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!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2021. You may share or link to anything here, but you must reference this site if you do. You can support my writing my buying a super-handy Pocket Chemist from Genius Lab Gear using the code FLASK15 at checkout (you’ll get a discount, too!) or by buying me a coffee – the button is right here…
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Faking Lateral Flow Tests: the problem with pH

Fruit juices can be used to generate a fake positive on COVID-19 LFTs

On Thursday last week, I got a message from Prof Mark Lorch — my sometime collaborator on supercharacter-based ramblings.

“Have you seen the reports of kids fooling the Covid lateral flow tests and getting false +ve results by adding orange juice to the devices?” he wondered.

At this point, I had not – but I quickly got up to speed. Mark had previously made an excellent video explaining how lateral flow test (LFT) devices work, so it was just a case of working out, firstly, whether the false positives were reproducible, and secondly, speculating what, exactly, was causing them.

Thus ensued some interesting discussion which ultimately led to a couple of articles from Mark. One at The Conversation and another, slightly more recently, at BBC Future.

I won’t delve into LFT-related science, because Mark has covered it (really, check the video and those articles), but I am going to talk a little bit about pH – the scale chemists use to measure how acidic or alkaline solutions are – because as soon as news of this started to gain traction people, predictably, started trying it out themselves. And that was when things got really interesting.

Image

The buffer included with LFTs is effective at neutralising the pH of solutions, for example, cola

Now, firstly, and importantly: the test kits come with a small vial of buffer solution. Buffers are substances which resist pH changes. As I’ve written before, our bodies naturally contain buffer systems, because keeping the pH of our blood and other body fluids constant is important. In fact, if blood pH varies even a little, you’re in all sorts of serious trouble (which is how we can be certain that so-called “alkaline” diets are a load of hooey). Anyway, the important message is: don’t mix any liquid you’re testing with the contents of that phial, because that will neutralise it.

If you want to try this for yourself, just drop the liquid you want to test directly into the window marked S on the test.

That out of the way, let’s get back to pH. It’s a scale, usually presented as going from 0–14, often associated with particular colours. The 0 end is usually red, the 7 in the middle is usually green, while the 14 end is usually dark blue.

These colours are so pervasive, in fact, that I’ve met more than one person with the idea that acids are red, and alkalis are blue. This isn’t the case, of course. The red/green/blue idea largely comes from universal indicator (UI), which is a mixture of dyes that change colour at different pH values. There’s also a common indicator called litmus (people sometimes mix up UI and litmus, but they’re not the same) which is also red in acid and blue in alkali.

Some species of hydrangea produce pink flowers in alkaline soil, blue in acid soil.

There are actually lots of pH indicators, with a wide variety of colour changes. Phenolphthalein, for example, is bright pink in alkali, and colourless in acids. Bromocresol purple (they have such easy-to-spell names) is yellow in acids, and violet-purple in alkalis.

Many plants contain natural indicators. Just to really mix things up, some species of hydrangea produce flowers that are blue-purple when they’re grown in acidic soil, and pink-red in alkaline conditions.

Bottom line? Despite the ubiquitous diagrams, pH has nothing to do with colour. What it is to do with is concentration. Specifically, the concentration of hydrogen ions (H+) in the solution. The more H+ ions there are, the more acidic the solution is, and the lower the pH. The fewer there are, the less acidic (and the more alkaline, and higher pH) it is.

In fact, pH is a log scale. When the concentration changes by a factor of 10, the pH changes by one point on the scale.

This means that if you take an acid with pH of 2, and you dilute it 1 part to 10, its pH changes to 3 (i.e. gets one point more alkaline, closer to neutral). Likewise, if you dilute an alkali with a pH of 10 by 1:10, its pH will shift to 9 (again, closer to neutral).

And what this means is that the pH of substances is not a fixed property.

Louder for anyone not paying attention at the back: the pH of substances is not a fixed property!

Yes, we’ve all seen diagrams that show, for example, the pH of lemon juice as 2. This is broadly true for most lemons, give or take, but if you dilute the lemon juice, the pH rises.

Apple juice dropped directly into the test window gives an immediate “positive” result.

I am by no means an expert in commercial, bottled lemon juice, but I reckon a lot of them have water added – which may well explain why @chrismiller_uk was able to get a positive result, while @BrexitClock, using a French bottle of lemon juice, couldn’t.

Mark and I concluded that the pH you need to aim for is probably around 3–4. Go too low, and you don’t get a positive (and you might wipe out the control line, too). Likewise, too high also won’t work.

Myself, I tried apple juice. I couldn’t find the indicator colour key for my indicator paper (I really must clear out the drawers one of these days) but it’s broadly the same as Mark’s cola photo, up above. In other words, the apple juice is about pH 3. And it gives a beautiful positive result, immediately.

