Chemistry World Podcast - February 2009
00:12 -- Introduction
02:13 -- Life on Mars? Carbonates and methane
05:15 -- Chemists edge closer to recreating early life
08:12-- Jeff Long reveals the magic of MOFs
14:56 -- How to strengthen the taste of umami
17:28 -- Synthetic cannabis mimic found in herbal incenses
20:32 -- Philip Kraft discusses the quest for new odour molecules for perfumes
26:23 -- InChIs helps chemists search the web
30:06 -- Periwinkles programmed to produce potential drugs
32:46 -- The chemical conundrum - do you know what molecule gives the jasmine note to fine fragrances
(Promo)
Brought to you by the Royal Society of Chemistry, this is the Chemistry World Podcast.
(End Promo)
(00:12 -- Introduction)
Interviewer - Chris Smith
Hello! Welcome to February's edition of the Chemistry World with Richard Van Noorden and James Mitchell Crow, Nina Notman and Phil Broadwith. I'm Chris Smith. Coming up, Methane on Mars so does this mean that there is life there too.
Interviewee - Richard Van Noorden
Methane might be being produced by microbes, methanogens, that feed on hydrogen and carbon dioxide and spit out methane and in fact some of those exist on earth for example deep under sea where sunlight can't reach them and they have to rely on radioactivity to split apart water and feed on the hydrogen and spit out methane. So we know that can happen and that could be why the methane is coming out.
Interviewer - Chris Smith
So have NASA finally answered David Bowie's question, Richard Van Noorden has been watching the space for us and he'll be here shortly. Also there is a new kid on the chemical blog that's got scientists very excited.
Interviewee - Jeffrey Long
The beautiful thing about this chemistry is you can actually tailor the surfaces of these high-surface area materials such that they might have a selective affinity for certain types of molecules and so you might be able to selectively capture CO2 out of a flue and let the nitrogen and other components pass through the solvent.
Interviewer - Chris Smith
That's Jeffrey Long and he works on MOFs, metal organic frameworks, which could help scientists to selectively sieve out the bad guys from exhaust gases plus we'll be finding out why flower power could be said to make a comeback.
Interviewee - Phillip Broadwith
They take a root culture, just part of the root and grow it separate from the plant and not the whole plant and feed it within an unnatural version of its natural food. It then incorporates that into a much more complex molecule which we would find very difficult to synthesize in a land.
Interviewer - Chris Smith
Phil Broadwith who will be explaining how scientists are using periwinkle to make complex chemicals for them.
(Promo)
The Chemistry World podcast is brought to you by the Royal Society of Chemistry. Look us up online at chemistryworld dot org
(End Promo)
(02:13 -- Life on Mars? Carbonates and methane)
Interviewer - Chris Smith
One of the big unanswered questions must be, is there anybody out there. In other words does ET exist? Not surprisingly, scientists are focused this so far on our nearby cosmic neighbour Mars and that search took a dramatic step forward recently when scientists announced they found signs of methane emerging from hot spots on the planet's surface. Richard van Noorden has been taking a look at the story so far. Richard, tell us more.
Interviewee - Richard Van Noorden
Well this is pretty exciting Chris, but we are not yet at life on Mars. This is a team lead by Michael Mumma at NASA and he and his team have reported seeing three plumes of methane on Mars in three different areas. Now before you get all excited about what this means, methane has been seen before on Mars in 2003 and in 2004, but these observations are just much clearer and they really definitively confirm that there is methane on Mars and they show that it occurs in these hot spots, which is quite exciting.
Interviewer - Chris Smith
Why is it so important that is seeing methane and could that not just be a vestige of the planet's past history and secondly why the hot spots?
Interviewee - Richard Van Noorden
What is important that they are seeing methane because methane might be being produced by microbes, methanogens, that feed on hydrogen and carbon dioxide and spit out methane and in fact some of those exist on earth. For example deep under sea where sunlight can't reach them and they have to rely on radioactivity to split apart water and feed on the hydrogen and spit out methane. So we know that can happen and that could be why the methane is coming out. Now it may be geological, it may be that water and rocks perhaps all have been combining in a, some kind of, volcanic activity, methane is coming out there and it may be that the methane is bursting out clathrate trapped methane structures as a result of past activity a long time ago and we are just seeing that happening. So it could be any one of those three explanations, but obviously microbes are one of them and water is involved in two of them.
