Chemistry at the Synchrotron

This month, we celebrate the international year of chemistry by exploring the wide range of chemical discoveries and research taking place at Diamond. We investigate the role of...
05 December 2011
Presented by Meera Senthilingam


This month, we celebrate the international year of chemistry by exploring the wide range of chemical discoveries and research taking place at Diamond. We investigate the role of chemistry in pitting erosion, photovoltaics and nanowires as well as reveal how Diamond has been used to unearth a new source of mercury poisoning... plus all the latest news and event from diamond including a wake up call revealing the benefits of caffeine!

In this episode

01:35 - Chemistry at the Synchrotron

Designer molecules, pitting corrosion and solar cells...

Chemistry at the Synchrotron
with Trevor Rayment, Diamond Light Source

Meera –One place the path of chemistry is being paved is the Diamond Synchrotron, where everything from designer molecules, pitting corrosion and solar cells are being investigated. Diamonds Director of Physical Sciences, Trevor Rayment, explains the importance of this versatile subject...

Trevor – As a chemist, my passion and my background over many years, you won’t be surprised if I say that I think it’s the central science. It’s the science that so many other topics interface to and without which they wouldn’t succeed. So I think of it spanning into physics where high temperature superconductors came out of a chemistry background, solid state chemistry. I think of biology, chemists are the people who actually make the molecule that go to form drugs. Oh there are all sorts of areas such as catalysis, the clean cars, and new sources of energy, in all of those cases, a knowledge of chemistry is vital and in fact, chemistry makes all of these things possible. So perhaps you can see that I’m biased, but actually it’s a great subject and it’s central to so many other subjects.

Meera – And your own research within all if this is the use of chemistry and its role towards the field of materials science?

Trevor – Yes, I’ve been working on methods for many years that look at materials under their real operating conditions, looking at their surface chemistry and what I’m doing at the moment is working with a close colleague in Birmingham, Alison Davenport, to use those skills to look at corroding layers. To look at pitting corrosion, where little black dots in stainless steel corrode, it’s quite an important form of corrosion. Looking at the chemistry of those corroding pits.

Meera – And what have you been able to find out about them so far and is it the aim to then prevent this occurring?

Trevor – What we’ve learned is that the chemistry at the bottom of these corroding pits is important and for the first time we’ve identified the compounds, chemical compounds, that are found at the bottom of a corroding pit and now what we’ve discovered, or it’s Alison’s group that have really discovered, is how that chemistry influences the rate of corrosion. Often it is very difficult to prevent corrosion and so what you really want to understand is ‘how long will it be before it is really important and that is where the work is really progressing; taking the insights that we get from chemistry to predict the lifetime of a device. The lifetime, for example, of a canister that might store radioactive waste. The data that we’re providing, Alison’s group are providing, is allowing us to have really good models of how they might corrode over a period of a decade, 20 years, 10 thousand years.

Meera – Now you did mention that chemistry stems into a variety of fields such as biochemistry and physics as well, so what perhaps is some of the more current research taking place here at Diamond that stems into these areas?

Trevor – I think I’d like to point out 2 areas; one is the general field of energy. There is, as everyone knows, a real pressing need to reduce the amount of energy we use and reduce the impact of our industrial processes on the environment that we live in. So if we think about energy itself, then we might think about hydrogen storage. There has been a great deal of work over many, many years to improve methods for storing hydrogen and one of the favoured topics at the moment, one of the favoured areas, is the so-called metal organic frameworks. Central to all of this is designing frameworks of molecules that will absorb hydrogen and it turns out that the synchrotron is the ideal place to determine the structure of these complex materials. On the other hand there’s a lot of interest in designing solar cells. We’re all familiar with solar cells on roofs, they’re made of silicon and it’s very good, but silicon is an expensive material and it using quite a lot of energy to process it and the thought has been ‘can we make lighter weight, cheaper, solar cells made of polymers, plastics?’ and what matters there is knowing the structure and the behaviour of those layers, which are very thin, studying that and determining that and synchrotrons are ideal for that.