One more interesting observation: Mark recorded some time-lapse video comparing orange juice to (sugar-free) cola. It shows the cola test line developing a lot more slowly. We’re not entirely sure why, but it may be pH again: orange juice almost certainly has a lower pH than cola.

For any parents reading this thinking we’re being terribly irresponsible, fear not: as Prof Lorch has made clear in his articles, you can identify a fake by waiting a few minutes and then dropping some of the buffer solution provided in the test window. As I said above, this will neutralise the pH, and the positive test line will disappear. Extra buffer won’t change a genuinely-positive test, because the antibodies bind very tightly (more technical info here). To quote Mark: “you’d need a swimming pool’s worth of buffer to have any chance of washing [the antibodies] off.”

Alternatively, you can just watch your teenager as they do their tests, and make sure they’re not getting up to anything nefarious…

Have you tried to trick an LFT? If you have, share your results! Look us up on Twitter: @chronicleflask and @Mark_Lorch or add a comment below. We’d love to see your photos!


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!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2021. You may share or link to anything here, but you must reference this site if you do. You can support my writing my buying a super-handy Pocket Chemist from Genius Lab Gear using the code FLASK15 at checkout (you’ll get a discount, too!) or by buying me a coffee – the button is right here…
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Vibrant Viburnum: the fascinating chemistry of fragrant flowers

There’s a Viburnum carlesii bush (sometimes called Koreanspice) near my front door and, right now, it smells amazing. It only flowers for a relatively short time each year and otherwise isn’t that spectacular – especially in the autumn when it drops its leaves all over the doorstop, and I’m constantly brushing them out of the house.

But it’s all worth it for these few weeks in April, when everyone who has any reason to come anywhere near our door says, ‘ooh, what is that smell? It’s gorgeous!’ We also rear butterflies at this time of year, and they love the flowers once they’ve emerged from their chrysalids. (No, of course this isn’t an excuse to include all my butterfly photos in a post. Painted lady, since you ask.)

But let’s talk chemistry – what is in the Viburnum carlesii’s fragrance? Well, it’s a bit complicated. Fragrances, as you might imagine, often are. We detect smells when volatile (things that vaporise easily) compounds find their way to our noses which are, believe it or not, great chemical detectors.

Well, I say great, many animals have far better smell detection: dogs, of course, are particularly known for it. Their noses have some 300 million scent receptors*, while humans “only” have 5-6 million but, and this is the really fantastic part, by some estimates we’re still able to detect a trillion or so smells. We (and other animals) inhale air that contains odour molecules, and those molecules bind to the receptors in our noses, triggering electrical impulses that our brains interpret as smell.

Most scents aren’t just one molecule, but are actually complex mixtures. Our brains learn to recognise combinations and to associate them with certain, familiar things. It’s not that different from recognising patterns of sound as speech, or patterns of light as images, it’s just that we often don’t think of smell in quite the same way.

Viburnum carlesii flowers have a fragrance often described as sweet and spicy.

So my Viburnum bush – and the flowers I’ve cut and put on my desk – is actually pumping out loads of different molecules right now. After a bit of hunting around, I tracked them down to (brace yourself for a list of chemical names) isoeugenol, eugenol, methyleugenol, 4-allylsyringol, vinyl-guaiacol and methyl nicotinate, plus the old favourites methyl salicylate (this stuff turns up everywhere), methyl benzoate (so does this), indole, cinnamic aldehyde and vanillin, and then some isovaleraldehyde, acetoin, hexanal, (Z)-3-hexen-1-ol and methional.

Phew.

Don’t worry, I’m not going to talk about the chemistry of all of those. But just for a moment consider how wondrous it is that our noses and brains work together to detect all of those molecules, in their relevant quantities, and then send the thought to our conscious mind that oh, hey, the Viburnum is flowering! (It’s also pretty astonishing that, in 2021, I can just plug all those names into a search engine and, with only a couple of exceptions, get all sorts of information about them in seconds – back in the old days when I was studying chemistry, you had to use a book index, and half the time the name you wanted wasn’t there. You kids don’t know how good you’ve got it, I’m telling you.)

Anyway, if you glance at those names, you’ll see eugenol popping up quite a bit, so let’s talk about that. It’s a benzene ring with a few other groups attached, and lots of chemicals like this have distinctive smells. In fact, we refer to molecules with these sorts of ring structures as “aromatic” for this exact, historical reason – when early chemists first isolated them, they noticed their distinctive scents.

Eugenol is an aromatic compound, both in terms of chemistry and fragrance (image source)

In fact there are several groups of molecules in chemistry that we tend to think of as particularly fragrant. There are esters (think nail polish and pear drops), linear terpenes (citrus, floral), cyclic terpenes (minty, woody), amines (fishy, rot) and the aromatics I’ve just mentioned.

