Visualising the invisible - The chemistry of almost everything (19/31)

Take one clear solution and add to it another clear solution.
And what happens?
Apparently not a lot.
A lot of chemistry is like this, invisible, but there are reactions that are not.
Take this one, for instance.
When we mix these two clear solutions, something quite spectacular happens.
And what we're setting up here is an oscillating reaction.
By manipulating the ingredients and the concentrations,
we can get this solution going from clear to opaque, back to clear again,
over and over again.
This is a highly visible reaction that's used in lecture demonstrations
to illustrate the excitement of chemistry.
But we have to go beyond that.
And chemistry's the study of processes
that take place at a completely different level,
At the atomic or molecular level.
How do we get a feel for this invisible world?
The starting point, a shed in Loughborough.
John Leaston makes models.
Not aeroplanes or trains but representations of atoms
and the bonds between them.
He teaches children the idea of how molecules are made up.
Children wouldn't be interested in something they can't see,
unless you can give them something tangible,
like a cube of wood with holes in, which is what my models are.
Put the chlorine one on there.
They already have a grasp of what some fairly complex molecules look like.
What they've got is a model of the molecular world.
It isn't real, these blocks and sticks aren't how
atoms and molecules look in reality.
But the atoms make the right number of bonds with other atoms or groups.
Carbon atoms make four bonds, oxygen too, and hydrogen one.
The model fits the first rule of any attempt to explain real life.
Make it as simple as you can get away with.
That rule applies all the way up the chemical scale.
Put two chemists together and, sooner or later,
they'll start drawing this sort of stuff.
Another model which shows the shape of molecules.
The dotted lines show that the group at the end is pointing down into the paper.
It's a language,
an attempt on paper to say that chemistry happens in three dimensions.
And it's doing the same job as the children's blocks.
As is this. Toys for chemists?
No, an indication of the significance of the shape of molecules,
especially when we want to use them in the body.
A colourless liquid added to another colourless liquid.
We had to get back to them sooner or later.
We're in the laboratory of a commercial drug company which is
trying to solve a medical problem.
AIDS.
And they use their own models to attack the virus responsible for the disease.
This is the protein we're interested in.
It's a protein from the AIDS virus and it carries out a vital function
in making really important parts of the virus.
If we can actually stop it carrying out that function,
then we should be able to stop the virus in its tracks.
The chemical structures that we're dealing with are real.
They're three-dimensional solid objects, just as you and I are three-dimensional,
they're just much, much smaller than we are.
When we make our models, we see this three-dimensional nature to them.
What this tool really helps me, as a chemist, do,
is actually get a feel for the shape.
It's certainly a great help to the chemists when they come in and actually
see their structures displayed in three dimensions.
So, a lot of the time, I'll use it as a guide.
It'll help me along the way, it'll give me an indication of
the sorts of molecules I might want to try and make.
So, what are they up to? What compound are they making here?
The hole in the middle you can see here is actually the active site
and that's the bit of the protein which carries out all the interesting chemistry.
That's the bit of the protein which actually carries out the function
that we want to stop.
If we can make a compound that fits into that active site,
locks up that space completely, it'll just stay there.
And there's no chance then of that protein carrying out the normal function.
Nothing else can get into that space, it's completely blocked
and it will stay blocked,
and that's the end of the story as far as that protein's concerned.
All the manipulations, all the cookery in the laboratory,
can be seen in terms of a three-dimensional object.
I hope you can see from looking at this one, just how close that fit is.
Every little bit of the protein which could be filled up
is actually filled up with this inhibitor that we've designed in our chemistry labs.
We can compare the different sizes and shapes of these things
at a very concrete level, and a way that our brains are good at understanding.
The tightness of the fit gives a good indication of how potent it's going to be
as an inhibitor of this protein.
How well it's going to stop that protein from carrying out its normal function.
So, if they've designed something that works,
why aren't they world headline news?
We've come a long way already and the compound is very good.
However, there's still quite a long way to go.
We've got to work out what the compound's going to do when
we actually give it to human beings.
And there's a lot of things that can go wrong.
The compound might be toxic, it might not be very selective.
But also, when we actually give it to people,
it might not last very long inside the body.
So, there's a lot of other tests we have to do on the compound to really find out
whether this will actually be a compound we'd actually like to take to Man
and really find out whether it'll actually stop the AIDS disease.
Filling out all the space that the protein occupies shows just how good a fit
their candidate drug is,
and confirms the worth of the model in getting a picture of the invisible.
A lesson which holds at all levels.
They're little round things.
So, everything in the world is made of the tiny round things,
much too small to see, even with a microscope.
The models that we make are good approximations of reality
but they're not reality.
The model's only a model, and it will be wrong, in certain cases.
We don't believe our models, we use them because they're useful,
and as soon as they stop becoming useful we discard them
and build a different model which better serves our purpose.
It's a very practical, pragmatic tool.