Chemical jigsaw puzzles: how do chemists identify molecules?

Front cover of Great ExplanationsA quick thing before I get into this month’s chemistry ramble: I’m guessing that you, lovely reader, enjoy reading about science stuff. Especially stuff written by an amazing crowd of hard-working science communicators, one of whom is yours truly. So, please consider spreading the word about this awesome book: Great Explanations. Or even better, pledge! There are some fabulous rewards at the different pledge levels. Either way, thank you x

Okay, back to it! Recently, a bit of an argument blew up on Twitter regarding what is, and isn’t, in covid vaccinations. The particular substance du jour being graphene oxide. The @TakeThatChem account pointed out that one of the sources being touted by some as ‘evidence’ for its presence (the article in question was by Robert O Young, remember him? Yes, the one that did actual jail time) didn’t describe the use of any sort of technique that could identify graphene oxide. Which, just to be clear, is absolutely not an ingredient in covid vaccinations.

The debate culminated with questions about how, exactly, scientists do identify substances on the molecular level. @TakeThatChem wondered if one of the users who had become embroiled in the debate even understood how a chemist might work out a molecule’s structure, and then posted an image.

Screenshot of tweet by @TakeThatChem showing an NMR spectrum (link in text)

This tweet illustrated a technique that can be used to identify molecules.

British students of chemistry first meet images like this somewhere around the age of 17–18, so although this is somewhat advanced, it’s still essentially school-level. Which means that for a chemist, it’s one of those things that’s so familiar that, half the time, we probably forget that the rest of the world will have absolutely no idea what it is.

But for those that have never studied A level chemistry or similar: what is it?

The answer is that it’s a proton NMR, or nuclear magnetic resonance, spectrum. Now, NMR is quite tricky. Bear with me, I’m about to try and explain it in a paragraph…

Here goes: you know magnets? And how, if you put one magnet near another magnet, it moves? Now imagine that certain types of atomic nuclei are basically tiny magnets. If you put them in a really powerful magnetic field, they sort of move. If you then alter that magnetic field, they move as the field varies. A computer records and analyses those changes, and spits out a graph that looks like that one back there – which chemists call a spectrum.

Photo of MRI equipment

Medical MRIs use essentially the same technology as the one used to generate the spectrum

Did I nail it? There’s a lot more to this, not surprisingly. In particular, radio waves are involved. My quick and dirty explanation is the equivalent of describing a car as a box on wheels – it’s broadly true from a distance if you squint a bit, but if you said it in the presence of a qualified mechanic they’d wince and start muttering words like ‘head gasket’ and ‘brake discs’ and ‘you do know this is a diesel engine, yes?’

Anyway, it’ll do for now. If you’re studying NMR at a more advanced level, take a look at this episode of Crash Course Organic Chemistry written by… someone called Kat Day. No idea who that is 😉

The same technique, by the way, is used in medicine – but there you know it as MRI, or magnetic resonance imaging. It turns out that if you shove a human (or pretty much anything that contains a lot of carbon-based molecules) into a powerful magnetic field, the atomic nuclei do their thing. You might imagine that having all your atoms do some sort of cha-cha would hurt, but no – as anyone who’s ever had an MRI will attest, it’s mostly just very loud and a bit dull. The end result is an image with different contrast for different types of tissue. Fatty tissue, for example, tends to show up as areas of brightness, while bone tends to look darker – so it’s useful for diagnosing all sorts of problems.

Photo of jigsaw pieces

Interpreting a proton NMR spectrum can be a bit like looking at a jigsaw pieces

But back to chemistry. Chemists, preferring a simpler life (haha), are often working with single substances. Or at least trying to. If we imagine a molecule as a picture, looking at a proton NMR spectrum is a bit like looking at a mixed-up jigsaw puzzle of that picture. Each individual piece – or peak – in the spectrum represents an atom or a group of atoms.