But back to eugenol: it’s a yellowish, oily liquid that can be extracted from plants such as nutmeg, cloves, cinnamon, basil and bay leaves. This might give you an idea of its scent, which is usually described as “spicy” and “clove-like”.

Not surprisingly, it turns up in perfumes, and also flavourings, since smell and flavour are closely linked. It’s also a local antiseptic and anaesthetic – you may have used some sort of eugenol-based paste, or perhaps just clove oil, if you’ve ever had a tooth extracted.

Plants, of course, don’t go to the trouble and biological expense of making these chemicals just so that humans can walk past and say, “ooh, that smells nice!” No, the benefit for the plant is in attracting insects, which (hopefully) help with pollination. Which explains why my butterflies like the flowers so much. (Another butterfly pic? Oh well, since you insist.) Eugenol, it turns out, is particularly attractive to various species of orchid bee, which use it to synthesise their own pheromones. Nature’s clever, isn’t she?

By the way, notice I mentioned anaesthetics back there? Eugenol turns out to be too toxic to use for this in large quantities, but the study of it did lead to the development of the widely-used drug propofol which, sadly, is pretty important right now – it’s used to sedate mechanically ventilated patients, such as those with severe COVID-19 symptoms. You may have seen some things in the news earlier this year about anaesthetic supply issues, precisely for this reason.

Isoeugenol has the same “backbone” as eugenol, with just a difference to the position of the C=C bond on the right. (image source)

Back in that list of chemical names, you’ll see “eugenol” forming parts of other names, for example isoeugenol. This points back to a time when chemicals tended to be named based on their origins. Eugenol took its name from the tree from which we get oil of cloves, Eugenia, which was in turn named after Prince Eugene of Savoy – a field marshal in the army of the Holy Roman Empire. And then other molecules with the same “backbone” were given the same name with prefixes and suffixes added on to describe their differences. As I said in my last post, this sort of naming system it was eventually replaced with more consistent rules, but a lot of these older substances have held onto their original names.

Still, regardless of what we call the chemicals, the flowers smell delightful. I’m off to replenish the vase on my desk while I still can. Roll on May, vaccines and (hopefully) lockdown easing!

Take care and stay safe.


*it’s even been suggested dogs’ super-powered sense of smell might be able to detect COVID-19 infections.


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Confusing chemical names: why do some sound so similiar?

It’s the end of March as I write this and, here in the UK at least, things are starting to feel a little bit hopeful. We’ve passed the spring equinox and the clocks have just gone forward. Arguments about the rights and wrongs of that aside, it does mean daylight late into the day, which means more opportunities to get outside in the evenings. Plus, of course, COVID-19 vaccines are rolling out, with many adults having had at least their first dose.

Some COVID-19 vaccines contain polyethylene glycol (PEG), a safe substance found in toothpaste, laxatives and other products, according to Science magazine and health expertsAh, yes. Speaking of vaccines… a couple of weeks ago I spotted a rather strange item trending on Twitter. The headline was: “Some COVID-19 vaccines contain polyethylene glycol (PEG), a safe substance found in toothpaste, laxatives and other products, according to Science magazine and health experts.”

Apart from being a bit of mouthful, this seemed like the most non-headline ever. And also, isn’t it the kind of thing that might raise suspicions in a certain mind? In a, “yeah, and why do they feel the need to tell us that, huh” sort of way?

Why on earth did it even exist?

A little bit of detective work later (by which I mean me tweeting about it and other people kindly taking the time to enlighten me) and I had my answer. The COVID-19 sceptic Alex Berenson had tweeted that the vaccine(s) contained antifreeze. Several people had immediately responded to say that, no, none of the vaccine formulations contain antifreeze. Antifreeze is ethylene glycol, which is definitely not the same thing as polyethylene glycol.

I’m not going to go much further into the vaccine ingredients thing, because actual toxicologists weighed in on that, and there’s nothing I (not a toxicologist) can really add. But this did get me thinking about chemical names, how chemists name compounds, and why some chemical names seem terrifyingly long while others seem, well, a bit silly.

A lot of the chemical names that have been around for a long time are just… names. That is, given to substances for a mixture of reasons. They do usually have something to do with the chemical makeup of the thing in question, but it might be a bit tangential.

formic acid, HCOOH, was first extracted from ants

For example, formic acid, HCOOH, takes its name from the Latin word for ant, formica, because it was first isolated by, er, distilling ant bodies (sorry, myrmecologists). On the other hand limestone, CaCO3, quicklime, CaO, and limewater, a solution of Ca(OH)2, all get their names from the old English word lim, meaning “a sticky substance,” which is also connected to the Latin limus, from which we get the modern word slime — because lime (mostly CaO) is the sticky stuff used to make building mortar.