Meera – Now that work is done by David Lidzey who we’ve had on the podcast in the past and I think an interesting thing with that research is that although the efficiency may not be as great as the photovoltaics, the fact that they’re cheaper and more flexible and perhaps have a wider array of uses means that they’re quite important.

Trevor – If you’re trying to create new energy sources, then ultimately you have to compete with other sources on economic terms and into that equation come lots of things like the original cost, the efficiency, ease of installation, so it’s really quite complicated. And into an environment like that, having control of the chemistry is really important.

Meera – And so you’ve touched on these areas that chemistry stems into but what about, I guess, more fundamental chemistry, that’s looked into here?

Trevor – Another area that stems out of the control that chemists have over the shape of molecules is the notion that if you take a small molecule that is simple to make, how can you use that? Well one way of doing it which is very attractive is simply to take that small molecule, as like a Lego brick, and make it sufficiently clever that it’s got bumps and holes in it, so that those bricks will automatically assemble if you put them together. That notion of building big molecules from small molecules by using specially designed locks and keys is in fact the area of supramolecular chemistry.

Meera – That was Trevor Rayment, Director of Physical Sciences at Diamond Light Source.


07:54 - Supramolecular Chemistry

Large molecules, with interesting properties...

Supramolecular Chemistry
with Harry Anderson, University of Oxford

Meera – An exciting area emerging from research at Diamond is the synthesis of new, specialist molecules, known as supramolecular chemistry and the scientist pioneering this field is Harry Anderson from the University of Oxford.

Harry – I’m interested in organic molecules with strongly coupled electrons and controlling their properties often using non-covalent, weak, reversible interactions.

Meera – And what kinds of molecules are these?

Harry – Well they tend to be coloured compounds, a bit like dyes, a lot of the molecules we work with are made from porphyrins, which are naturally occurring pigments. But the ones we work with are not naturally occurring, I mean we make them ourselves from scratch but they’re related to the compounds that make blood red and grass green.

Meera – So are you essentially building molecules and then working with them from there?

Harry – Yes, we do synthesis from very simple starting components and we make compounds and design the compounds. So we are making compounds that have never existed anywhere ever before and so we’re interested in learning about their properties and relating the properties to the molecular structure.

Meera – The actual molecules you’re making are quite big, so how do you actually set about constructing these from scratch?

Harry – It’s a classical, organic synthesis except we also use templates quite a lot. So a template is a molecule around which you can build another molecule which determines the shape of the components in the right places as you link them together and then you can remove the template afterwards. So we’ve developed new ways of using templates to make bigger molecules.

Meera – And is it then hoped that they can have some new applications as well?

Harry – Yeah, of course. So the sort of molecules we work with have strongly coupled electrons which means they are often semiconductors. Organic semiconductors have one important area of application in devices like, well, display devices, electroluminescent displays, but also their interaction with light. They are often fluorescent and have unusual ways of interacting with light that can be used in optical switching devices. And some of the materials which we work with generate singlet oxygen which can be useful in medical applications.

Meera – and could you give an example of a particular molecule that you’ve worked on recently? So how you’d set about making it, why you wanted to make it and maybe some of the uses that it could now have?

Harry – One of the sorts of molecules that we’re excited about are molecular wires that are in rings rather than being straight. So we’ve worked on, what we call, molecular wires which are straight molecules down which you can transfer electrons, but recently we’ve realised that it’s possible to make rings of these molecules. So part of the challenge is just to make a molecular wire into a ring and then look at the charge mobility around the ring but for this particular class of molecules, then it’s not that easy to identify applications here, but we think that it may have unusual properties, maybe magnetic properties, than can get them to behave like little loops of magnetic wire. So we’re just investigating them to see how they behave.

Meera – What are the applications of the first set of molecular wires that were created, the linear ones?

Harry – Yes, potentially in molecular electronics, that means molecular scale electronics, transistors or electronic devices on the molecular scale, the ultimate in miniaturisation as integration circuits get smaller and smaller. So a lot of people are working in that area but it’s still a very long way from being useful. On the other hand in devices made on a larger scale, using larger amounts of material, like solar cells and maybe also organic transistors, it’s useful to have materials which can transfer charge efficiently. The molecular wires might be components in a material, perhaps in a solar cell.

