Neem: nice, nasty or… not sure?

A few days ago it was sunny and slightly breezy outside (yes, it’s August, but I live in the UK – this isn’t as common as you might imagine) and I thought, I should make the most of this and do something about my orchids.

Now, anyone that reads this blog regularly will know that my Dad is a horticulturist. I, however, am not. My fascination with bright colours, interesting smells and complicated naming conventions went down the chemistry route. But I am, oddly, quite good with Phalaenopsis, aka, moth orchids. I don’t really know why, or how, but I seem to have come to some sort of agreement with the ones that live on my kitchen windowsill. It goes along the lines of: I’ll water you once a week, and you make flowers a couple of times a year, and we’ll otherwise leave each other alone, okay?

Scale bugs secrete honeydew, which encourages the growth of sooty moulds

Well, this was fine for years, until we somehow acquired an infestation of scale bugs. These tiny but extremely annoying pests feed by sucking sap from leaves of plants, and they excrete a sticky substance called honeydew. Trust me, it’s not as nice as it sounds. Firstly, it really is sticky, and makes a horrible mess not just of the orchid leaves, but also the area around the plants.

Then it turns out that certain types of mould just love this stuff, so you end up with black spots on the leaves. And, not surprisingly, all this weakens the plant.

So, what’s the answer? Well, there are several. But the one I tend to default to is neem oil.

This stuff is a vegetable oil from the seeds of the Azadirachta indica, or neem, tree. It has a musty, nutty sort of smell, and is fairly easy to buy.

It’s indigenous to the Indian subcontinent and has been historically important in traditional medicine. In fact, The Sanskrit name of this evergreen tree is ‘Arishtha’, which means ‘reliever of sickness’.

So it’s a natural vegetable oil and people have been using it as a remedy for thousands of years – must be totally safe, right? Right?

Well… I’ve said it before, but some of the very best horribly toxic things are entirely natural, and neem is yet another example. Ingestion of significant quantities can cause metabolic acidosis (finally, something that really does have the potential to change blood pH! Er… but not… in a good way), kidney failure, seizures, and brain damage in children. Skin contact can cause contact dermatitis. It’s been shown to work as a contraceptive and, more problematically, it’s a known abortifacient (causes miscarriage).

Neem oil is easy to buy, but it needs to be handled with caution

All this said, as always, the dose make the poison.

One case study in the Journal of The Association of Physicians of India reported on a 36-year-old man who swallowed 30–50 ml (about three tablespoons) of neem oil, in the hope of treating the corns on his feet. As far as I can tell, it didn’t help his corns. It did cause vomiting, drowsiness, a dangerous drop in blood pH and seizures. There’s no specific antidote for neem poisoning, but the hospital managed his symptoms. Luckily, despite the hammering his kidneys undoubtedly took, he didn’t need dialysis, and was discharged from hospital after just over a week.

Now, okay, you’re unlikely to accidentally swallow three tablespoons of any oil, especially not neem which does have quite a strong, not entirely pleasant, smell and (reportedly – I haven’t tried for obvious reasons) a bitter taste. But nevertheless, it’s wise to be cautious, particularly around children who have a smaller body mass and therefore are much more likely to suffer serious effects – up to and including death. In one reported case, a mother gave a 3-month-old child a teaspoon of neem oil in the hope of curing his indigestion – fortunately he survived, but not without some seriously scary symptoms.

Nimbin, a chemical found in neem oil, is reported to have all sorts of beneficial effects [image source]

Okay, so those are the dangers. Let’s talk chemistry. The Pakistani organic chemist Salimuzzaman Siddiqui is thought to be the first scientist to formally investigate the various compounds in neem oil. In 1942 he extracted three compounds, and identified nimbidin as the main antibacterial substance in neem. He was awarded an OBE in 1946 for his discoveries.

I will confess, at this point, to running into a little bit of confusion with the nomenclature. Nimbidin is described, in some places at least, as a mixture of compounds (collectively, tetranortriterpenes) rather than a single molecule. But either way, it has been shown to have anti-inflammatory properties – at least in rats.

Another of the probably-mostly-good substances in neem is nimbin: a triterpenoid which is reported to have a whole range of positive properties, including acting as an anti-inflammatory, an antipyretic, a fungicide, an antiseptic and even as an antihistamine. Interestingly, I went looking for safety data on nimbin, and I couldn’t find much. That could mean it’s safe, or it could mean it just hasn’t been extensively tested.