The trouble with this sort of system, though, is that it gets out of control. The number of organic compounds listed in the American Chemical Society‘s index is in excess of 30 million. On top of which, chemists have an annoying habit of making new ones. Much as some people might think forcing budding chemists to memorise hundreds of thousands of unrelated names is a jolly good idea, it’s simply not very practical (hehe).

It’s the French chemist, Auguste Laurent, who usually gets most of the credit for deciding that organic chemistry needed a system. He was a remarkable scientist who discovered and synthesised lots of organic compounds for the first time, but it was his proposal that organic molecules be named according to their functional groups that would change things for chemistry students for many generations to come.

Auguste Laurent (image source)

Back in 1760 or so, memorising the names of substances wasn’t that much of a chore. There were half a dozen acids, a mere eleven metallic substances, and about thirty salts which were widely known and studied. There were others, of course, but still, compared to today it was a tiny number. Even if they were all named after something to do with their nature, or the discoverer, or a typical property, it wasn’t that difficult to keep on top of things.

But over the next twenty years, things… exploded. Sometimes literally, since health and safety wasn’t really a thing then, but also figuratively, in terms of the number of compounds being reported. It was horribly confusing, there were lots of synonyms, and the situation really wasn’t satisfactory. How can you replicate another scientist’s experiment if you’re not even completely sure of their starting materials?

In 1787 another French chemist, Guyton de Morveau, suggested the first general nomenclature — mostly for acids, bases and salts — with a few simple principles:

  • each substance should have a unique name, as short and specific as possible
  • the name should reflect what the substance consisted of, that is, describe its “composing parts”
  • unknown substances should be assigned names with no particular meaning, being sure not to suggest something false about the substance (if you know it’s not an acid, for example, don’t name it someinterestingname acid)
  • new names should be based on old languages, such as Latin

His ideas were accepted and adopted by most chemists at the time, although a few did attack them, claiming they were “barbarian, incomprehensible, and without etymology” (reminds me of some of the arguments I’ve had about sulfur). Still, his classification was eventually made official, after he presented it to the Académie des Sciences.

Chemists needed a naming system that would allow them to quickly identify chemical compounds.

However, by the middle of the 1800s, the number of organic compounds — that is, ones containing carbon and hydrogen — was growing very fast, and it was becoming a serious problem. Different methods were proposed to sort through the messy, and somewhat arbitrary, accumulation of names.

Enter Auguste Laurent. His idea was simple: name your substance based on the longest chain of carbon atoms it contains. As he said, “all chemical combinations derive from a hydrocarbon.” There was a bit more to it, and he had proposals for dealing with specific substances such as amines and aldehydes, and of course it was in French, but that was the fundamental idea.

It caused trouble, as good ideas so often do. Most of the other chemists of the time felt that chemical names should derive from the substance’s origins. Indeed, some of the common ones that chemistry professors are clinging onto today still do. For example, the Latin for vinegar is acetum, from which we get acetic acid. But, since organic chemistry was increasingly about making stuff, it didn’t entirely make sense to name compounds after things they might have come from, if they’d come from nature — even when they hadn’t.

So, today, we have a system that’s based on Laurent’s ideas, as well as work by Jean-Baptiste Dumas and, importantly, the concept of homology — which came from Charles Gerhardt.

Homology means putting organic compounds into “families”. For example, the simplest family is the alkanes, and the first few are named like this:

Like human families, chemical families share parts of their names and certain characteristics.

The thing to notice here is that all the family members have the same last name, or rather, their names all end with the same thing: “ane”. That’s what tells us they’re alkanes (they used to be called paraffins, but that’s a name with other meanings — see why we needed a system?).

So the end of the name tells us the family, and the first part of the name tells us about the number of carbons: something with one carbon in it starts with “meth”. Something with five starts with “pent”, and so on. We can go on and on to much bigger numbers, too. It’s a bit like naming your kids by their birth order, not that anyone would do such a thing.

There are lots of chemical families. The alcohols all end in “ol”. Carboxylic acids all end in “oic acid” and ketones end in “one” (as in bone, not the number). These endings tell us about certain groups of atoms the molecules all contain — a bit like everyone in a family having the same colour eyes, or the same shaped nose.

A chemist that’s learned the system can look at a name like this and tell you, just from the words, exactly which atoms are present, how many there are of each, and how they’re joined together. Which, when you think about it, is actually pretty awesome.

Which brings me back to the start and the confusion of glycols. Ah, you may be thinking, so ethylene glycol and polyethylene glycol are part of the same family? Their names end with the same thing, but they start differently?

Well, hah, yes and no. You remember a moment ago when I said that there are still some “common” names in use, that came from origins — for example acetic acid (properly named ethanoic acid)? Well, these substances are a bit like that. The ending “glycol” originates from “glycerine” because the first ones came from, yes, glycerine — which you get when fats are broken down.