Each piece tells you something and, at the same time, it also tells you about the bits that are joined to it. In the same way that you might look at a jigsaw piece and think, ‘well, this has a sticky-out bit so the piece that goes next to it must have an inny-bit,’ chemists look at a spectrum and say, ‘well, this bit looks like this, so its carbon atom must be attached to group of atoms like that.’

Okay, so what do the pieces in the spectrum @TakeThatChem posted show us? Well, reading spectra takes practice but, like most things, if you do that practice, after a while you get into the habit of spotting things straight away.

For example, it’s fairly obvious to me that whatever-it-is it probably has a carboxylic acid (COOH) group, and it definitely has a benzene ring. I can also see that the benzene ring has things bonded to opposite points, in other words, if you numbered the carbons in the ring from 1 to 6, it has things attached at carbon 1 and carbon 4. There’s a chain of carbons, which is branched, and there’s another CH3 group somewhere. To get more precise I’d have to look more carefully at the integrals (the differently-sized ∫ symbols over the peaks), hunt for a data sheet and study the scale on the horizontal axis along the bottom.

Photo of white pills

The spectrum is of a common drug substance, but which one…

My brain got as far as ‘hm, maybe it’s aspirin, oh no, it can’t be, because…’ before I came across the already-posted answer. I won’t give it away – spoilers, sweetie – but let’s just say it’s a molecule not a million miles different from aspirin.

So yes, chemists do have the means to identify individual molecules, but it requires a fair bit of knowledge and training to both carry out the techniques and to interpret the results. Despite what Hollywood might have us believe, we don’t (yet) have a machine that intones ‘this material is approximately 40% isobutylphenylpropionic acid, captain’ when you plop a sample into it.

The fact that real chemistry (and science in general) is not simple is precisely why pseudoscience peddled by the likes of Robert O Young is so appealing: it’s nice and easy, it follows a sort of ‘common sense’ narrative, it’s not swathed in all sorts of technical language. Anyone can read it and, without any other training, feel as if they understand it perfectly.

None of us knows what we don’t know. If someone comes along with an easy explanation, it’s tempting to believe it – particularly if they go on to play into our anxieties and tell us what we were hoping to hear.

Which brings me to a thread by the lovely Dr Ben Janaway, one tweet of which said, extremely eloquently:

Please do not harass [people protesting covid vaccines]. Please do not blame them. My education is a privilege they have not been afforded. They do not lack intelligence, they lack being taught how to make sense of very complicated things, most of it hidden. What can we do, listen and talk.

Photo of a facemask, syringe and vaccine vials

Please get vaccinated

His point is a good one. All we can do is keep spreading the word as clearly as possible and just hope that, maybe, it will change one mind somewhere. Because maybe that mind will change another, and maybe sense will spread.

Take care, stay safe, and get vaccinated. Get your flu jab, too, if it’s that time of year in your part of the world.


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Do you want something non-sciency to distract you from, well, everything? Why not take a look at my fiction blog: the fiction phial? You can also find me doing various flavours of editor-type-stuff at the horror podcast, PseudoPod.org – so head over there, too!

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Are we really wasting a valuable natural resource at parties?

Solar_eclipse_1999_4_NR

This particular inert gas was discovered by an astronomer observing a solar eclipse.

A couple of weeks ago I wrote a (tongue in cheek) post about a very inert gas, nitrogen. Silliness aside though, nitrogen is a bit, well boring. I mean, we’ve known about it for nearly 250 years, it makes up nearly 80% of our atmosphere and it mostly just sits around doing nothing. Even plants, who’ve mastered the spectacular trick of making solid stuff out of sunlight and carbon dioxide, can’t do much with it in its gaseous form (with a few exceptions).

There are much more interesting inert gases. There’s one that wasn’t even discovered on Earth. In fact, it was first spotted on the Sun by Jules Janssen, an astronomer who was taking advantage of a total solar eclipse to study the Sun’s atmosphere. After some more experiments astronomer Norman Lockyer and chemist Edward Frankland named the element after the Greek word for the Sun. It was the first element to be discovered somewhere other than Earth.