Meera – So would the circular forms have different applications? So you’ve mentioned that they could perhaps alter magnetic fields and so on. So changing the shape of them could give them different properties and other uses?

Harry – Yes, just like a bit of wire, if it’s in a solenoid shape it behaves quite differently to if it’s in a straight shape. That’s one of the amazing things about molecules that just changing the shape, thinking about the shape, often relates to the properties.

Meera – And how do you use Diamond in all of this? How do you use synchrotron radiation to perhaps aid this process?

Harry - For structurally characterising the compounds that we make, proving that they are actually the compounds which we think they are, and for getting information on the shapes. So there are two techniques that we use at Diamond; small angle x-ray scattering of solutions, is very useful for getting low resolution information on the shapes of the molecules. It hasn’t been used much before for synthetic molecules, it has been used a lot for proteins, and it’s useful because you don’t have to grow crystals, you can take a compound and take a dilute solution and just from the small angle x-ray scattering you can get information on the 3-dimensional shape of the molecule. And the other thing that we use at Diamond is x-ray crystallography, and it gives much higher resolution information than the solution phase scattering.

Meera – Is there a particular molecule that has perhaps been your most successful to date in terms of how far you’ve managed to go with it?

Harry – Well, I suppose we’ve worked most on porphyrin-based molecular wires. Perhaps they’ve been most successful because they’re so versatile. That a similar group of molecules can have potential applications in medicine and photodynamic therapy and also in molecular electronics and there are lots of other potential applications too, they have such a rich range of properties.

Meera - Harry Anderson, Professor of Chemistry from the University of Oxford.

14:26 - Diamond News Update

The latest news and research from Diamond...

Diamond News Update
with Sarah Boundy, Diamond Lightsource Communications Team

Meera - Let’s join Sarah Boundy from Diamond’s Communication Team for a round of up of the latest news and events from the synchrotron, starting with a good reason to drink that cup of coffee in the morning...

Sarah – Yes, so it seems that coffee could offer a key ingredient for new treatments for Parkinson’s disease and one of our Industrial Users has used our micro-focus macromolecular crystallography beamline – I24 – to solve the structure of a protein that’s involved in Parkinson’s disease and other neurological disorders. The team was from Heptares Therapeutics and they were looking at the adenosine A2A receptor which is responsible for regulating the effects of neurotransmitters in the brain, in cardiovascular and immune systems, and they were also looking at how xanthine based drugs, such as caffeine, bind to their target.

Meera - And so what effects did they see, how does it bind?

Sarah – Well although it was known that caffeine inhibits the action of the adenosine, the exact molecular mechanism involved was not fully understood until now. So the structural information that Heptares got from I24 has helped to understand what is happening at the molecular level when the drug binds to its target and blocks the receptors response. So this information is enabling them to develop a highly optimised, next generation drug candidates for Parkinson’s disease and other neurological disorders.

Meera – Staying on the field of structural biology, other research taking place here at Diamond was looking into another disease and that’s heart disease.

Sarah – Yep, so scientists from Imperial College London and Diamond worked at the membrane protein laboratory at Diamond and their research was recently reported in Nature. They revealed the structure of a cholesterol-lowering drug target. Their findings could hopefully lead to much more effective drugs to tackle high cholesterol levels, which is a big cause of heart disease.

Meera – and what is this target and how could it make a difference?

Sarah – Well for the first time they determined the structure of bacterial homolog of the apical sodium-dependent bile acid transporter protein, or ASBT for short, and ASBT is a target for high cholesterolemia drugs because it can affect the level of cholesterol in the blood. So there are currently a number of existing ASBT inhibitors effective in animal models, and they were developed without structural knowledge of the protein. Now that they know the shape and the size of the drug binding site within the bacterial model of the protein, it should be possible to work on the design of improved drugs which are much more targeted and which will fit much better.

Meera – So two very important diseases of today, currently being targeted here?

Sarah – Yeah, the life sciences makes up about 40% of Diamond’s research work so we’re working on a lot of important diseases.

Meera – And staying with Structural Biology still, you’ve quite a notable scientist in this field visit Diamond recently?