Polyethylene glycol (PEG) is a polymer, with very different properties to ethylene glycol (image source)

Things that end in glycol are actually diols, that is, molecules which contain two -OH groups of atoms (“di” meaning two, “ol” indicating alcohol). Ethylene glycol is systematically named ethane-1,2-diol, from which a chemist would deduce that it contains two carbon atoms (“eth”) with alcohol groups (“ol”) on different carbons (1,2).

Polyethylene glycol, on the other hand, is named poly(ethylene oxide) by the International Union of Pure and Applied Chemistry (IUPAC), who get the final say on these things. The “poly” tells us it’s a polymer — that is, a very long molecule made by joining up lots and lots of smaller ones. In theory, the “ethylene oxide” bit tells us what those smaller molecules were, before they all got connected up to make some new stuff.

Okay, fine. So what’s ethylene oxide? Well, you see, that’s not quite a systematic name, either. Ethylene oxide is a triangular-shaped molecule with an oxygen atom in it, systematically named oxirane. Why poly(ethylene oxide), and not poly(oxirane), then? Mainly, as far as I can work out, to avoid confusion with epoxy resins and… look, I think we’ve gone far enough into labyrinth at this point.

The thing is, polyethylene glycol is usually made from ethylene glycol. Since everyone tends to call ethylene glycol that (and rarely, if ever, ethane-1,2-diol), it makes sense to call the polymer polyethylene glycol. Ethylene glycol makes polyethylene glycol. Simple.

Plastic bags are made from polythene, which has very different properties to the ethene that’s used to make it.

Polymers are very different to the molecules they’re made from. Of course they are, otherwise why bother? For example, ethene (also called ethylene, look, I’m sorry) is a colourless, flammable gas at room temperature. Poly(ethylene) — often just called polythene — is used to make umpteen things, including plastic bags. They’re verrrrry different. A flammable gas wouldn’t be much use for keeping the rain off your broccoli and sourdough.

Likewise, ethylene glycol is a colourless, sweet-tasting, thick liquid at room temperature. It’s an ingredient in some antifreeze products, and is, yes, toxic if swallowed — damaging to the heart, kidneys and central nervous system and potentially fatal in high enough doses. Polyethylene glycol, or PEG, on the other hand, is a solid or a liquid (depending on how many smaller molecules were joined together) that’s essentially biologically inert. It passes straight through the body, barely stopping along the way. In fact, it’s even used as a laxative.

So the headlines were accurate: PEG is “a safe substance found in toothpaste, laxatives and other products.” It is non-toxic, and describing it as “antifreeze” is utterly ridiculous.

In summary: different chemicals, in theory, have nice, logical, tell-you-everything about them names. But, a bit like humans, some of them have obscure nicknames that bear little resemblance to their “real” names. They will insist on going by those names, though, so we just need to get on with it.

The one light in this confusingly dark tunnel is the internet. In my day (croak) you had to memorise non-systematic chemical names because, unless you had a copy of the weighty rubber handbook within reach, there was no easy way to look them up. These days you can type a name into Google (apparently other search engines are available) and, in under a second, all the names that chemical has ever been called will be presented to you. And its chemical formula. And multiple other useful bits of information. It’s even possible to search by chemical structure these days. Kids don’t know they’re born, I tell you.

Anyway, don’t be scared of chemical names. They’re just names. Check what things actually are. And never, ever listen to Alex Berenson.

And get your vaccine!


If you’re studying chemistry, have you got your Pocket Chemist yet? Why not grab one? It’s a hugely useful tool, and by buying one you’ll be supporting this site – it’s win-win! If you happen to know a chemist, it would make a brilliant stocking-filler! As would a set of chemistry word magnets!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2021. You may share or link to anything here, but you must reference this site if you do. If you enjoy reading my blog, and especially if you’re using information you’ve found here to write a piece for which you will be paid, please consider buying me a coffee through Ko-fi using the button below.
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Sunshine, skin chemistry, and vitamin D

The UK is on the same latitude as Northern Canada (Image Source: Wiki Commons)

As I write this it’s the last day of September in the U.K., which means we’re well into meteorological autumn and summer is, at least here, a distant memory. The weather is cooler and the days are getting shorter. Soon, the clocks will go back an hour, and we’ll shift from BST (British Summer Time) to GMT (Greenwich Mean Time).

Seasons in the U.K. are particularly marked because of our northerly latitude. British weather tends to be fairly mild (thanks, Gulf Stream), and it’s easy to forget just how far north we are – but a quick look at a globe makes it clear: London is actually further north than most of the major Canadian cities, while the Polar Bear Provincial Park in Ontario is roughly on the same latitude as Scotland’s capital city, Edinburgh.

Yes, I hear you say, but what on Earth (hoho) does this have to do with chemistry?

Well, a clever little piece of chemistry happens in human skin, and, if you live in the U.K., it’s about to stop. At least, until next spring.