Azadirachtin, another chemical found in neem, is a known pesticide [image source]

The substance that seems to do most of the pesticide heavy lifting is azadirachtin. This is a limonoid (compounds that are probably best known for their presence in citrus fruits). It’s what’s called an antifeedant – a substance produced by plants to deter predators from munching on them. Well, mostly. Humans have a strange habit of developing a taste for plants that produce such substances. Take, for example, odoriferous garlic, clears-out-your-sinuses horseradish, and of course the daddy of them all: nicotine.

Azadirachtin is known to affect lots of species of insects, both by acting as an antifeedant and as a growth disruptor. Handily, it’s also biodegradable – and breaks down in a few days when exposed to light and water.

That makes it appealing as a potential pesticide, and it’s also generally described as having low toxicity in mammals – its reported LD50 tends to fall into the grams per kilogram range, which makes it “moderately to slightly toxic“. Wikipedia quotes a value (without a source, as I write this) of >3,540 mg/kg in rats.

But… I did find another page quoting 13 mg/kg in mice. That’s quite dramatically different, and would make it extremely/highly toxic. Unfortunately I couldn’t get my hands on the original source, so I haven’t been able to verify it’s not a transposition error.

Let’s assume it isn’t. It would be odd to have such a big difference between mice and rats. Things that poison mice tend to poison rats, too. There might be some confusion over pure azadirachtin vs. “neem extract” – it could be the case that the mixture of chemicals working together in neem create some sort of synergistic (toxic) effect – greater than the sum of all the individual substances. It could be an experimental error, including a contaminated neem sample, or something to do with the way the animals were exposed to the extract.

Neem soap is widely available online, but that may not be a good thing…

It’s difficult to say. Well, it’s difficult for me to say, because I don’t have access to all the primary sources. (Any toxicologists out there, please do feel free to weigh into the comments section!) But either way, as I’ve already mentioned, several case studies have fingered azadirachtin as one of the substances likely to be causing the well-reported nasty side effects.

If you’re asking this chemist? I say be careful with the stuff. If you decide to use it on your plants, keep it out of reach of children, and wear some good-quality disposable gloves while you’re handling it (I put some on after I took that photo back there). If you’re pregnant, or trying to become pregnant, the safest option is to not use it at all.

Which brings me to neem soap.

Yup. It’s sold as a “natural” treatment for skin conditions like acne. I won’t link to a specific brand, but it’s easy to find multiple retailers with a simple Google search. I looked at one selling soap bars for £6.99 a pop, containing 10% (certified organic, because of course) neem oil. Did I mention back there that neem is known to cause contact dermatitis? I’m fairly sure I did. None of the products I saw had obvious safety warnings, and I certainly found nothing about safety (or otherwise) for pregnant women.

Plus – worryingly, not least because children are more likely to get things in their mouth – you can also buy kids and babies versions, again purporting to contain 10% neem oil.

I even found neem toothpaste. Which… given people often swallow toothpaste… yikes.

My moth orchids are looking much healthier now I’ve got rid of all the scale bugs!

Now again, and for the umpteenth time, the dose makes the poison. The case studies I’ve mentioned involved, at a minimum, swallowing a teaspoon of pure neem oil, and you’re not getting that sort of quantity from smears of toothpaste. But, at the same time, when it comes to pregnancy and babies, it’s generally sensible to apply a precautionary principle, especially for things like soap and toothpaste for which alternatives with well-established safety profiles exist.

Bottom line? Would I use these products? I would not.

But I do use neem to treat the scale bugs on my orchids, and they’re doing much better than they were. Fingers crossed for more flowers!


Do you want something non-sciency to distract you from, well, everything? Why not take a look at my fiction blog: the fiction phial? You can also find me doing various flavours of editor-type-stuff at the horror podcast, PseudoPod.org – so head over there, too!

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

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

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

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

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

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

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

Image

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


Do you want something non-sciency to distract you from, well, everything? Why not take a look at my fiction blog: the fiction phial? You can also find me doing various flavours of editor-type-stuff at the horror podcast, PseudoPod.org – so head over there, too!

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

20th May is World Bee Day, the aim of which is to raise awareness of the importance of bees and beekeeping. So, hey, let’s do that!