Sarah – That’s right, at our annual User Meeting, the keynote address was given by Professor Venki Ramakrishnan, who is the joint winner of the 2009 Nobel prize in Chemistry. He spoke about his work on the structure of the ribosome and they way discoveries in macromolecular crystallography have accelerated over the past decade thanks to more powerful beamlines and better detectors and increased automation. So the User Meeting saw about 200 scientists from across the UK gather at Diamond to discuss the latest developments in synchrotron science. It was a really successful meeting and we hope it will lead to much more exciting developments and collaborations between our users.

Meera – So that’s a benefit for the users, but you’ve also done a lot lately to benefit the public in terms of the multimedia content that you’ve got online?

Sarah – Yes, so Diamond News is hot of the press. The latest issue includes articles on research work into protect herbarium staff from mercury contaminated specimens, we’ll hear about that from John Fellows from the University of Manchester later on. Also, looking at the role of gold nanoparticles in cancer treatment and there’s also a feature on polarised light which will help to explain more about our nanoscience beamline I06 and much more. Copies are available from our website.

Meera – In addition to this, there’s also visual content, so videos.

Sarah – That’s right, I mentioned them last time. We’ve now got a whole host of video case studies available and you can find them on our YouTube channel and they cover all kinds of things that Diamond is involved in such a structural biology, Industry innovation and impact and also environmental and health research, so this gives the viewer a great insight into Diamond, but if they actually want to come here and see it in the flesh, our next Inside Diamond public open day is going to be the 14th January.

Meera – Thanks Sarah. Sarah Boundy from Diamond’s Communications Team

Plastic - a polymer

19:25 - Synchrotrons for Structural Chemistry

Structural chemistry and its applications in our daily lives...

Synchrotrons for Structural Chemistry
with Tony Ryan, University of Sheffield

Tony – So I study the structure of polymers, plastics and colloid suspensions. So one example might be the structure of molecules that make up a shampoo bottle and also the structure of the molecules that make up the shampoo.

Meera – and how do you set about looking into this?

Tony – Well we do various things in the labs, we synthesise special molecules, we synthesise molecules that we can label so we know where they are and then we use the synchrotron as a source of high-intensity x-ray beams that allows us either to penetrate deep into a sample, or to look at a sample on its surface as it is doing its stuff and we can work out where the atoms are and how the whole molecules are organised.

Meera – And so what’s your real aim here, so what are you actually trying to find out about the molecules?

Tony – So, if we take the example of a shampoo bottle, then we are wanting to know when the material was processed, how the stretching of the molecules affected the way they crystallised. So when you make a bottle, you take a liquid and essentially you blow a bubble in the liquid to a special shape, that’s the shape of the bottle, and the stretching and the cooling causes the polymer molecules to organise themselves so that they crystallise and we study the stretching and the cooling and the crystallisation by following what the molecules do, in real time, by x-ray scattering.

Meera – and what have been, perhaps, some of your key findings having monitored the molecules in this way?

Tony – Well we’ve just had a paper published that compares the crystallisation of synthetic polymers like polyethylene, with the crystallisation of silk, from a silk worm. By using the synchrotron and by using other techniques in the lab at home, we’ve been able to estimate the energy needed to do the processing and we find out that the silk worm uses about 10% of the energy that we use to process polyethylene to make a fibre. So silk worms are much better a making fibres than people.

Meera – So is the aim then to really find out a bit more about how the silk worm does this to reduce our energy needs, or usages?

Tony – So what we can do from what we’ve learned about how silk worms go about processing silk, we’ve learned that it’s a different mechanism to the mechanism that’s used in making fibres of synthetic polymers. So what we can do is look to mimic the silk worms’ method in engineering materials. What the synchrotron has allowed us to do is compare the energetic of the 2 processes; learn that one process is much less energy intensive than the other and now we understand both how and why it’s less energy intensive to try and replicate that methodology in synthetic materials. So it actually means going back to the molecular drawing board and doing synthetic chemistry again.

Meera – Could you perhaps give a bit of insight into an even wider range of areas of chemistry that the synchrotron can be used for and that benefits other scientists?