Some clever chemistry happens in human skin.

There’s a substance in your skin called 7-dehydrocholesterol (7-DHC). It is, as the name suggests, something to do with cholesterol (which, despite its bad press, is an essential component of animal cell membranes). In fact, 7-DHC is converted to cholesterol in the body, but it’s also converted to something else.

You will have heard of vitamin D. It helps us to absorb calcium and other minerals, and if children, in particular, don’t get enough it can lead to rickets – which leads to weak bones, bowed legs and stunted growth. Vitamin D deficiency has also been linked to lots of other health problems, including increased risk of certain cancers, heart disease, arthritis and even type one diabetes.

More recently, vitamin D has been linked to COVID-19. It’s estimated that around 80-85% of people who contract COVID-19 experience mild or no symptoms, while the rest develop severe symptoms and, even if they recover, may suffer life-altering after-effects for many months. Early data suggest that patients with low vitamin D levels are much more likely to experience those severe symptoms. There’s a plausible mechanism for this: vitamin D helps to regulate the immune system and, in particular, helps to reduce the production of cytokines.

It’s possible that having inadequate levels of vitamin D may increase your chances of a severe response to COVID-19.

Cytokines are small proteins which are important in cell signalling, but if the body starts to produce too many in response to a virus it can cause something called a cytokine storm, which can lead to organ failure and death.

It’s proposed that having the right levels of vitamin D might help to prevent such cytokine storms, and therefore help to prevent a severe COVID-19 response. This is all early stages, because everyone is still learning about COVID-19, and it may turn out to be correlation without causation, but so far it looks promising.

One thing you many not know is that vitamin D is, technically, misnamed. Vitamins are, by definition, substances which are required in small quantities in the diet, because they can’t be synthesised in the body.

But vitamin D, which is actually a group of fat soluble molecules rather than a single substance, can be synthesised in the body, in our skin. The most important two in the group are ergocalciferol (vitamin D2) and cholecalciferol (vitamin D3), sometimes known collectively as calciferol.

Shiitake mushrooms are a good source of vitamin D2.

Vitamin D2 is found in fungi, but it’s cleared more quickly from the body than D3, so needs to be consumed in some form daily. Mushrooms are a good source (especially if they’ve been exposed to UV light), so if you like mushrooms, that’s one way to go. Vitamin D3 is hard to obtain from diet – the only really good source is oily fish, although other foods are fortified – but that’s okay because, most of the time, we don’t need to eat it.

Which brings us back to 7-DHC. It’s found in large quantities in the skin, although exactly how it gets there has been the subject of some debate. It used to be thought it was formed from cholesterol via an enzymatic reaction in the intestine wall and then transported to the skin via the bloodstream. But the trouble with this idea is that the blood would pass through the liver, and 7-DHC would be reconverted to cholesterol, never having a chance to build up in skin. A more robust theory is it’s actually synthesised in the skin in the first place, particularly since higher levels are found in a layer closer to the surface (the stratum spinosum) than in the deeper dermis.

We make vitamin D in our skin when we’re exposed to UVB light from the sun.

Anyway, the important thing is that 7-DHC absorbs UV light, particularly wavelengths between 290 and 320 nm, that is, in the UVB range, sometimes called “intermediate” UV (in contrast with “soft” UVA, and “hard” UVC). When exposed to UVB light, one of the rings in the 7-DHC molecule breaks apart, forming something known pre-D3, that then converts (isomerises) to vitamin D3 in a heat-sensitive process.

In short, we make vitamin D3 in our skin when we’re in the sunshine. Obviously we need to avoid skin damage from UV light, but the process doesn’t take long: 10-15 minutes of midday sunlight three times a week, in the U.K. in the summer, is enough to keep our levels up.

Sun exposure is by far the quickest, and certainly the cheapest, way to get your vitamin D. If you live somewhere where that’s possible.

Here’s the thing, though, if you live in the U.K., for a chunk of the year, it’s just not. I’ve pinched the graph here from my husband, whose work involves solar panels, because it makes a nice visual point.

The amount of sunlight we’re exposed to in the U.K. drops sharply in autumn and winter.

From April – September, there’s plenty of energy available from sunlight. But look at what happens from October – March. The numbers drop drastically. And here’s the thing: it turns out that vitamin D production in human skin only occurs when UV radiation exceeds a certain level. Below this threshold? Well, no photocoversion takes place.

In short: if you live in the U.K. you can’t make vitamin D in your skin for a few months of the year. And those few months are starting… round about now.

The NILU has a web page where you can calculate how much vitamin D you can synthesise in your skin on a given day.

If you want to experiment, there’s a website here, published by the Norwegian Institute for Air Research (NILU), where you can enter various parameters – month, longitude, cloudiness etc – and it will tell you how many hours during a given a day it’s possible to synthesise vitamin D in your skin.

