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!


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Puzzling pool problems?

We’re half way thorough the Rio 2016 Olypics, and it will have escaped no one’s notice that there have been a few little problems with one of the pools.

Maria Lenk Aquatic Enter, Tuesday, Aug. 9, 2016. (AP Photo/Matt Dunham)

Maria Lenk Aquatic Enter, Tuesday, Aug. 9, 2016. (AP Photo/Matt Dunham)

First, the water turned a mysterious green colour. Then there were reports of a ‘sulfurous’ smell, with German diver Stephan Feck reported as saying it smelled like a “fart”.

The diving pool seemed to be the worst affected, but the water-polo pool next to it also suffered problems, and competitors complained of stinging eyes.

So what on earth was happening? An early suggestion was that copper salts were contaminating the water. It’s not unheard of for copper compounds to get into water supplies, and it would certainly explain the colour; copper chloride solutions in particular are famously greeny-blue. But what about that sulfurous smell? Copper chloride doesn’t smell of sulfur.

Was the strange pool colour due to algae bloom?

Was the strange pool colour due to an algae bloom, like this one in Lake Erie?

The most likely culprit was some sort of algae bloom – in other words rapid algae growth – with the smell probably coming from dimethyl sulfide, or DMS. There’s a singled-celled phytoplankton called Emiliania huxleyi which is particularly famous for producing this smelly compound. In fact, it actually has more than one very important role in nature: the smell is thought to alert marine life that there’s food nearby, but it also seeps into the atmosphere and helps with cloud formation, helping to control our planet’s temperature. Without these reactions, Earth might not be nearly so habitable.

But how did algae manage to grow in the pool? The pool chemicals should have prevented it, so what had happened? An Olympic official then went on to make the comment that “chemistry is not an exact science,” which of course led to much hilarity all around. Chemistry is, after all, incredibly exact. What chemistry student doesn’t remember all those calculations, with answers to three significant figures? The endless balancing of equations? The careful addition of one solution to another, drop by drop? How much more ‘exact’ would you like it to be?

But I had a bit of sympathy with the official, because I suspect that what they actually meant – if not said – was that swimming pool chemistry is not an exact science. And while that, too, is hardly accurate, it is true that swimming pool chemistry is very complicated and things can easily go wrong, particularly when you’re trying to work on an extremely tight schedule. They could hardly, after all, close down all the pools and spend several days carrying out extensive testing in the middle of the sixteen-day-long Olympic Games.

Rio 2016 Olympics Aquatics Stadium (Image: Myrtha Pools)

Rio 2016 Olympics Aquatics Stadium (Image: Myrtha Pools)

When a pool is first built and filled, things are, theoretically, simple. You know exactly how many cubic litres of water there are, and you know exactly how much of each chemical needs to be added to keep the water free of bacteria and other nasties. Those chemicals are added, possibly (particularly in a pool this size) via some kind of automated system, and the pH is carefully monitored to ensure the water is neither too alkaline (basic) nor too acidic.

There’s a certain amount of proprietary variation of swimming pool chemicals, but it essentially all comes down to chlorine, which has been used to make water safe now for over 120 years.

Originally, water was treated to make it alkaline and then chlorine gas itself was added. This produced compounds which killed bacteria, in particular sodium hypochlorite, but the practice was risky. Chlorine gas is extremely nasty stuff – it has, after all, been used as a chemical weapon – and storing it, not to mention actually using it, was a dangerous business.

However, hundreds of people swimming in untreated water is a recipe for catching all kinds of water-borne disease, so it wasn’t long before alternatives were developed.

The Chemistry of Swimming Pools (Image: Compound Interest - click for more info)

The Chemistry of Swimming Pools (Image: Compound Interest – click graphic for more info)

Those alternatives made use of the chemistry that was happening anyway in the water, but  allowed the dangerous bit, with the elemental chlorine, to happen somewhere else. And so hypochlorite salts began to be manufactured to be used in swimming pools.

As the lovely graphic from Compound Interest illustrates, sodium hypochlorite reacts with water to form hypochlorous acid, which in turn goes on to form hypochlorite ions. These two substances sit in an equilibrium, and both are oxidants, which is good because oxidants are good at blasting bacteria. The equilibria in question are affected by pH though, which is one reason why, quite apart from the potential effects on swimmers, it’s so important to manage the pH of pool water.

There are a couple of different chemicals which can be added to adjust pH. Sodium bicarbonate, for example, can be used to nudge the pH up if needed. On the other hand, sodium bisulfate can be used to lower pH if the water becomes too alkaline.

Open-air pools have particular problems

UV light breaks down the chemicals that are used to keep swimming pool water clean.

This can all be managed extremely precisely in an unused, enclosed pool. But once you open that pool up, things become less simple. Open-air pools have a particular problem with UV light. Chlorine compounds are often sensitive to UV – this is why CFCs are such a problem for the ozone layer – and hypochlorite is no exception. In the presence of UV it breaks down in a process called photolysis to form chloride ions and oxygen. This means that outdoor pools require more frequent treatments, or the addition of extra chemicals to stabilise the ‘free available chlorine’ (FAC) levels.

Sadly, I haven’t managed to make it over to Rio, but from what I’ve seen the Aquatic Centre has a roof which opens up, which means that the pool water is indeed being exposed to UV light.

So perhaps the chemical levels simply dropped too low, which allowed algae to proliferate? Possibly aggravated by environmental conditions? Indeed, initially this seemed to be the explanation. FINA, the international governing body of aquatics, issued a statement on Wednesday afternoon which said:

“FINA can confirm that the reason for the unusual water color observed during the Rio diving competitions is that the water tanks ran out of some of the chemicals used in the water treatment process. As a result, the pH level of the water was outside the usual range, causing the discoloration. The FINA Sport Medicine Committee conducted tests on the water quality and concluded that there was no risk to the health and safety of the athletes, and no reason for the competition to be affected.”

This prompted people to wonder how on earth chemical levels were allowed to run out in an event as significant as the Olympics – did someone forget to click send on the order? – but still, it seemed to explain what had happened.

FINA issued a new statement

FINA issued a new statement on Sunday

Until today (Sunday), when more information surfaced as Olympic officials announced that they were going to drain at least one of the swimming pools and refill it. This is no small feat and will involve considerable cost: after all, we’re talking about millions of gallons of water. But it seems to be necessary. As Rio 2016’s director of venue management Gustavo Nascimento said:

“On the day of the Opening Ceremonies of the Games, 80 litres of hydrogen peroxide was put in the water. This creates a reaction to the chlorine which neutralises the ability of the chlorine to kill organics. This is not a problem for the health of anyone.”

Whoops. Yes indeed. Hydrogen peroxide reacts with chlorine to produce oxygen and hydrochloric acid. In fact, hydrogen peroxide is actually used to dechlorinate water which contains levels of chlorine that are too high. It might not be the very worst thing you could add to the water (when you think of all the things that could end up swimming pools) but it’s definitely up there.

Why and how this happened doesn’t, at the moment, appear to be clear. Presumably someone is for the high jump, and not just on the athletics field.

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