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.
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.

 

One Flash of Light, One Vision: Carrots, Colour and Chemistry

“White” light is made up of all the colours of the rainbow.

Sometimes you have one of those weeks when the universe seems to be determined to yell at you about a certain thing. That’s happened to me this week, and the shouting has been all about light and vision (earworm, anyone?).

I started the week writing about conjugated molecules and UV spectrometry for one project, was asked a couple of days ago if I’d support a piece of work on indicators for the RSC Twitter Poster Conference that’s happening from 2-3rd March, and then practically fell over a tweet by Dr Adam Rutherford about bacteria that photosynthesise from infrared light in a hydrothermal vent*.

Oh well, who am I to fight the universe?

Light is awesome. The fact that we can detect it is even awesome-er. The fact that we’ve evolved brains clever enough built all sorts of machines to measure other kinds of light that our puny human eyes cannot detect is, frankly, astonishing.

The electromagnetic spectrum covers all the different kinds of light. (Image source)

Let’s start with some basics. You probably met the electromagnetic (EM) spectrum at some point in school. Possibly a particularly enthusiastic physics teacher encouraged you to come up with some sort of mnemonic to help you remember it. Personally I like Rich Men In Vegas Use eXpensive Gadgets, but maybe that’s just me.

The relevant thing here is that the EM spectrum covers all the different wavelengths of light. Visible light, the stuff that’s, well, visible (to our eyes), runs from about 400 to 700 nanometres.

A colour wheel: when light is absorbed, we see the colour opposite the absorbed wavelengths. (Image source)

Now, we need another bit of basic physics (and biology): we see light when it enters our eyes and strikes our retinas. We see colours when only certain wavelengths of light make it into our eyes.

So-called “white” light is made up of all the colours of the rainbow. Take one or more of those colours away, and we see what’s left.

For example, if something looks red, it means that red light made it to our eyes, which in turn means that, somewhere along the way, blue and green were filtered out.

(Before I go any further, there are actually several causes of colour, but I’m about to focus on one in particular. If you really want to know more, there’s this book, although it is a tad expensive…)

Back to chemistry. Certain substances absorb coloured light. We know them as pigments. Carrots are orange, for example, largely because they contain a pigment called beta-carotene (or β-carotene). This stuff appears, to our eyes, as red-orange, and the reason for that is that it absorbs green-blue light, the wavelengths around 400-500 nm.

β-Carotene is a long molecule with lots of C=C double bonds. (Image source.)

Why does it absorb light at all? Well, β-carotene is a really long molecule, with lots of C=C double bonds. These bonds form what’s called a conjugated system. Without getting into the complexities of molecular orbital theory, that means the double bonds alternate along the chain, and they basically overlap and… smoosh into one long thing. (Look, as the saying goes, “all models are wrong, but some are useful,” – it’ll do for now.)

When molecules with conjugated systems are exposed to electromagnetic light, they absorb it. Specifically, they absorb in the ultraviolet region – the wavelengths between about 200 and 400 nanometres. Here’s the thing, though, those wavelengths are right next to the violet end of the visible spectrum – that’s why it’s called ultraviolet after all.

Molecules with really long conjugated systems start to absorb in the coloured light region, as well. And because they’re absorbing violet and blue, possibly a smidge of green, they look… yup! Orangey, drifting into red.

So now you know why carrots are orange. Most brightly coloured fruit, of course, is that way to attract animals and birds to eat it, and thus spread its seeds. As fruit ripens, it usually changes colour, making it stand out better against green foliage and easier to find. This is the link with indicators that I mentioned at the start: many fruits contain anthocyanin pigments, and these often have purple-red colours in neutral-acidic environments, and yellow-green at the more alkaline end. In other words, the colour change is quite literally an indicator of ripeness.

But the bit of the carrot that we usually eat is underground, right? Not particularly easy to spot, and they don’t contain seeds anyway. Why are carrots bright orange?

Modern carrots are mostly orange, but purple and yellow varieties also exist.

Well, they weren’t. The edible roots of wild plants almost certainly started out as white or cream-coloured, as you might expect for something growing underground, but the carrots which were first domesticated and farmed by humans in around 900 CE were, most probably, purple and yellow.