Have a play and you’ll see that, for London, vitamin D synthesis drops off to zero somewhere around the end of November, and doesn’t restart until sometime after the 20th of January. In Edinburgh, the difference is even more marked, running from the first week or so of November to the first week of February.

It’s important to realise that it tails off, too, so during the days either side of these periods there’s only a brief period during midday when you can synthesise vitamin D. And all this assumes a cloudless sky which in this country… is unlikely.

The skin pigment, melanin, absorbs UVB. (Image Source: Wiki Commons)

The situation is worse still if you have darker skin because the skin pigment, melanin, absorbs UVB. On the one hand, this is a good thing, since it protects skin cells from sun-related damage. But it also reduces the ability to synthesise vitamin D. In short, wimpy autumn and winter sunshine just isn’t going to cut it.

Likewise, to state the obvious, anyone who covers their skin (with clothing or sunblock), also won’t be able to synthesise vitamin D in their skin.

Fortunately, there’s a simple answer: supplements. The evidence is fairly solid that vitamin D supplements increase blood serum levels as well as, if not better than, sunshine – which, for the reasons mentioned above, can be difficult to obtain consistently.

Now, as I’ve said many times before, I’m not a medical doctor. However, I’m on fairly safe ground here, because Public Health England do actually recommend everyone take a vitamin D supplement from October to May. That is, from now. Yes, now.

I do need to stress one point here: DO NOT OVERDO IT. There always seems to be someone whose reasoning goes along the lines of, “if one tablet is good, then ten will be even better!” and, no. No. Excessive doses of vitamin D can cause vomiting and digestive problems, and can lead to hypercalcemia which results in weakness, joint pain confusion and other unpleasant symptoms.

If you live in the U.K. you should be taking a vitamin D supplement from October-May.

Public Health England recommend everyone in the U.K. take 10 micrograms per day in autumn and winter. Babies under one year should also be given 8.5–10 micrograms of vitamin D in the form of vitamin drops, unless they’re drinking more than 500 ml of infant formula a day (because that’s already fortified).

Amounts can get a little confusing, because there are different ways to measure vitamin D doses, and in particular you may see IU, or “international units“. However, if you buy a simple D3 supplement, like this one that I picked up at the supermarket, and follow the dose instructions on the label, you won’t go far wrong.

So, should you (and everyone else in your family) be taking a simple vitamin D supplement right around now? If you live in the U.K., or somewhere else very northerly, then yes. Well, unless you’re really keen to eat mushrooms pretty much every day. At worst, it won’t make much difference, and at best, well, there’s a chance it might help you to avoid a really unpleasant time with COVID-19, and that’s got to be a good thing.

But, look, it’s not toilet roll. Don’t go and bulk buy vitamin D, for goodness sake.

Until next time, take care, and stay safe.


If you’re studying chemistry, have you got your Pocket Chemist yet? Why not grab one? It’s a hugely useful tool, and by buying one you’ll be supporting this site – it’s win-win!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2020. You may share or link to anything here, but you must reference this site if you do. If you enjoy reading my blog, and especially if you’re using information you’ve found here to write a piece for which you will be paid, please consider buying me a coffee through Ko-fi using the button below.
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Chemical connections: dexamethasone, hydroxychloroquine and rheumatoid arthritis

The chemical structure of dexamethasone (image from Wikimedia Commons)

It’s been widely reported today that a “cheap and widely-available” steroid treatment has been shown to be effective in patients suffering the most severe COVID-19 symptoms, significantly reducing the risk of death for both patients on ventilators and those on oxygen treatment.

Most of the reports have understandably focused on the medical aspects, but this is a chemistry blog (mostly) so *cracks chemistry knuckles* what is dexamethasone, exactly?

Its story starts a little over 60 years ago when, in 1958, a paper was published on “clinical observations with 16a-methyl corticosteroid compounds”. Bear with me, I shall explain. Firstly, corticosteroids are hormones which are naturally produced in our bodies. They do all sorts of nifty, useful things like regulate our immune response, reduce inflammation and help us to get energy from carbohydrates. Two of the most familiar names are probably cortisol and cortisone—both of which are released in response to stress.

The discovery of corticosteroids was an important one. So important, in fact, that a few years earlier, in 1950, Tadeusz ReichsteinEdward Calvin Kendall and Philip Showalter Hench had been awarded a Nobel Prize in Physiology and Medicine for “discoveries relating to the hormones of the adrenal cortex”.

The adrenal glands are two small glands found above the kidneys. The outermost part of these glands is called the adrenal cortex (“cortex” from the Latin for (tree) bark and meaning, literally, an outer layer). In the mid-1930s Kendall and Reichstein managed to isolate several hormones produced by these glands. They then made preparations which, with input from Hench, were used in the 1940s to treat a number of conditions, including rheumatoid arthritis.

