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!

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Rhubarb rhubarb rhubarb

rhubarb‘Tis the season for rhubarb.  I know this because my Dad, who is a professional grower of green stuff, brought me some last week.  Sadly I didn’t inherit his green thumb (and fingers, and probably toes) but I can knock up a half decent rhubarb crumble*, and I can make custard from scratch.  Yes really, no packet or anything.  Impressive eh?

But anyway, Dad suggested we might grow rhubarb in our garden, since we have a shady, slightly soggy patch of ground near the house where, apparently, it might do well even with my appalling track record of plant abuse and neglect.  (If there were a Royal Society for the Protection of Plants, trust me I’d be top of their most wanted list.)  This led me to to some musings about safety, since we have both a cat and a small person in the house.  I vaguely recalled that the leaves were poisonous, and Dad confirmed that this particular piece of information wasn’t merely a product of my fevered brain, but was in fact correct.

“So what’s in rhubarb leaves then?” Asked Dad.

“Erm, oxalic acid I think…” I said.  And it occurred to me, before the inevitable “what’s that then?” question, that I didn’t actually know very much about oxalic acid.

Oxalic acid fire diamondSo being a motivated learner, I went and looked it up.  The first thing that drew my eye was its fire diamond.  That description conjures up images of impressive gemstones, but sadly it’s not quite that cool.  Fire diamonds are those red, blue, yellow and white diamonds that you see on the side of big chemical containers.  They’re useful because they summarise the key safety and hazard information at a glance, without anyone needing to mess about reading text on a warning label or having to find a knowledgable, if slightly hysterical, scientist to explain the dangers in the middle of a disaster.

The first thing you need to know about these diamonds is that 0 is pretty safe, and 4 is very bad.  As for the colours: blue is for health and basically covers toxicity, yellow is for reactivity (is it likely to explode or generally do something unpleasant and probably loud), red is predictably for flammability and white is for ‘special’.  Special in this case meaning, ‘does something else nasty’.

The 3 in the blue bit means oxalic acid is pretty toxic. Chlorine gas has a 3, as does pure ammonia.  The official description is “short exposure could cause temporary incapacitation or possible residual injury”.  Eeek.

oxalic acid moleculeSo is it time to put child-safe locks on your rhubarb patch?  It’s probably not necessary.  Rhubarb leaves have roughly 0.5% oxalic acid by weight.  There are various lethal doses mentioned out there, but even the more conservative is about 0.6 g per kg of body weight.  A small child, weighing say 10 kg, would need to consume about 6 g of oxalic acid, or about 1.2 kg of rhubarb leaves to receive a lethal dose.  There are other harmful things in rhubarb leaves, of which more later, so they might be quite a bit more dangerous than this implies, but even a determined toddler probably isn’t going to much their way through enough of the pretty horrible-tasting leaves to give them more than a tummy ache.  Still, I don’t recommend you leave them to experiment.

There is, in fact, also a bit of oxalic acid in the petioles (the stalks), but not very much.  Most of the acidity in the stalks is due to malic acid, which turns up all over the place (it’s one of those mysterious ‘fruit acids’ beloved of skincare product manufacturers) and is fairly harmless.  Cooking helps to break it down what tiny bit of oxalic acid is present, but it’s such a small quantity that even if you ate nothing but raw rhubarb stalks it probably wouldn’t be dangerous.  The occasional crumble certainly isn’t going to be a worry.  And, I checked, a little bit of stewed rhubarb is safe for babies.

Why is oxalic acid (in largish quantities) poisonous?  It’s not because it’s an acid; as I’ve mentioned before, lots of things are acids and are pretty harmless.  It turns out that oxalic acid is nephrotoxic, which means it damages your kidneys.  Oxalic acid reacts with iron and calcium ions in the body to form crystals which are then excreted in urine.  This is bad for two reasons, firstly it’s removing calcium and iron from the body, and they’re both quite important.  Secondly calcium oxalate is the main component of kidney stones, which are at best agonisingly painful and at worst can cause a nasty infection if they block the urinary tract.  It can also cause joint pain because similar precipitates form in the joints.  Interestingly, ethylene glycol (used in antifreeze) will produce oxalic acid in the body if you drink it (not recommended), so can generate the same kinds of problems.

The salt of oxalic acid is oxalate, remember that
acid + base –> salt + water
which is why the word oxalate keeps cropping up.  Oxalates turn up in lots of other foods as well as rhubarb, including parsley, spinach, and tea.  They’re not harmful in the quantities usually eaten, and the plants invariably contain all kinds of other beneficial nutrients that more than make up for the presence of a bit of oxalate.  Still, best not to go all Popeye and try to live off spinach.

During World War I rhubarb was briefly recommended as a vegetable, and this led to some deaths.  This mistake might have been caused when the gardener of the Earl of Shrewsbury at Alton Towers (now home of the theme park) had a letter published in Gardeners Chronicle some decades before which said that rhubarb leaves had been used as a food there for many years.  He apparently later wrote again to say he meant the stalks, and the correction was published, but by then the information was out there in print and perpetuated.  These days it would be so much easier wouldn’t it?  Someone could just write one of those “FORWARD THIS TO ALL YOUR FRIENDS NOW!!!!!!” emails and the information would be round the world in a flash.

As I mentioned earlier it’s not just oxalic acid in rhubarb leaves that’s dangerous, although exactly why the leaves are so toxic doesn’t seem to be well understood.  It might be anthraquinones, ring-shaped molecules used to make dyes and in paper-making.  There is definitely more to the story than oxalic acid, because post mortems of some of deaths supposedly due to rhubarb leaves didn’t find lethal quantities of oxalic acid.

rhubarb leavesIt’s possible that some of these cases weren’t  entirely due to the leaves themselves, but something on them such as a pesticide (bearing in mind that some quite scary things have been chucked around as pesticides in times gone by, with little if any controls).  Rhubarb leaves have a large surface area and are slightly cone-shaped, and it’s not beyond the realms of possibility that something harmful could accumulate in them and then be eaten.  As far as I can establish, no one has carried out a recent study on the toxicity of rhubarb leaves (if you know differently, please let me know!) so it’s difficult to be sure.

So there we have it.  Rhubarb leaves contain oxalic acid, and it’s toxic, so don’t eat them.  Your pets are likely to be safe since, as most gardeners will tell you, few animals will willingly eat rhubarb leaves.  Children are also unlikely to try munching the huge green leaves, but it might be wise to keep an eye on them.  The stalks, on the other hand, make delicious crumble.  And look out for fire diamonds.

And what do you know, I posted this and then caught up with today’s episode of Pointless, and oxalic acid was a pointless answer in the first round.  What are the chances of that?  I love Pointless.

* Handy rhubarb hint: if you don’t want to use extra sugar, or should I say sucrose, add a chopped and peeled apple and banana to your rhubarb – it sweetens it up nicely.  I’m not giving up my custard recipe.  Sorry.