Helium_spectrum

Spectral lines of helium

As it turns out, this element is the second most abundant element in the universe (after hydrogen), but one of the least abundant elements on Earth – with a concentration of just 8 parts per billion in the Earth’s crust.

Today, almost all of us meet it as very young children. In balloons.

It’s helium, the second-lightest element in the periodic table and also, perhaps, the ultimate non-renewable resource.

Most of us meet this element as children.

We all learnt what ‘non-renewable’ means in school: it refers to something we’re using up faster than we can ever replace it. Almost anyone can tell you that crude oil is non-renewable. But the thing is, there are alternatives to crude oil. We can use bioethanolbiodiesel and their cousins to power vehicles and provide power. Bioethanol can act as a route to plastics, too. Scientists are also investigating the potential of algae to produce oil substitutes. These alternatives may (at the moment) be relatively expensive, and come with certain disadvantages, but they do exist.

We have no way to make helium. At least, no way to make it in significant quantities (it’s a by-product in nuclear reactors, but there we’re talking tiny amounts). And because it’s so light, when helium escapes into the atmosphere it tends to float, well, up. Ultimately, it escapes from our atmosphere and is lost. Every time you get fed up with that helium balloon that’s started to look a bit sorry for itself and stick a pin in it (perhaps taking a few seconds to do the squeaky-voice trick first) you’re wasting a little bit of a helium.

But so what? We could all live without helium balloons right? If we run out, balloons will just have to be the sinking kind. What’s the problem?

Liquid helium is used to cool the magnets in MRI machines.

Liquid helium is used to cool the magnets in MRI machines.

The problem is that helium has a lot more uses than you might realise. Cool it to -269 oC – just 4 degrees warmer than absolute zero, the lowest termperature there is – and it turns into a liquid, and that liquid is very important stuff. It’s used to cool the superconducting magnets in MRI (magnetic resonance imaging) scanners in hospitals, which provide doctors with vital, non-invasive, information about what’s going on inside our bodies. MRI techniques have made diagnoses more accurate and allowed surgery to become far more precise. Nothing else (not even the lightest element, hydrogen) has a lower boiling point than helium, so nothing else is quite as good for this chilly job. Scientists are working hard on developing superconducting magnets that work at warmer temperatures, but this technology is still in its infancy.

There’s another technology called NMR (nuclear magnetic resonance) which chemists use all the time to help them identify unknown compounds. In fact, MRI was born out of NMR – they’re basically the same technique applied slightly differently – but the medical application was renamed because it was felt that patients wouldn’t understand that the ‘nuclear’ in NMR refers to the nuclei of atoms rather than nuclear energy or radiation, and would balk at the idea of a ‘nuclear’ treatment. Possibly imagining that they’d turn into the Hulk when they went into the scanner, who knows.

Since it works in essentially the same way, NMR also relies on superconducting magnets, also often cooled with liquid helium. Without NMR, whole swathes of chemical research, not to mention drug testing, would run into serious problems overnight.

It doesn’t stop there. Helium is also used in deep-sea diving, in airships, to cool nuclear reactors and certain other types of chemical detectors. NASA also uses massive amounts of helium to help clean out the fuel from its rockets. In summary, it’s important stuff.

But if we can’t make it, where does all this helium come from?

The Earth’s helium supplies have largely originated from the very slow radioactive alpha decay that occurs in rocks, and it’s taken 4.7 billion years to build them up. Helium is often found sitting above reserves of natural oil and gas. In fact that’s exactly how the first helium reserve was discovered: when, in 1903, an oil drilling operation in Kansas produced a gas geyser that wouldn’t burn. It turned out that although helium is relatively rare in the Earth overall, it was concentrated in large quantities under the American Great Plains.

The National Helium Reserve

Show me the way to… The National Helium Reserve

Of course this meant that the United States quickly became the world’s leading supplier of helium. The US started stockpiling the gas during World War I, intending to use it in barrage balloons and later in airships. Helium, unlike the other lighter-than-air gas hydrogen, doesn’t burn. This made things filled with helium safer to handle and, of course, more difficult to shoot down or sabotage.