Interviewer - Chris Smith
But why not just be a vestige of the planet's past history that's why they are seeing this in the atmosphere. Could it not just have been hanging around for a very long time?
Interviewee - Richard Van Noorden
Well what Mumma has discovered is that while in 2003, there was a lot of methane just above the northern hemisphere in the summer, by 2006, there was a very low concentration of methane. So the methane is not constant. It comes in bursts. Now it actually takes sunlight and photochemical process some 300 to 350 years to breakdown methane. So it sounds like that methane is coming in seasonal bursts and that suggests that there is some kind of volcanic activity or some kind of microbe activity where perhaps it's churned out in the summer but less in the winter and that's why they think, well it's just not hanging around from ages ago. It may be that there happens a catch or clathrate dispersing and methane coming out, but they think it's going to be more seasonal than that.
Interviewer - Chris Smith
So I guess Richard, we just have to watch the space. Boo..boom.
(05:15 -- Chemists edge closer to recreating early life)
Interviewer - Chris Smith
So, James from life on Mars to the early earth, tell us about this.
Interviewee - James Mitchell Crow
Well Chris, this is potentially a finding that could give some answers to how life on earth might have started. A group at the Scripps Research Institute in California led by Gerald Joyce have been experimenting on this test tube based system that actually displays lot other properties that you would associate with life and so these molecules can self-replicate and they actually evolve as well. So it's a bit of survival of the fittest going on.
Interviewer - Chris Smith
What are the molecules are they playing with?
Interviewee - James Mitchell Crow
They are playing with pairs of RNA molecules. They pair up just like DNA does, sort of Watson and Crick base pairing and what these molecules do is obviously RNA encode information RNA can also act as a catalyst. So basically they have this pair of, let's call them a left and right and the left molecule catalyzes the synthesis of the right and then the right molecule catalyzes the synthesis of a new molecule of the left from just a pool of free nucleotides. The team have shown that if you basically give the system an endless supply of free nucleotides then these RNA pairs will go on self-replicating forever which is obviously one of the important things for life.
Interviewer - Chris Smith
And how did they make the discovery in the first place?
Interviewee - James Mitchell Crow
Well what they were doing was testing quite a longstanding theory, which is called the 'RNA world' theory which is the before DNA-based life forms emerged, there were RNA-based life forms which are a bit simpler and the theory goes that RNA could both carry information and also act as a catalyst. So when you think about current life forms it accesses both the DNA and also the enzymes that are protein-based catalysts.
Interviewer - Chris Smith
Because the same group had a discovery then last year, where they were showing that the same sorts of systems could evolve overtime and become better and better doing the sorts of processes that you mentioned. So I guess, they are going to place it into the same hands, doesn't?
Interviewee - James Mitchell Crow
Yes that's right. You can actually set up a system where you have got several pairs of RNA molecules and if you just set these going over a long enough period of time and give them plenty of free nucleotides to keep chewing on, these RNA molecules will actually form hybrids; so say you've got 12 pairs of RNA, then RNA left 7 will make RNA right 7, but there may be RNA right 7 or make an RNA 7-12 hybrid and eventually these hybrids come to dominate the population levels.
Interviewer - Chris Smith
So much survival of the fittest except it's the survival of the RNA fittest.
Interviewee - James Mitchell Crow
Exactly, that's right. These particular hybrids have some sort of chemical benefit within this system. They are obviously able to compete better for the free nucleotides than the original RNA molecules and that's why they come to dominate the system.
Interviewer - Chris Smith
An intelligently designed experiment to reveal the workings of evolution in front of your very eyes thank you James.