As carrot cultivation became popular, orange roots began to appear in Spain and Germany in the 15th/16th centuries. Very orange carrots, with high levels of β-carotene, appeared from the 16th/17th centuries and were probably first cultivated in the Netherlands. Some have theorised that they were particularly selected for to honour William of Orange, but the evidence for this seems to be a bit slight. Either way, most modern European carrots do descend from a variety that was originally grown in the Dutch town of Hoorn.

In other words, brightly-coloured carrots are a mutation which human plant breeders selected for, probably largely for appearances.

But wait! There was an advantage for humans, too – even if we didn’t realise it straight away. β-carotene (which, by the way, has the E number E160a – many natural substances have E numbers, they’re nothing to be frightened of) is broken up in our intestines to form vitamin A.

Vitamin A is essential for good eye health.

Vitamin A, like most vitamins, is actually a group of compounds, but the important thing is that it’s essential for growth, a healthy immune system and – this is the really clever bit – good vision.

We knew that. Carrots help you see in the dark, right?

Hah. Well. The idea that carrot consumption actually improves eyesight seems to be the result of a World War II propaganda campaign. During the Blitz, the Royal Air Force had (at that time) new, secret radar technology. They didn’t want anyone to know that, of course, so they spread the rumour that British pilots could see exceptionally well in the dark because they ate a lot of carrots, when the truth was that those pilots were actually using radar.

But! It’s not all a lie – there is some truth to it! Our retinas, at the back of our eyes, have two types of light-sensitive cells. Cone cells help us distinguish colours, while rod cells help us detect light in general.

In those rod cells, a molecule called 11-cis-retinal is converted into another molecule called rhodopsin. This is really light-sensitive. When it’s exposed to light it photobleaches (stops being able to fluoresce), but then regenerates. This process takes about thirty minutes, and is a large part of the reason it takes a while for your eyes to “get used to the dark.”

Guess where 11-cis-retinal comes from? Yep! From vitamin A. Which is why one of the symptoms of vitamin A deficiency is night blindness. So although eating loads of carrots won’t give you super-powered night vision, it does help to maintain vision in low light.

Our brain interprets electrical signals as vision.

How do these molecules actually help us to see? Well, when rhodopsin is exposed to light, the molecule changes, which ultimately results in an electrical signal being transmitted along the optic nerve to the brain, which interprets it as vision!

In summary, not only is colour all about molecules, but our whole visual system depends on some clever chemistry. I told you chemistry was cool!

Just gimme fried chicken 😉


*Ah. I sort of ran out of space for the weird hydrothermal bacteria thing. At least one of the relevant molecules seems to be another carotenoid, probably chlorobactene. The really freaking amazing thing is that there seems to be an absorption at 775 nm, which is beyond red visible light and into the infrared region of the EM spectrum. Maybe more on this another day…


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.
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.

 

Is there NO way to stop COVID-19?

UK trials have begun of a nasal spray that could prevent COVID-19 infections

A few weeks ago, it was announced that UK trials were beginning of a nasal spray proven to kill 99.9% of the coronavirus that causes COVID-19. The idea, broadly, is that you’d use the spray first thing in the morning, during the day after social interactions, and then again in the evening — and it would prevent the virus from taking hold and making you ill.

Awesome, right? Simple, cheap, portable. Sort of like cleaning your teeth regularly: prevention rather than cure. Combined with a vaccine, particularly for anyone at high risk such as those in healthcare settings, it could put a stop to the whole thing — and might also turn out to be effective on other, less deadly but still annoying, viruses.

But, I hear you ask, what is it? Because if I’m going to squirt something up my nose several times a day, I have questions…

Nitric oxide has the chemical formula NO

Fair enough. It’s actually, mostly, nitric oxide, which has the chemical formula NO.

Yes, there are plenty of wordplay options here. The researchers have already jammed the letters NO into their company name, and done the acronym thing, to get SaNOtize Nitric Oxide Nasal Spray (NONS). If the trials are successful, it’s probably only a matter of time before we get: “Say NO to coronavirus!” marketing. (Any ad agencies reading this, I’m claiming copyright.)