Tony – So my colleagues in the chemistry field use the synchrotron for many, many reasons. So they do spectroscopy that they can’t do anywhere else to see what the local environment of individual atoms are, how catalysts work, like the catalytic converter in your car, other colleagues use it to study the crystallisation of drugs. So you can separate polymorphs, different forms of drugs because drugs crystallise in different ways and if you have the wrong sort of crystals in a tablet, they don’t work. But they can even work out how proteins interact with each other, so how proteins interact with drugs using a different set of scattering techniques called macromolecular crystallography. So there’s a whole variety of different techniques, imaging techniques, spectroscopy techniques that chemists use to study many, many different aspects of science. Whether it be; how rain clouds form or how drugs are taken into the marketplace.

Meera – And I guess with the opening of the new beamlines, which you must know about as well being on the Board of Directors and so on, this just must increase as well as each beamline opens as well?

Tony – The new beamline proposals open new areas of science, so for example, parts of what we do in terms of molecular engineering have been transformed by the availability of microbeams. So you can look in very fine detail in large parts. You only need very small crystals to be able to solve the structure. So all the time the techniques ands the technology at the synchrotron are pushing the envelope of what we can do and that generates new scientific opportunities with it.

Meera – What will you be looking into next then? What will be your next use for the synchrotron for your own work?

Tony – Well I’m really interested in how we use catalysts to clean up the environment so I’ve been working with and artist on making catalytic clothes and so what we want to do is to stick tiny catalyst particles to peoples clothes so they can walk around and take out environmental pollution - to use people and their clothing as catalyst supports. But to do that we need to understand how the catalyst particles stick to fibres and so my next project at the synchrotron will be to understand this process of depositing nanoparticles on to fibres. And we’ll use both imaging and scattering techniques to do that.

Meera – That’s a really interesting idea and so if you can just get a certain percentage of the population to wear that, that could make quite a big difference.

Tony – Yes, it would actually have to be quite a large proportion of the population. Each person could take out about 3 grams of nitric oxide a day, which doesn’t sound like very much but once you have a million people doing it then they take out 3 tonnes of pollution a day and once you start to get those sorts of numbers of people involved then you can have a significant impact on the urban environment.

Meera – So how can people get involved with this and find out more?

Tony – So there’s a great website called and there’s been lots of social media activity around this. At some point we’re going to be doing a pop-up laundry and we may even run a pop-up laundry at Diamond.

Meera – Tony Ryan from the University of Sheffield.

Element mercury (Hg), liquid form.

26:18 - Mercury Poisoning from Museum Samples

Some museum samples could be harbouring volatile compounds of mercury...

Mercury Poisoning from Museum Samples
with John Fellowes, University of Manchester

Meera – It seems some museum samples could be harbouring volatile compounds of mercury. But no need to fear, as it is only the people handling the samples themselves that need to watch out. To help them, John Fellowes from the University of Manchester is on the case at the University’s Herbarium to stop these vapours in their tracks.

John – Mercury salts were widely used to preserve museum specimens against damage from bacteria, insects, fungi and so on and so forth, and you can tell by the state of the preservation that these mercury salts have worked, but over time, and what’s been noted, is the initial mercury solutions, you’re talking pretty concentrated mercury solutions, one recipe out there has it a 30g per litre of mercury chloride dissolved into methylated spirits, which were then either sprayed on or paint brushed on or the samples themselves were dipped into this solution and what’s been happening over time is that this mercury chloride has been converted into different forms of mercury, one of which is volatile mercury which is then being released from the samples.

Meera – so is the problem then that when the people go to work with these samples and open them up, they’re being exposed to these volatile levels of mercury?

John – Well, that was one of the things we were investigating, yeah. The first thing we had to test for was making sure there were no dangerous effects in the area. The samples themselves were located in the herbarium and the first thing we tested was the mercury content of the air in the herbarium and we found it was well below the guidelines. So we had 1.7 micrograms per cubic metre of mercury when the guidelines are up at over 25.

Meera – What were the concerns with this to mean you’re are analysing these samples to see the levels of mercury within?