(08:12-- Jeff Long reveals the magic of MOFs)
Interviewer - Chris Smith
And now to another piece of intelligent design but this time involving metal organic frameworks or MOFs which scientists think might hold the key to storing hydrogen to power cars or sieving out the chemical nasties from exhaust gases. Jeff Long.
Interviewee - Jeffrey Long
So, these are not molecules as you'd ordinarily think about them because the bonds within these structures extend throughout the crystal from one side to another and so they are really three-dimensional network solids with chemical bonds extending throughout the network of the crystal.
Interviewer - Chris Smith
What are they made of?
Interviewee - Jeffrey Long
So, the ones we are interested in are in particular made of metal nodes that are connected through organic bridging ligands. So organic molecules connecting for example transitional metal elements.
Interviewer - Chris Smith
That's quite unusual chemistry because we are quite comfortable with the fact that you have a metal and you have all the metal atoms in this sea of electrons around them. You have no metals and crystalline solids and things. You have now married the two together. So how do you actually get a metal to unite within an organic molecule in this sort of structure?
Interviewee - Jeffrey Long
Lot of these transition metals you can put them in solution and then in solution they have a particular structure, where they might have six solvent molecules surrounding them and then you can use some organic molecule that's capable of linking two or more of those transition metals together and the reaction involves displacing the solvent molecules on the transition metal with this bridging organic ligand and the bridging propagates until you grow this three-dimensional network solid that forms at the bottom of the flask.
Interviewer - Chris Smith
And does it form a regular lattice, so that you end up with a very organized structure resembling a crystal to all other intents and purposes?
Interviewee - Jeffrey Long
You do get nice crystalline materials with periodic arrangement of the atoms.
Interviewer - Chris Smith
And how are you seeking to use these interesting molecules.
Interviewee - Jeffrey Long
In our research, we've been particularly interested in seeing if the materials can be used for hydrogen storage applications and those applications would be of relevance for example to the storage system in a hydrogen-powered car.
Interviewer - Chris Smith
How do you actually use the crystal to store the hydrogen though?
Interviewee - Jeffrey Long
The three-dimensional architecture of the network is such that it has pores within this structure and as formed initially, those pores contain solvent molecules, but it turns out that the architecture is so stable that you can apply a vacuum and with little bit of heating you can pull out all of the gas solvent molecules and so as a result you have this porous network structure which is then going to give you a very high surface area for the material.
Interviewer - Chris Smith
Hydrogen is notoriously small and therefore notoriously hard to hang onto. How do you keep the hydrogen in the pool?
Interviewee - Jeffrey Long
So the whole trick about this is creating a material that has strong affinity for hydrogen.
Interviewer - Chris Smith
On what sorts of ways they are doing that?
Interviewee - Jeffrey Long
Most of these metal organic framework compounds don't have metal sides that are open and available to except gas molecules binding at the site whereas we are trying to create ones that do have these open metal sites and those are sites where hydrogen can stick quite strongly.
Interviewer - Chris Smith
Why do we need a material like this to do that? Why don't we just have a big cylinder of gaseous hydrogen in the back of the car that can power the engine anyway?
Interviewee - Jeffrey Long
The existing hydrogen cars for the most part do use compressed hydrogen gas. There is real problems with doing this however, if you want to be able to drive your car as we do a gasoline powered car today, then you really need to store about 5 kilograms of hydrogen on board and so to do that, you know with pressurized hydrogen gas in a cylinder, requires really a very large volume or you are going to an extremely high pressure, which becomes a safety concern and also pressurizing the hydrogen to that extent uses a lot of the energy content of the hydrogen as a fuel.
Interviewer - Chris Smith
But how do these molecules therefore solve that problem. How do they pack in more hydrogen at lower pressure than a cylinder can?
Interviewee - Jeffrey Long
Within a cylinder, you're really relying on the interactions between hydrogen molecules themselves to form a dense form of the solid or gas or liquid hydrogen. In our materials, what we are relying on is the interaction between the hydrogen molecules and the surface of our solid and that interaction can be much stronger such that you can organize the hydrogen molecules more closely together.