But that aside, unless you’re a chemist you might be thinking about some half-remembered chemical names and frowning at this point. Isn’t that… used in rocket fuel? Or… wait… isn’t that… the nasty smoggy stuff that causes lung problems?

Ah, well, there are several nitrogen oxides. Let me summarise:

Nitric oxides in the atmosphere cause photochemical smog.

There are other nitrogen oxides, not to mention ions — but let’s not spend all day on this. Nitrogen forms this confusing hodgepodge of oxides because it has five electrons in its outermost shell (it’s in group 15 of the periodic table) and because there’s not much difference in the electronegativities of oxygen and nitrogen. So essentially, it can share electrons with oxygen to form bonds in a number of different ways to obtain a stable, full outer shell.

For any students reading this, I’m sorry. You… pretty much just have to remember these. Yes, I know. That’s why experienced chemists so often use the shorthand NOx — we just can’t be bothered keeping all the names straight. (Okay, before someone shouts at me, actually NOx is handy because we’re often talking about more than one oxide at a time, and it allows us to easily express that.)

Back to NO. It’s a colourless gas, and it has an unpaired electron, which makes it a free radical. And… here we go again. Aren’t we supposed to eat lots of antioxidant-rich fruit and vegetables to mop up free radicals? They’re bad, aren’t they?

Viagra (Sildenafil) makes use of the nitric oxide pathway which causes blood vessels to dilate…

Yes and no. Free radicals are reactive species which damage cells and can cause illness and ageing. Too much exposure to free radicals causes something oxidative stress, which is definitely bad. But. It turns out that nitrogen oxide is an important signalling molecule, that is, a molecule which is the body uses to send chemical signals from one place to another. In particular, nitrogen oxide “tells” the smooth muscle around blood vessels to relax, causing those blood vessels to dilate, and increasing blood flow. Viagra (aka Sildenafil) uses the nitric oxide pathway, and I think we all know what that does, don’t we? Good.

Nitric oxide has also been shown to reduce blood pressure, which is generally considered a good thing — up to a point, obviously. This is why you can buy lots of so-called nitric oxide supplements, which, since nitrogen oxide is a gas at room temperature, don’t actually contain nitric oxide on its own. Rather, they’re a mixture of amino acids and other things that supposedly help the body to make NO. But it might be cheaper, and healthier, to eat plenty of beetroot or drink beetroot juice, since there’s evidence that does the same sort of thing.

As always, the dose makes the poison. Too much nitric oxide is definitely problematic, but administered in the right way and in appropriate doses, it’s extremely safe.

It’s suggested that the nitric oxide in the SaNOtize nasal spray destroys the virus and also helps to stop viral replication within cells. Plus, it blocks the receptors that the virus uses to enter cells in the first place. Essentially, it locks the doors and rains down fire on the potential intruders — nice work.

You only need to use the spray occasionally, because developing a COVID-19 infection isn’t instant. First the virus gets into your nose, then it attaches to cells, then it replicates, and then it sheds into your lungs. There are timescales involved here — so long as the spray is used every so often it should do the trick.

Another advantage is that this should, theoretically, work on other strains — where the current vaccines may not. So it could provide a very important stopgap when vaccination isn’t immediately available.

This is only in the early stages of clinical trials so, for now, wear your mask.

All sounds fabulous, doesn’t it? It might be, but, we’re in the early stages with this. Clinical trials have now started in the UK, are already in Phase II in Canada and have been approved to start in the USA. Researchers are hopeful, but we need to wait for the evidence.

So in the meantime, wear a mask, wash your hands, and take a vaccine if you’re offered one. Stay safe out there!


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.
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.

 

 

Colour me! STEM Heroes colouring book

Someone reminded me the other day of a podcast I hosted in January 2020, in which I hoped that 2020 would bring everyone lots of good things.

Well, if nothing else, we’ve proved that I definitely don’t have prophetic abilities, eh?

But 2020 hasn’t been all unpleasantness. There have been some bright spots, and I’m about to tell you about one! Back in November the science historian and writer, Dr Kit Chapman (@ChemistryKit), tweeted:

“If I were to commission a colouring book of scientists as heroes/villains (they get to pick what they want to be shown as – superheroes, princesses, wizards etc), would you be up for being a model? Colouring book would be free for all. Just a charity thing for inspiring kids.”

