends to split into two fragments, one of which will have a positive charge, just like the molecular ion. By varying the strength of the magnetic field, the machine can measure the mass of each of the different charged fragments that are produced. This is very helpful for identifying the compound.
The relative molecular mass of a compound is very useful
information to have, but what if we compare two compounds with the same mass?
Figure 4 shows a mass spec reading for the compound hexanol and figure 5 shows
a diagram of the compound, which is an alcohol with 6 carbon atoms, just like
hexane is an alkane with 6 carbon
atoms. (Strictly speaking, this compound is hexan-2-ol, because the alcohol
group [-OH] is bonded to the second carbon atom in the chain.)The molecular ion
peak is at 102, showing us that hexanol has the same relative molecular mass as
2-ethoxybutane. There are other similarities, too. Both have peaks at 45, 57
and 87. But the other peaks are different. The first chart has peaks at 29 and
73, whereas the second chart has peaks at 27, 69 and 84.
Figure 4: A mass spec chart for the compound hexan-2-ol
Figure
5: hexan-2-ol
Let’s start by looking at one of the peaks that they have in
common – the one with a mass of 57. In both cases this is caused by a fragment
called butyl, which looks like this:
Figure 6 shows how each compound splits up to generate the
butyl fragment. As the molecular ion fragments, a bond breaks. The bond that
breaks in each compound is shown by the wiggly yellow lines. What this tells us
is that both of the compounds we are analysing contain a section formed from a
sequence of 4 carbon atoms bonded to the corresponding number of hydrogen
atoms. Now remember, we are looking at the mass spec readings with full knowledge
of the compounds they represent but normally, that is not what happens.
Normally, a scientist is looking at a mass spec reading in order to work out what compound they have. From the peaks at 57
in each diagram, the scientist can tell that both compounds contain butyl
groups.
Figure 6: How the two
compounds fragment to create butyl groups
Now let’s consider one of the peaks that the two compounds
don’t share. The chart for hexanol shows a peak for a fragment with a mass of
84. This corresponds to a fragment that is left over when a water molecule is
lost, which is shown in figure 7. What happens is that the –OH group is
separated from the molecular ion. On its way, it snatches a hydrogen atom from
the molecular ion to become a water molecule. The relative molecular mass of
water is 18 (two hydrogen atoms with masses of 1 each, plus one oxygen atom
with a mass of 16). If we subtract 18 from the overall mass of 102, we get 84,
which gives us the peak. Why doesn’t 2-ethoxybutane also lose a water molecule
in the same way? If you look at the diagram for 2-ethoxybutane, you will notice
that the oxygen atom is bonded to a carbon atom on either side. In order for
that oxygen atom to include itself in a water molecule, it would have to break
both its bonds to its neighbouring carbon atoms and snatch not just one but two
hydrogen atoms from somewhere else. Compare this with the oxygen atom in the
other compound, hexanol. It is already bonded to one hydrogen, so all it has to
do is break one bond and find one hydrogen, which is obviously much easier and
therefore much more likely to happen.
Figure 7: Hexanol fragments
to form a water molecule and another fragment
So what's the deal with relative abundance? Remember that
your droplet of pure sample contains trillions and trillions of molecules of
the same compound. It's not that you put in one molecule and it splits up into
two fragments. Instead, each molecule that breaks down has a few different
options of what they might do. Looking back at the charts of our compounds,
they both have peaks at 57 but they are different heights. What this means is
that molecules of 2-ethoxybutane, which has the higher peak, is much more
likely to break apart into the butyl fragment and whatever is left over than
hexanol is. So the mass spec chart shows you all of the different fragments that the compound turns into and the
relative abundance shows you how many of each of the different fragments are
produced.
Mass spec can be gone into in much greater detail but this
has already gone on for a long time. In the end, it comes down to this: compounds
generally give unique mass spec readings. The precise reasons for the position
and size of the different peaks are very complicated, but in combination they
can be viewed as a fingerprint. Also there are other ways of analysing substances
but mass spec is a common way for scientists to figure out what a mystery
substance might be.