John – The samples themselves may or may not have been contaminated with mercury because the problem is, is that over the course of several hundred years, ‘cause these collections date back hundreds of years, they have been homogenised and sort of rearranged and resorted and reset out, so they don’t know which samples have actually been treated. And the boxes that these samples are kept in are these little airtight containers or little cardboard boxes which are essentially air tight and what we were mostly concerned with was that this build-up of mercury within these boxes, if someone could open this case, then you would have this kind of waft of mercury, which overall across the entire area is not a significant concentration, but it’s that initial opening of the box that we wanted to look at.

Meera – So how have you set about doing that?

John – Ok, so the other aspect we were looking at is, part of my work as a biogeochemistry really is to analyse how efficient our biogenic selenium nanoparticles are, that’s selenium nanoparticles that which been precipitated by bacteria, and one thing that’s been published out in the literature is that selenium is very, very good at capturing this elemental mercury phase, so it was kind of a two-fold research in that one, we wanted to identify, quantify any mercury present within the samples, and secondly to find a way if we could test our selenium nanoparticles and how good they were at capturing this mercury.

Meera – How have you gone about doing that?

John – What we made is little filter membranes. Our selenium starts off as a suspension and you can filter them out onto these filter membranes which are these 0.22 micron filters, and then allow them to air dry and we placed them in some of the boxes where we knew samples had been contaminated with mercury and see if we could capture the mercury as it was coming off the samples.

Meera – So I guess essentially what, you would be making these membranes to soak up the mercury just prior to opening up samples? Or how would this process work if these are proven to be effective at soaking it up?

John – The samples themselves we would be leaving inside the boxes permanently, so hopefully it will decrease any chances of a build up of mercury within the boxes.

Meera – And so how have you been using Diamond to try and visualise this?

John – Diamond was crucial really because we needed to investigate the form of the mercury present which will help us to understand the fate of what happens to the mercury, but also, because the samples are so varied, some have been contaminated with mercury, some haven’t, some of the samples which have been contaminated are only contaminated in certain areas of the sample, so Diamond to start with, with the samples, was helping us to pinpoint where the mercury was and also tell us the kind of concentration we can expect and the form that it’s in. Secondly, it also helped us to characterise the phase the mercury takes once it’s been reacted with the selenium and ensure that it’s not about to come back off again.

Meera – And what were some of your key findings, how badly contaminated were the samples?

John – So within the herbarium there are numerous collections and the one we focussed on was the European Collection and once we’d identified a sample that had got the mercury, we needed to find out whereabouts it was. What we found is that the mercury itself tended to be as little crystalline mercury sulphide phases that happens which was Diamond helped us prove this. There was one particular sample which was really quite good and that was a collection of dust from one of the bottoms of these boxes and just to put this in context; the samples were stuck down onto A3 sheets, and then these A3 sheets were then piled one on top of the other within these cardboard boxes and what we found when we were looking through was, we’re trying to identify where this mercury is and none of the sheets really came very high on the scale of mercury. But when we analysed one of them we found the dust which had collected on the bottom of the box, so none was on the actual sheets it was in the dust at the bottom. When we analysed that we found quite a high mercury concentration which we picked out by XPF and then we sent off to Diamond for XAS. What we found on this is maybe a micron long particle contained on one of the dust particles, which was almost pure mercury sulphide. Once we analysed these samples in Diamond, they were able to scan across a sample set and pick out and say there’s a bright bit there, let’s go in and get our XAS spectrum from this little sample here.

Meera – Now that you’ve been able to see this spread and localisation of mercury within this variety of samples, what are you able to do with the information, what do these findings really mean?

John – So what we can do with this data now is help build up Health and Safety guidelines as to what people are to do with these samples. This will help to say what you want to do when you find one of these boxes is open the box and just leave for 5 minutes and then come back and go through the samples. Because it’s the elemental mercury phase, the volatile phase, which is the dangerous one, you want to watch out for. The mercury sulphide that’s going to be in those, not really too much concerned. We’d like to get to the stage where these selenium membrane filters are used within the boxes to help prevent this build up of mercury within the boxes, so that when someone comes along to look at one of these samples, they can lift off the lid and not have to worry about a waft of mercury coming out from the box.

Meera – So before these membranes are in use, mental note, leave the room when opening a museum sample, well, some of them anyway! That was John Fellowes from the University of Manchester.


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