Interviewer - Chris Smith
One presumes that the scope of this goes beyond just hydrogen though. Could you use this as a sort of selective molecular filter on thinking of things like flue gases? If you had a system like this, plumbed into the exhaust pipe of a car, could you scavenge just the bad gases and hang onto those for later elusion dumping or chemical modification and allow through the things that you don't mind so much.
Interviewee - Jeffrey Long
Absolutely. The beautiful thing about this chemistry is you can actually tailor the surfaces of these high surface area materials, such that they might have a selective affinity for certain types of molecules and so you might for example be able to selectively capture CO2 out of the flue stream and let the nitrogen and other components pass through the solid.
Interviewer - Chris Smith
How far are we away from being able to do that? Is this something which we're going to be seeing tangibly in the next few years or are we talking at least a decade away to use this?
Interviewee - Jeffrey Long
That's hard to say. You know, there are lot of potential applications for gas separations, where you might use these and some of these have been demonstrated in principle, but usually they are hard engineering targets that need to be met, so that these are competitive with alternative strategies, but I would except in the next five years or so that we might see some cases where metal organic frameworks really make sense for a broad application.
Interviewer - Chris Smith
Chemist, Jeff Long, on the exciting potential of MOFs, metal organic frameworks. He is based at the University of California at Berkeley.
Music
Interviewer - Chris Smith
This is the Royal Society of Chemistry's Chemistry World podcast with me Chris Smith. In just a moment, how scientists make smells. We'll be joining perfumer Philip Kraft to find out how he comes up with the clever combinations of molecules that make a person smell irresistible.
(14:56 -- How to strengthen the taste of umami)
Interviewer - Chris Smith
But first to how to make things taste irresistible too because researchers have discovered how to intensify the meaty umami flavour, which is brought to food by the presence of the amino acid glutamate and apparently the receptor looks a bit like a Venus flytrap, Nina.
Interviewee - Nina Notman
So Xiaodong Li, who is based in California and works for flavour enhancing company called Senomyx have been looking at Umami, which is one of our five flavours that we taste and we've trying to understand how the binding site works in order to help them make better flavours in the future and the key thing they've been looking at is how to strengthen the umami flavour. So they look at how glutamate, which is in all of our savoury foods bind to the umami and they've also been looking at synergic effect which has additional molecules like the ribonucleotides also binding the same receptor and enhance the binding and therefore the flavour of the umami.
Interviewer - Chris Smith
I get it. So in other words, what you've got going on is that you have a second molecule coming in, alongside the umami which is a natural ligand for the receptor and when the second molecule is present, you get a stronger signal for the same amount of umami than you would do otherwise.
Interviewee - Nina Notman
Yes, and they've been trying to understand why this is to help them further improve things in the future and get new flavours.
Interviewer - Chris Smith
What have hey found?
Interviewee - Nina Notman
So they found that another receptor is a Venus fly-trap type receptor. They've seen that the L-glutamate bind right into the middle of the receptor and the ribonucleotide they've been looking at bind right in the front and they two together make the receptor closes much more tightly which give them the effect that they were looking at.
Interviewer - Chris Smith
So when we are going to see more flavours in curries then?
Interviewee - Nina Notman
They've not told us that. They've also found a second reason for doing this. So the receptor which is used for the umami is a very common receptor and it may be of interest to drug companies and they're thinking there are a number of drugs which bind to very similar receptor and they think the information that they've managed to find may be useful for the drug manufacturing companies.
Interviewer - Chris Smith
So it's sort of a class effect. There are many potential therapeutics that could exploit the same mechanism to the same end and therefore knowing how this, sort of, steric effect effectively works, could be very useful in that respect.
Interviewee - Nina Notman
The scientists certainly hope so. They've also been using it to look at the sweet flavour as well, not in just the savoury.
Interviewer - Chris Smith
Which is nice; some people say sweet enough already, but how with that work.
Interviewee - Nina Notman
They haven't told us so far, I think they're going to be publishing it very soon.
Interviewer - Chris Smith
Terrific, thank you Nina.