Now, how cool is that idea? Kit set up a GoFundMe which raised (as I write this) over £300, and also sourced twenty different STEM “heroes” to feature in the colouring book. His goal was to ensure multiple ethnicities, gender identities and body types were represented, as well as members of the LGBTQ+ and disabled communities and scientists with mental health disorders. In other words: science is for everyone.

Kit is a science writer (a really good one, read his book) so, of course, he had to include at least one science writer in the book, luckily for me!
 My colouring page is Discworld-themed, because of course it is. It’s based on the Alchemists’ Guild, which on the Disc is… quite an exciting place. To quote a conversation between dwarf Cheery Littlebottom and Sam Vimes in the 19th Discworld book, Feet of Clay:

‘I was quite good at alchemy.’
‘Guild member?’
‘Not any more, sir.’
‘Oh? How did you leave the guild?’
‘Through the roof, sir. But I’m pretty certain I know what I did wrong.’

Like Cheery, I no longer work in a lab, but I do very much enjoy writing about horrible smells, scary acids and everyday chemistry.

You can download a full-size, high-resolution version of my colouring page from here, and you can download the entire book in one go, too — that should keep everyone busy in these slow days between Christmas and New Year!

If you do colour a page — any of them — please come and share it with me: @chronicleflask on Twitter.

I won’t say Happy New Year because, well, that didn’t work out so well last time. So, instead, let’s go with happy end of 2020!

See you all soon and remember, if you’re setting fire to a pudding, do keep it away from the curtains.


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 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.

Onerous ovens: why is cleaning the cooker such a chore?

As I write Thanksgiving was a few days ago, when most Americans traditionally cook a very large meal based around roasted turkey. Most Brits – and other countries of course – have the same thing coming up soon in the form of Christmas, and there are lots of other celebrations around this time of year that seem to feature cooking and food quite heavily.

Whatever your traditions, then, it’s a time when many of us frown critically at the dark, sticky depths of our oven and wonder if, perhaps, we should attempt to give it a clean. Or at least pay someone else to come and clean it.

Why is oven cleaning such a difficult and unpleasant job, anyway? It’s not that hard to clean other surfaces, is it? Why are ovens so particularly awful?

Well, to explain this, we first need to understand fats.

Fats vaporise during cooking.

Most of the grime in your oven is fat, combined with the carbonised remains of… something or other. The sorts of fats that are common in animal and plant products have boiling points around the 300 oC mark (animal fats typically having higher values than plant oils), but they start to form vapours at much lower temperatures, and certainly at typical cooking temperatures there’s plenty vaporised oil around. Besides, under typical conditions most oils will “smoke” – i.e. start to burn – long before they get close to boiling.

We’re all familiar with the idea that fats don’t mix well with water, and herein lies the problem: all that fatty gloop that’s stuck to the inside of your oven just doesn’t want to come off with standard cleaning methods, particularly when it’s built up over time.

Can chemistry help us here? What are fats, chemically? Well, they’re esters. Which may or may not mean anything to you, depending on how much chemistry you can remember from school. But even if you don’t remember the name, trust me, you know the smell. In particular, nail polishes and nail polish removers contain the simple ester known as ethyl acetate, otherwise known as ethyl ethanoate. (Some people say this chemical smells like pear drops which… only really helps if you know what pear drops smell like. Look, it smells of nail polish, okay?)

Fats are esters (image source)

Anyway, the point is that esters have a particular sequence of atoms that has a carbon bonded to an oxygen, which is bonded to another carbon, which is in turn double-bonded to oxygen. This is a bit of a mouthful, so chemists often write it as COOC. In the diagram here, oxygen atoms are red while carbon atoms are black.

There are actually three ester groups in fat molecules – which explains why fats are also known as triglycerides.

In terms of general chemistry, esters form when a carboxylic acid (a molecule which contains a COOH group) reacts with an alcohol (a molecule that contains an OH group). And this is where it all starts to come together – honest – because you’ve probably heard of fatty acids, right? If nothing else, the words turn up in certain food additive names, in particular E471 mono- and diglycerides of fatty acids, which is really common in lots of foods, from ice cream to bread rolls.

