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.

Support the Great Explanations book here!

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, – so head over there, too!

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Elements, compounds and misleading mercury

Elemental mercury isn't the same as mercury in compounds.

Elemental mercury isn’t the same as mercury in compounds.

Today I read an interesting article about some recent research carried out at the University of Illinois where they demonstrated that the best way to convince parents to vaccinate their children might be to show them the results of the diseases the vaccines prevent. (This, by the way, contradicts some research published in 2014 which showed that this tactic didn’t work. For an excellent discussion of the two, see here.)

Then, because I am just one of those people who can’t resist poking at ulcers with my tongue (you know what I mean) I had a quick look at some of the comments regarding that article. Reassuringly, most people were weighing in on the “yeah, vaccinate!” side of the argument. But not surprisingly there was also a small group of people posting the traditional anti-vaccine arguments. And then, this appeared:

mercury ppm

This is thoroughly silly, and I’ll tell you why.

Well, it did make be go “hmmmmm”, but for the reason you might imagine.

No, you see, what I thought was: “hmmmmm, someone else who has, possibly deliberately, failed to understood the difference between elements and compounds, and how chemical bonding changes properties.”

Allow me to start at the beginning. If you went to a school in the UK (and I would hope it’s similar elsewhere in the world) you learned about elements, compounds and mixtures when you were about 13 years old – if not before. You might have forgotten it since, but I can absolutely, categorically guarantee you that lesson happened. In fact, it was probably a few lessons.

iron sulfide experiment

The much-loved reaction between iron and sulfur.

One experiment much beloved of chemistry teachers since year dot is to take a mixture of sulfur (a yellow powder) and some iron filings (grey) and show that they can be separated with a magnet. Then heat the mixture up so that the two react, with a rather beautiful red glow, to form iron sulfide. This is a blackish solid which is in theory not magnetic (but in practice almost always is) and demonstrate that now the two elements cannot be separated.

Thus we have demonstrated that elements (the iron and the sulfur) have different properties to the compound they formed (iron sulfide), and also that mixtures can be separated fairly easily, whereas breaking compounds up into their constituent elements is much harder. Lovely. Job done.

And yet… so many people seem to have been asleep that day. Or perhaps just didn’t grasp it well enough to continue to apply the principle to other things.

pouring mercury

Elemental mercury

For example, mercury. Mercury, the element (the runny, silvery stuff that you used to find in thermometers) is a heavy metal. Like most of its compatriots, such as cadmium, lead and arsenic, it’s toxic. It can be absorbed through the skin and mercury vapour can be inhaled, so containers need to be tightly sealed. The increasing awareness of the toxicity of mercury is why older readers might remember seeing it ‘in the flesh’, so to speak, at school, whereas younger ones will not – these days it’s rarely even used in thermometers for fear of breakages.

That said, it does occur naturally in the environment, particularly as the result of volcanic eruptions – and very low levels aren’t considered harmful. The dose, as they say, makes the poison. It also occurs as the result of industrial processes, particularly coal-fired power plants and gold production, and occupational exposure is a genuine concern. In particular, chronic exposure is known to cause cogitative impairment. It might the source of the ‘mad dentist’ myth. It’s almost certainly the origin of the phrase ‘mad as a hatter‘.

So in summary, don’t mess about with elemental mercury; it’s not good for your health.

However, as I took some pains to establish, elements and compounds are different things. So what about compounds which contain mercury?

The compound thiomersal

The compound thiomersal

This is where vaccines come in. There is a substance that used to be used as a preservative in (some) vaccines called thiomersal (or thimerosal, in the U.S). You may have heard its name; it comes up quite a lot. Incidentally, it hasn’t just been used in vaccines, but also in various other things including skin-test antigens and tattoo inks.

Now, to be clear, thiomersal IS potentially toxic, however it’s quickly metabolised in the body to ethyl mercury (C2H5Hg+) and thiosalicylate and, although ethyl mercury does, clearly, still contain atoms of mercury, it does not bioaccumulate. In other words, your body gets rid of it. At very low doses (such as those in vaccines) there is no good evidence that thiomersal is harmful.