(17:28 -- Synthetic cannabis mimic found in herbal incenses)
Interviewer - Chris Smith
And James talking about making things taste better like a bit of spice too.
Interviewee - James Mitchell Crow
Well I don't know if that tastes better, but this might make you hungry Chris. It might give you the munches. So governments around Europe are rising to try and ban this. It is being sold as an herbal mixture known as spice and it turns out that it contains low levels of molecule that actually has exactly the same effects on the body as THC tetrahydrocannabinol.
Interviewer - Chris Smith
Where does this molecule come from?
Interviewee - James Mitchell Crow
Well it's a synthetic molecule so it is added to this supposedly natural spice mix artificially and where it actually came out of was a lab at Clemson University in South Carolina in the mid '90s. A group led by John. W. Huffman and the compound is actually called JWH-018 after his initials. What this group were actually doing was looking for molecules to study structure activity relationships so looking at receptors basically and how molecules activate those receptors and they are looking at the cannabinoid receptors and they found this particular structure was very effective activator of this receptor. Even those actually are quite structurally different to THC and quite have this stuffs ending up in the spice mixtures. I am not quite sure about some people are using.
Interviewer - Chris Smith
So people are actually eating this.
Interviewee - James Mitchell Crow
No I think, well it is sold as incense. So I think people are smoking this stuff. It's actually quite a mystery as to whether these spice mixtures add any real effect on the body or if it was purely just placebo effect. But a company in Germany called THC Pharma who were analyzing these mixtures happened to have been making JWH-018 couple of years back. They actually, they are a company that make medicinal compounds based on THC and so happened to have all the spectra of this compound on their files. So when they analyzed this Spice mixture, they found that this stuff was in there. We talked to John Huffman about his molecule and I asked him a few questions including whether there are any potential medical applications for this stuff and he said all that he had found was that was for getting it high.
Interviewer - Chris Smith
Presumably he didn't tell you, how he knew that?
Interviewee - James Mitchell Crow
No, he didn't mention that.
Interviewer - Chris Smith
I guess now the position we find ourselves in is with the design the drugs boom of the '70s and '80s where something is not illegal until there is a piece of paper saying that this particular molecule is illegal. So there's something out, they are on the market at the moment that has cannabis like effects but won't get you arrested.
Interviewee - James Mitchell Crow
Well yes, in the short term, although as I mentioned governments are rushing to try and ban this stuff. So it's not currently illegal in many countries, but no doubt it soon will be, as soon as governments can catch up.
Interviewer - Chris Smith
So I think you'll have to get rid of those joy sticks from the Chemistry World office James.
(20:32 -- Philip Kraft discusses the quest for new odour molecules for perfumes)
Interviewer - Chris Smith
And now on the subject of things with interesting smells. Here's Philip Kraft who is a perfumer with a chemical form of synesthesia. When he sees a molecule he knows intuitively what it will smell like.
Interviewee - Philip Kraft
So I design smelling molecules, odorants. My job is more or less to invent new smells, that key perfumery creation.
Interviewer - Chris Smith
I would think that the majority of people, myself included, think that when perfumers go out into world saying around, we want new smell, they just go and look in nature and steal something. How has modern day chemistry changed our approach to designing fragrances?
Interviewee - Philip Kraft
The main component is from naturals, say like vanilla beans vanillin or coumarin from tonka beans. These have been identified and synthesized and then there was a second period where one looked into not the main principle but some of the trace components of nature and took them as key for design, for instance from the rose is the damascones which are smelling like plum and not necessarily typical for rose but which are very essential in providing natural rose odour and now if you have the second generation, you can go one step further and for instance design compounds where you cut a few atoms from the damascones and mixed with some seco and these material can then provide additional lift and you can have this idea then to learn from the natural principles how to design an odorant.
Interviewer - Chris Smith
So do you have a sort of chemical synesthesia where when you smell a molecule you end up with the picture forming in your mind as to what must the chemical structure of that molecule? So you can begin to work how it might interact with other molecules and so on.