Glycerol is a polyol — a molecule that contains several alcohol groups (image source)

Well, this reaction is reversible, and as a result fats (which are esters, remember) break up into fatty acids and glycerol – which is a polyol, that is, a molecule with several alcohol groups. Or, to look at it the other way around: fats are made by combining fatty acids with glycerol.

And the reason it’s useful to understand all this is that the way you break up esters, and therefore fat, is with alkalis. (Well, you can do it with acid, too, but let’s not worry about that for now.)

Strong alkalis break up fats in a chemical reaction called hydrolysis — the word comes from the Greek for water (hydro) and unbind (lysis) and so literally means “split up with water”. Humans have known about this particular bit of chemistry for a long time, because it’s fundamental to making soap. As I said a few months ago when I was banging on about hand-washing, the ancient Babylonians were making soap some 4800 years ago, by boiling fats with ashes – which works because alkaline compounds of calcium and potassium form when wood is burnt at high temperatures.

The grime in ovens is mostly fat.

The really clever thing about all this is that two things are happening when we mix alkali with fat: not only are we breaking up the fat molecules, but also the substances they break up into are water-soluble (whereas fats, as I said at the start, aren’t). Which makes them much easier to clean away with water. Obviously this is the very point of soap, but it’s also handy when trying to get all that baked-on gunk off your oven walls.

Now, in theory, this means you could get some lye (aka sodium hydroxide, probably), smear it all over your oven and voilà. But I don’t recommend it, for a few reasons. Firstly, it’s going to be difficult to apply, since sodium hydroxide is mostly sold as pellets or flakes (it’s pretty easy to buy, because people use it to make soap).

Sodium hydroxide, sometimes called lye, is often sold in the form of pellets.

But, you say, couldn’t I just dissolve it in water and spray or spread it on? Yes, yes you could. But it gets really, really hot when you mix it with water. So you need to be incredibly careful. Because, and this is my next point, chemically your skin is basically fat and protein, and this reaction we’re trying to do on oven sludge works equally well on your skin. Only, you know, more painfully, and with scarring and stuff. In short, if you’re handing lye, wear good nitrile on vinyl gloves and eye protection.

Actually, regardless of how you’re cleaning your oven you should wear gloves and eye protection, because the chemicals are still designed to break down fats and so… all of the above applies. It’s just that specially-designed oven cleaners tend to come with easier (and safer) ways to apply them. For example, they might come as a gel which you can paint on, and/or with bags that you can put the racks into, and may also be sold with gloves and arm protectors (but rarely goggles – get some separately). They might also have an extra surfactant, such as sodium laureth sulfate, added to help with breaking down grease. The main ingredient is still either potassium hydroxide or sodium hydroxide, though.

Well, possibly, but also not really, if you’re sensible.

As an aside, it makes me smile when I come across an article like this which talks about the “serious” chemicals in oven cleaners and more “natural” ways to clean your oven. The “natural” ways are invariably weak acids or alkalis such as lemon juice or baking soda, respectively. They’re essentially ineffective ways of trying to do exactly the same chemistry.

And okay, sure, the gel and the bag and so on in the modern kits are newer tech, but the strong alkali? Nothing more natural than that. As I said at the start, humans have literally been using it for thousands of years.

A point which really cannot be repeated enough: natural does not mean safe.

Fumes can be irritating to skin, eyes and lungs.

Speaking of which, you will get fumes during oven cleaning. Depending on the exact cleaning mixture involved, these will probably be an alkaline vapour, basically (haha) forming as everything gets hot. Such vapour is potentially irritating to skin, eyes and lungs, but not actually deadly toxic. Not that I recommend you stick your head in your freshly-scrubbed oven and inhale deeply, but you take my point. It might give food a soapy, possibly bitter (contrary to what’s stated in some text books, not all alkalis taste bitter, but do not experiment with this) taste if you really over-do it.

In short, if you’re cleaning your oven yourself: follow the manufacturer’s instructions, make sure your kitchen is well-ventilated, leave the oven door open for a while after you’ve finished and, to be really sure, give all the surfaces an extra wash down with plenty of water.

Put the cleaning off until January – after all, the oven’s only going to get dirty again.