Still, due to continuing public health concerns, thiomersal has been phased out of most U.S. and European vaccines. In the UK, thiomersal is no longer used in any of the vaccines routinely given to babies and young children in the NHS childhood immunisation programme. And at the moment, all routinely recommended vaccines for U.S. infants are available only as thimerosal-free formulations or contain only trace amounts of thimerosal (≤1 than micrograms mercury per dose).

Let me just say that again. The evidence suggests it’s safe, but it’s been removed anyway as a precaution. If you live in the UK, it’s not in your child’s vaccines, and that includes the new nasal-spray vaccine for flu which has been rolled out over the last few years. If you live in the U.S. it’s probably not, and thimerosal (thiomersal) free versions exist. It does turn up most often in flu vaccines (hence the meme image at the start) but thiomersal-free versions of those also exist in the U.S.

So chances are it’s not in your vaccines. Not in there. Got it? Ok.

ethyl vs methyl mercury

methyl mercury (left) is not the same as ethyl mercury (right)

Now, you may have heard about mercury in seafood. It is an issue, particularly for women who are pregnant, trying to become pregnant or breastfeeding, and is the reason such women are advised not to eat shark and swordfish, and to keep their tuna consumption low. But here’s the thing: it’s a different kind of mercury. In this case, it’s methyl mercury (remember, thiomersal breaks down to ethyl mercury, which is not the same).

Methyl mercury is more toxic than ethyl mercury. Methyl mercury binds to parts of amino acids much more readily than its ethyl cousin, and it’s able to pass through the blood brain barrier and into nerve cells where it causes damage. In addition, ethyl mercury is much more quickly eliminated from the body than methyl mercury. Because of all this, methyl mercury does bioaccumulate (build up in the body), and that’s why large top-of-the-food-chain fish like shark and tuna can have significant levels of it, and why certain groups of people should be careful about eating them.

The FDA’s action level (the limit at or above which FDA will take legal action) for methyl mercury in fish is 1000 ppb (1 ppm). But remember, that’s for the much more dangerous methyl mercury, not ethyl mercury. I’ve been unable to find an equivalent figure for the UK, but I’d imagine it’s similar.

So, where does the 200 ppb mercury figure in the image at the top come from? Well the Environmental Protection Agency does indeed set a ‘maximum contaminant level goal’ for inorganic mercury of 0.002 mg/L or 2 ppb in water supplies. Methyl and ethyl mercury are not inorganic mercury; compounds that fall into this category include mercuric chloride, mercuric acetate and mercuric sulfide, which largely get into water as the result of industrial contamination.

In summary, that meme image at the start is basically comparing apples and oranges. The EPA limit isn’t relevant to vaccines, because it’s for inorganic mercury, which the substance in vaccines isn’t. While we’re about it, the levels applied to fish don’t apply either, because that’s methyl mercury, not ethyl mercury. They’re not the same thing. And all that aside, it’s highly unlikely (if you live in the UK, no chance at all) that there are 50,000 ppb of ethyl mercury in your flu vaccine anyway. AND, let’s not forget, there’s no evidence that the tiny quantities of thiomersal used in vaccines are harmful in the first place.


You may note that I’ve studiously avoided the word ‘autism’ in this post so far. But yes, that’s the big concern; that exposure to thiomersal in vaccines could cause autism. Despite multiple, huge, studies in several countries looking for possible links between vaccines and autism, none have been found. Vaccines don’t cause autism. It’s time we stopped wasting enormous amounts of time and resources on this non-link and spent it instead on finding out what does cause it. Wouldn’t that be far more useful and interesting?

Now… if you’re hardcore anti-vaccine and you’ve read this far, and you’re about to hit the comment button and tell me that all this research is just Big Pharma covering things up so they can make money from the ‘million(/billion/trillion) dollar vaccine industry’, just wait a moment.


Think about this: how much money could the medical industry make from people actually catching measles, mumps, polio, TB, whooping cough and all the others? Just think of all the money they could make selling antivirals and antibiotics, all the money to be made from painkillers, antipyretics, drugs to treat respiratory symptoms of one kind or another, and everything else? Believe me, it would be much, much more than they make from a single 2 ml dose of vaccine. Why ‘cover up’ research that’s, if anything, reducing their profits?

All these diseases are horrible, and some can be fatal or have genuinely life-changing consequences. That’s proven. Please vaccinate your children, and yourself.


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