This was hugely significant at the time, because until this point the treatments for this painful, debilitating condition were pretty limited. Aspirin was known, of course, but wasn’t particularly effective and long-term use had potentially dangerous side effects. Injectable gold compounds (literally chemical compounds containing Au atoms/ions) had also been tried, but those treatments were slow to work, if they worked at all, and were expensive. The anti-malarial drug, hydroxychloroquine (which has also been in the news quite a lot), had been tried as a “remittive agent”—meaning it could occasionally produce remission—but it wasn’t guaranteed.

Rheumatoid arthritis causes warm, swollen, and painful joints (image from Wikimedia Commons)

Corticosteroids were a game-changer. When Hench and Kendall treated patients with what they called, at the time, “compound E” (cortisone) there was a rapid reduction in joint inflammation. It still caused side effects, and it didn’t prevent joint damage, but it did consistently provide relief from painful symptoms.

Fast-forward to the 1958 paper I mentioned earlier, and scientists had discovered that a little bit of fiddling with the molecular structure of steroid molecules caused them to have different effects in the body. The particular chemical path we’re following here started with prednisolone, which had turned out to be a useful treatment for a number of inflammatory conditions. However, placing a methyl group (—CH3) on the 16th carbon—which is, if you have a look at the diagram below, the one on the pentagon-shaped ring, roughly in the middle—changed things.

The steroid “nucleus”: each number represents a carbon atom (image from Wikimedia Commons)

In 1957, four different molecules with methyl groups on that 16th carbon were made available for clinical trial. One of them was 16a-methyl 9a-fluoroprednisolone, more handily known as dexamethasone.

(Quick aside to explain that on the diagram of dexamethasone at the start of this post, the methyl group on the 16th carbon is represented by a dashed wedge-shape. It’s a 2D diagram of a 3D molecule, and the dashed wedge tells us that the methyl group is pointing away from us, through the paper, or rather, screen. This matters because molecules like this have mirror image forms which usually have very different effects in the body—so it’s important to get the right one.)

Dexamethasone is on the WHO Model List of Essential Medicines

It turned out that dexamethasone had a much stronger anti-inflammatory action than plain prednisolone, and it was also more effective the other molecules being tested. It caused a bigger reduction in symptoms, at lower doses. A win all round. It did still have side effects—weight gain, skin problems and digestive issues—but these were no worse than other steroids, and better than some. In fact, salt and water retention were less with dexamethasone, which meant less bloating. It also seemed to have less of an effect on carbohydrate metabolism, making it potentially safer for patients with diabetes.

Skipping forward to 2020, and dexamethasone is routinely used to treat rheumatoid arthritis, as well as skin diseases, asthma, COPD and various other conditions. It is on the WHO Model List of Essential Medicines—a list of drugs thought to be the most important for taking care of the health needs of the population, based on their effectiveness, safety and relative cost.

In the wake of more and more evidence that COVID-19 disease was leading to autoimmune and autoinflammatory diseases, scientists have been looking at anti-inflammatory drugs to see if any of them might help. The Recovery Trial at the University of Oxford was set up to investigate a few different drugs, including hydroxychloroquine (there it is again) and dexamethasone.

It’s not a miracle cure but, in the most severe cases, dexamethasone—a cheap, 60+ year old drug—might just make all the difference.

And that brings us back to today’s news: in the trial, 2104 patients were given dexamethasone once per day for ten days and compared to 4321 patients who were given standard care. The study, led by Professor Peter Horby and Professor Martin Landray, showed that dexamethasone reduced the risk of dying by one-third in ventilated patients and by one fifth in other patients receiving only oxygen.

It’s not a miracle cure by any means: it doesn’t help patients who don’t (yet) need respiratory support, and it doesn’t work for everyone, but, if you find yourself on a ventilator, there’s a chance this 60+ year-old molecule that was first developed to cure rheumatoid arthritis might, just, save your life. And that’s pretty good news.

EDIT 17th June 2020: Chemistry World published an article pointing out that “the trial results have yet to be released leading some to urge caution when interpreting them” and quoting Ayfer Ali, a specialist in drug repurposing, as saying “we have to wait for the full results to be peer reviewed and remember that it is not a cure for all, just one more tool.


If you’re studying from home, have you got your Pocket Chemist yet? Why not grab one? It’s a hugely useful tool, and by buying one you’ll be supporting this site – it’s win-win!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2020. You may share or link to anything here, but you must reference this site if you do. If you enjoy reading my blog, and especially if you’re using information you’ve found here to write a piece for which you will be paid, please consider buying me a coffee through Ko-fi using the button below.
Buy Me a Coffee at ko-fi.com

Want something non-sciency to distract you from, well, everything? Why not check out my fiction blog: the fiction phial.