And that’s… it, really. Whether you’re cleaning your own oven or getting someone else to do it for you, the chemistry involved is really, really old. And yes, the chemicals involved are hazardous, but not because they’re not “natural”. Quite the opposite.

Or you could just leave it. I mean, it’s only going to get dirty again when you cook Christmas dinner, right?


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

Monstrous Moles: Happy Mole Day!

Happy Mole Day! It’s the 23rd of October and, at least where I am right now, it’s still between 6:02 am and 6:02 pm, so that means it’s time for chemists to celebrate! Of course, I’m in the U.K., so the date thing doesn’t quite work — for me this is 23/10, not 10/23 — but since there are only 12 months in a year (even in 2020) the British system is a bit unsatisfactory, so I’ll go with the American date format for the day.

There are literally loads of atoms in everything

What’s a mole? Well, to paraphrase Douglas Adams: atoms are small. You just won’t believe how vastly, hugely, mind-bogglingly small they are. I mean, you may think the latest incarnation of the walnut whip is small, but that’s just peanuts to atoms. Or even walnuts.

There are literally loads and loads of atoms in everything. There are so many of the blasted things that the numbers are a real pain to deal with. A teaspoon of table sugar, for example, has about 7,400,000,000,000,000,000,000 sucrose molecules in it, and since each sucrose molecule contains 45 atoms, that’s a whopping 330,000,000,000,000,000,000,000 atoms. And that’s not even a heaped teaspoon.

Even if we used standard form and wrote that last number as, for example, 3.3 x 1023 it’s a bit of a pain. And chemists are far too busy to write things out in full — why do you think they came up with all these symbols in the first place? — so what we do is we pick a convenient amount, which turns out to be 6.022 x 1023, and call that a “mole”. It’s just like calling twelve eggs “a dozen” only, you know, bigger.

I’m not going to explain the origin of the actual number further than this. There’s an awesome graphic here from Compound Interest and, if you want to know more, just click through.

What I am going to do are some… interesting mole calculations. People usually do grains of sand or coins or something. But those are so boooorrring. It’s nearly Halloween, right? I say we go gruesome.

Let’s start with blood!

A healthy adult has about 35 trillion red blood cells in their body at any given moment. (Vampires, presumably, have even more… although… do vampires make their own blood supply? Interesting question…).

35 trillion is a big number, right? A trillion is a million million (on the short scale, which everyone uses, don’t start), 1,000,000,000,000, or 1012, so 35 trillion is 3.5 x 1013.

But that’s only 0.000000000058 of a mole! Even if we count everyone on the planet, we only get to 0.45 of a mole. Yes, that’s right. Even if we drained the blood out of every, single human on the planet, we’d only about half a mole of red blood cells.

Ooh, how about bacteria? We have a lot of those on us, right? In fact, we have more microbes in and on our bodies than human cells! (Well, we can argue about the definition of “human” here, I suppose, but… let’s not.) Apparently there are around 3.8 x 1013 bacteria in our colons which means… damn. This is the blood cells thing all over again, isn’t it? If we took all the humans on the planet, sucked out their gut bacteria (don’t ask) and collected it all together (really, don’t) we’d have, yes, a little under half a mole of microbes.

Don’t tell the tooth fairy’s boss. She really IS scary.

Okay, this is all very well, but it’s not helping us get an idea of scale, is it? All right. Let’s try human teeth. Why not? I mugged the tooth fairy for this one (she’s much tougher than she looks), and it’s about 8 mm long. Adult teeth are a bit larger, of course, but the fairy has less of those. Let’s assume 1 cm to make things easier. That’s 0.01 m. If we had a mole of human teeth they would stack up to… 6.02 x 1021 metres, or 6.02 x 1018 km, or (we need to ramp this up a bit) about 640,000 light years. That would reach a little dwarf galaxy in the constellation of Canes Venatici, somewhere in the general neighbourhood of the Milky Way. Or, alternatively, to Neptune and back…. some 670 million times. Gosh.

What about… hair? A fine human hair is about 0.05 mm across, which means a mole of (fine) hair would be 3.01 x 1019 metres thick. The diameter of the Earth is 12,700,000 metres so that’s about… 2,400,000,000,000 times wider than the Earth. Even Rapunzel might struggle with that much hair.