In 1925 the US government set up the National Helium Reserve in Amarillo, Texas. In 1927 the Helium Control Act came into force, which banned the export of the gas. At that point, the USA was the only country producing helium, so they had a complete monopoly (personally, I’d quite like to see a Monopoly board with ‘helium reserves’ on it, wouldn’t you?). And that’s why the Hindenburg, like all German Zeppelins, both famously and tragically had to use hydrogen as its lift gas.

Helium use dropped after World War II, but the reserve was expanded in the 1950s to supply liquid helium as a coolant to create hydrogen/oxygen rocket fuel during the Space Race and the Cold War. The US continued to stockpile helium until 1995. At which point, the reserve was $1.4 billion in debt. The government of the time pondered this and ended up passing the Helium Privatization Act of 1996, directing the United States Department of the Interior to empty the reserve and sell it off at a fixed rate to pay off the cost.

Right now, anyone can buy cheap helium in supermarkets and high street shops.

Right now, anyone can buy cheap helium in supermarkets and high street shops.

As a result cheap helium flooded the market and its price stayed fairly static for a number of years, although the price for very pure helium has recently risen sharply. This sell-off is why we think of helium as a cheap gas; the sort of thing you can cheerfully fill a balloon with and then throw away. Pop down to a large supermarket or your local high street and you might even be able to buy a canister of helium in the party section relatively cheaply.

The problem is that this situation isn’t going to last. The US reserves have been dramatically depleted, and at one point were expected to run out completely in 2018, although other reserves have since been discovered and other countries have set up extraction plants. It is also possible to extract helium from air by distillation, but it’s expensive – some 10,000 times more expensive. None of these alternatives are expected to really ease the shortage; they’ll just delay it by a few years.

So are helium party balloons truly an irresponsible waste of a precious resource? Well… the helium that’s used in balloons is fairly impure, about 98% helium (mixed with, guess what? Yep, we’re back to nitrogen again!) whereas the helium that’s needed for MRI and the like is what’s called ‘grade A’ helium, which is something like 99.997% pure, depending on whom you ask. Of course you can purify the low-grade helium to get the purer kind but this costs money, which is why grade A helium is so much more expensive.

NABAS logo

The National Balloon Association (‘the voice of the balloon industry’ – you can’t help wondering whether that’s a very high-pitched voice, can you?) argues that balloons only account for 5-7% of helium use and that the helium that goes into balloons – which they prefer to call ‘balloon gas’ because of its impurities – is mainly recycled from from the gas that’s used in the medical industry, or is a by-product of supplying pure, liquid helium, and therefore using it in balloons isn’t really a problem.

Dr Peter Wothers argues that helium balloons should be banned.

Dr Peter Wothers argues that helium balloons should be banned.

On the other hand, more than one eminent physics professor has spoken out on the subject of helium wastage. It costs about 30-50p to fill a helium balloon, but Professor Robert Richardson of Cornell University argued (before his death in 2013) that a helium party balloon should cost £75 to more accurately reflect the true scarcity value of the gas. Dr Peter Wothers of Cambridge University has called for an outright ban of them, saying that in 50 years’ time our children will be amazed that we ever used such a precious material to fill balloons.

Is it time to call for a helium balloon boycott? Perhaps, although it will probably take more than one or two scientifically-minded consumers refusing to buy them before we see any difference. Realistically, the price will sky-rocket in the next few years and, as Peter Wothers suggests, filling balloons with helium will become a ridiculous notion because it’s far too expensive.

Will images like this make no sense in the future?

Will images like this make no sense in the future?

It’s strange to think though, that in maybe 50 years or so the idea of a floating balloon might simply disappear. Just think of all the artwork and drawings that will no longer make sense.

Perhaps this quotation by the late Sir Terry Pratchett is even more relevant than it first appears:

“There are times in life when people must know when not to let go. Balloons are designed to teach small children this.”

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