Interviewee - Philip Kraft
Yeah, when I see a molecule I see the smell, I have an idea of which part could actually contribute to which facet. It is a learning process because I might be wrong, but it might be right and it's working like that. We make some derivatives and see if that's okay but you have to see, if well if you like the results but also the perfumers must love it.
Interviewer - Chris Smith
How much of this is in the nose of the beholder, in the sense that you make a molecule of a certain shape, but you have receptors in your nose that recognize that molecule and react to it in a certain way, but the next person because of genetic differences might not, so how do you take that into account?
Interviewee - Philip Kraft
Perception is actually an assay of 350 receptors and it gives a unique profile, but we learn to identify these profiles with nature, so we are sort of tuned in from our experience and the receptors might be different, but when we learn odours during our daily life, we associate certain patterns with certain odours like with rose and in a way we learn to recognize similar structural principles.
Interviewer - Chris Smith
What other sorts of applications are there for this sort of chemistry?
Interviewee - Philip Kraft
Oh lots, basically it's everything that is in use for odour purpose, but also for daily use. So it starts really with shampoo, washing detergents, deodorants, candles, even gas odorants so that people don't poison themselves with gas, so sometimes people ask for very stinky molecules but fine fragrances are still the motto of innovation.
Interviewer - Chris Smith
So given that we have a finite number of receptors in our noses to smell these smells and there must be a finite number of molecules you could make. Does that mean then eventually someone like you is going to make the last possible different smell we could make?
Interviewee - Philip Kraft
No, think, its pretty infinite, right if you think about one molecule is not just in one receptor, so its hopping, it might be 90% in this receptor, 5% in that receptor, 2% in that, 0.1% in another receptor, so usually you see an array, so the combinations would be something like (350)350 so its almost infinite really.
Interviewer - Chris Smith
Have tastes changed a lot in terms of what people want to wear in terms of perfumes these days and if you take a perfume that people were making, say, 50 years ago and smell that, does it smell goddamn awful to someone like you?
Interviewee - Philip Kraft
It really depends on the person, but obviously there are trends and the trends are going to more transparent, to more in a way lush and sexy still but not really very opulent smells and people get of course also both with the same fragrance all the times.
Interviewer - Chris Smith
And just to finish off, coming from someone who is a master, odorant specialist yourself, so what do you wear and what do you recommend?
Interviewee - Philip Kraft
Okay, I wear for myself this Puff Daddy fragrance 'Unforgivable' from Sean John because this has this specific champagne accord in it which features an overdose of my Pomarose molecule and the female edition also has this Pomarose in, but in a little bit different context. Yeah, I like also the Marc Jacobs men with the DKNY 'Be Delicious' and even some weird accords in S?cr?tions Magnifiques from Etat Libre d'Orange, they launched a small brand in Paris that has really crazy perfume ideas in a sense that should smell like blood salvia and this is really action smell but difficult to wear, but it is sometimes well, sort of, fun what you can do if you want to do something.
Interviewer - Chris Smith
I think I'll stick with my Calvin Klein. That was Philip Kraft from the research company Givaudan in Switzerland.
(26:23 -- InChIs helps chemists search the web)
Interviewer - Chris Smith
The Internet has revolutionized research and the dissemination of new discoveries, but chemists have got something of a problem because vast search engines like Google can find facts for you there are much less good at tracking down molecular structures. So how scientists are trying to solve this one, Richard.
Interviewee - Richard Van Noorden
Yeah, this is a pretty interesting one, Chris. There is so much chemical information out there on the web, but it is very difficult to search for it, because you can type in a molecule's name, but you really want to do as a chemist is search for a molecule's structure, search for a ring of six attached to a ring of five, you certainly can't do that in Google. So to address this in 1995 IUPAC, which is chemistry 's international governing body, invented this unique identifier, the string of texts that exactly identified what a molecule looked like and it is called the International Chemical Identifier or the InChI. Now the idea is that if every molecule on the web were tagged with this string, you could enter a little bit of this string that correspond to say a six n
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