There are about half a mole of red blood cells in all the humans on the planet.

Hang on, let’s go back to those red blood cells for a minute… okay, if there’s about half a mole of red blood cells in all the humans on the planet, and we assume a single red blood cell is 7.8 μm (0.0000078 m) if we put all those red blood cells in a line it would be…2.3 x 1015 kilometres long. The circumference of the sun is about 4,400,000 kilometres so…

… with all the people on the planet, we could make half a billion rings of blood around the sun, one cell thick.

There’s a thought.

In summary, the mole is a flipping big number. Too big, really, to count anything other than atoms (or molecules, or ions). But it is useful for that.

Happy Mole Day!


Look, these numbers are big, right. I’m going to be amazed if there isn’t some sort of order of magnitude mistake. Just… let me know.


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

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

More from Genius Lab Gear: Science Word Magnets

Magnets say: the results say we can inhale hot ketones

(Don’t try this at home. Or in the lab.)

The brilliant people at Genius Lab Gear (inventors of The Pocket Chemist) recently sent me a new toy: Science Word Magnets!

They are, as the name suggests, magnetic words, but with the twist that they have science and engineering themes. There are sets for ecology, engineering, microbiology, neuroscience, physics and, of course, chemistry. There’s also a science basics set, an academia set and a PhD balance set.

I’ve been messing about with the science basics set, the starter tile set ($3 extra with any order) and the chemistry set, and they really are loads of fun!

Board shows random magnets

These science word magnets have been specially designed by experts in each field to have technical depth while being fun to use.

Stick them on your fridge, your magnetic whiteboard, or anywhere you might usually persuade a magnet to stick.

And guess what? Yes, there’s a discount code! Use FLASKMAG1 when you check out to save $1 on each set you buy (so the more you buy, the more you save).

magnets read: question, method, experiment, scientific notebook, equations, formulas, results, publish, tequila

The magnets fit with other popular word magnet sets.

Follow this link and the code will be automatically applied.

By doing so, you’ll also be supporting this site, and helping to fund more cool chemistry articles — thank you!

Shipping is FREE for the USA and Canada (no tracking) and $5.90 for the UK, Europe, Japan, Korea and Australia. Shipping for elsewhere in the world is calculated at checkout. Add 4 sets to get $5 OFF and free expedited shipping in the USA!


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Lovely lollipops: the chemistry of sugary things

20th July is National Lollipop Day!

Today, July 20th, is apparently national lollipop day in the United States, and general news is… *waves hands* so it seems like a good excuse to write something with lots of pictures of brightly coloured sweets, right? Plus, sugar!

The idea of putting something sugary on a stick to hold and eat is an ancient one. The very earliest humans probably used sticks to collect honey from beehives. Later, the Chinese, Egyptians and people from the Middle East dipped fruits and nuts in honey and used sticks to make them easier to eat.

In the 17th century, boiled sugar sweets were made in England and, again, sticks inserted to make eating easier. This may be where the name “lollipop” originates, since “lolly” is a dialect word for tongue. Later, in the American Civil War era (early 1860s), some sources say hard candy was put on the tips of pencils for children. In 1931 an American named George Smith started making hard candies on sticks, and trademarked the name lollipop — but he reportedly took the name from a racehorse named “Lolly Pop”.

Table sugar is sucrose

Enough history, let’s get to the chemistry! Lollipops are made of sugar, with added colours and flavours. I’ve talked about sugar before, and it’s always worth remembering that we tend to use the word rather loosely in everyday speech.

There’s more than one type of sugar: in particular, the three that are probably most familiar are glucose, fructose and sucrose. Glucose is a simple sugar, and the one you might remember from photosynthesis and respiration equations. It’s essential for life, and you quickly run into serious trouble if your blood glucose levels drop too low (just ask a diabetic).

Like glucose, fructose is a monosaccharide (the simplest form of sugar), and is often called “fruit sugar” because, guess what, it’s common in fruits. Sucrose is what we know as “table sugar” and is a disaccharide, made up of a unit of glucose joined to a unit of fructose. In the body, sucrose is broken up into glucose and fructose.

Rock candy is made from sucrose but, unlike in most lollipops and hard candy, the sugar is allowed to form large crystals

The primary ingredient in lollipops is usually sucrose, which can be persuaded (more in a minute) to set nicely to produce a hard, shiny surface. However, commercial lollipops often also include corn syrup, or glucose syrup, which contains oligosaccharides: larger sugar molecules made from a number of simple sugar molecules joined together. Typically, as the name “glucose syrup” might suggest, these molecules contain units of glucose.

It’s worth mentioning here that corn syrup/glucose syrup isn’t the same as “high fructose corn syrup” or HFCS, in which the glucose molecules have been converted into fructose. This product is cheap, sweet and commercially easy to use, but it’s also controversial. Excessive consumption has been linked to obesity and non-alcoholic fatty liver disease, although the actual evidence is weak: a systematic review in 2014 concluded that there was little evidence it was worse than other forms of sugar. It’s really a problem of quantity: it’s easy and cheap for food manufacturers to throw HFCS into foods and drinks, and of course it tastes delicious, so as a consequence consumers end up eating too much of the stuff. In short: more water and fruit, less cake and fizzy drinks.

But having done the obligatory “eat healthily” thing, one lollipop isn’t going to hurt, is it? So back to that…

Fudge, perhaps surprisingly, contains the crystalline form of sugar

When it cools, sugar forms two different types of solid: crystalline and glassy amorphous (sometimes described as ‘amorphous solid’). Now, you might imagine that sugar as a crystalline solid is found in hard sweets/candies, but, no — it mostly turns up in soft things like fudge and fondant, which contain lots of very tiny crystals, giving an ever-so slightly granular texture. (An exception is rock candy, where the sugar is encouraged to form large crystals.)

The glassy amorphous form of sugar, on the other hand, can be literally like glass: hard, brittle, and transparent. In fact, “sugar glass” has in the past been used to make windows, bottles and so on for special effects in film and television, because it’s much less likely to cause injury than “real” glass. However, it’s very fragile and hygroscopic (meaning it absorbs water, causing it to soften over time) so these days it’s largely been replaced by synthetic resins.

Honey can be used as an inhibitor, to prevent crystallisation

The glassy amorphous form of sugar is achieved by starting with a 50% sugar solution which also contains an inhibitor, to prevent crystals forming spontaneously. Common inhibitors are the corn syrup I mentioned earlier, or cream of tartar (potassium bitartrate), honey or butter.

Exactly which you use depends on the recipe, but they all do essentially the same thing, namely, get in the way of the glucose molecules and prevent them ordering themselves into a regular (crystalline) structure. The mixture is heated to a high temperature (about 155 oC) until almost all the water evaporates — the final candy will only have about 1-2% water — and then cooled until glass transition occurs.

At the glass transition point, the sugar mixture becomes solid.

This is the clever bit, and only happens if crystallisation is inhibited (else crystals form instead). Glass transition happens around 100-150 oC below the melting point of the pure substance. For example, the melting point of pure sucrose is 186 oC, but it undergoes glass transition at around 60 oC.

Glass transition is a reversible change, which we might (if I didn’t generally dislike the concept) call a physical change. It’s a change of phase, where the sugar mixture changes from liquid to solid, but it’s different from crystallisation, because instead of the molecules becoming more ordered, they simply ‘freeze’ in their random, liquid positions. (It is, for the record, annoyingly difficult to show this in diagram form.)

Amorphous solid structures are sometimes called “supercooled liquids”. This isn’t wrong, but personally I think it’s unhelpful (and can lead to nonsense about glass flowing very slowly over time). Once cooled and set, glass, whether window glass or sugar glass, is absolutely not a liquid; it’s a solid.

Of course, to make lollipops, all sorts of colours and flavours are added to the mixture as well, and sometimes more than one mixture is used to create intricate, layered effects. There are even medicinal lollipops which contain, for example, the powerful painkiller fentanyl — the idea being that the patient can administer the dose gradually as needed.

Which brings me to the end. Happy National Lollipop Day! My favourites are Chupa Chups — if you’ve enjoyed this, how about popping over to Ko-fi so I can stock up? And if you’ve been eating sweets, do remember to clean your teeth!


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

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.