I’m helped this month by my horticulturist* dad who, while working in a public garden recently, discovered this honeybee swarm in a honeysuckle. (Me: “what sort of tree is that?” Dad: “a winter flowering Honeysuckle lonicera. It’s a shrub, not a tree!” Yes, despite his tireless efforts I’m still pretty clueless about plants.)

Now, Dad knows what he’s doing in such situations. He immediately called the professionals. One does not mess around with (or ignore) a swarm of bees – one finds a beekeeper, stat. Obviously bees can sting, but they’re also endangered and they need to be collected to protect them. Should you find yourself in such a situation, you can find someone local via the British Beekeepers Association website.

That out of the way, aren’t they gorgeous? A swarm like this is a natural phenomenon, that happens when new queen bees are born and raised in the colony. Worker bees stop feeding the old queen – because a laying queen is too heavy to fly – and then in time she leaves with a swarm. They cluster somewhere, as you see in the photo, while scout bees go looking for a new location to settle. Bees in swarms only have the honey or nectar in their stomachs to keep them going, so they’ll starve if they don’t find a new home, and nectar, quickly.

This is all fascinating, of course, but what does it have to do with chemistry? Well, quite a bit, because bees are brilliant chemists. Really!

Ethyl oleate is an ester and an important chemical for bees (image source)

Firstly, despite what DreamWorks might have taught us, bees don’t have vocal cords, and they don’t sound like Jerry Seinfeld. A lot of their communication is chemical-based (actually, it turns out this is a topic of hot debate in bee circles, but since this is a chemistry blog, I’m not doing waggle dances. No, not even if you ask nicely).

As you might imagine, there are multiple chemicals involved, and I won’t go into all of them. Many are esters, which are known for their sweet, fruity smells, and which are also (at least, the longer-chain ones) the building blocks of fats.

One such chemical is ethyl oleate which plants produce and which, interestingly, we humans also make in our bodies when we drink alcohol. Forager bees gather ethyl oleate and carry it in their stomachs, and they then feed it to worker bees. It has the effect of keeping those workers in a nurse bee state and prevents them from maturing into forager bees too early. But, as forager bees die off, less ethyl oleate is available, and this “tells” the nurse bees to mature more quickly – so the colony makes more foragers. Clever, eh?

In this situation, ethyl oleate is acting as a pheromone, in other words, a substance that triggers a social response in members of the same species. Another example is Nasonov’s pheromone, which is a mixture of chemicals including geraniol (think fresh, “green” smell), nerolic acid, geranic acid (an isomer of nerolic acid) and citral (smells of lemon).

The white gland at the top of the honeybee’s abdomen releases pheromones which entice the swarm to an empty hive (image source)

An interesting aside: geranic acid has been investigated as an antiseptic material. It can penetrate skin, and has been shown to help the delivery of transdermal antibiotics, which are being investigated partly as a solution to the problem of antibiotic resistance. Nature is, as always, amazing.

Anyway, worker bees (which, again contrary to DreamWorks’ narrative, are female) release Nasonov’s pheromone to orient returning forager bees (also female) back to the colony. They do this by raising up their abdomens and fanning their wings. Beekeepers can use synthetic Nasonov pheromone, sometimes mixed with a “queen bee pheromone” to attract honeybee swarms to an unoccupied hive or swarm-catching box.

As my Dad chatted to the beekeepers (partly on my insistence – I was on the other end of my phone texting questions and demanding photos) one substance they were particularly keen to mention was “the alarm pheromone,” which “smells of bananas.”

Ooh, interesting, I thought. Turns out, this is isoamyl acetate, which is another ester. In fact, depending on your chemistry teacher’s enthusiasm for esters, you might even have made it in school – it forms when acetic acid (the vinegary one) is combined with 3-methylbutan-1-ol (isoamyl alcohol).

Never eat a banana by a bee.

Isoamyl acetate is used to give foods a banana flavour and scent. But, funnily enough, actual bananas you buy in the shops today don’t contain very much of it, the isoamyl acetate-rich ones having been wiped out by a fungal plague in the 1990s. This has lead to the peculiar situation of banana-flavoured foods tasting more like bananas than… well… bananas.

Modern bananas can still be upset bees, though. There are numerous stories of unwary individuals who walked too close to hives while eating a banana and been attacked. So, top tip: if you’re going on a picnic, leave the bananas (and banana-flavoured sweets, milkshakes etc) at home.

The reason is that banana-scented isoamyl acetate is released when honeybees sting. They don’t do this lightly, of course, since they can’t pull out the barbed stinger afterwards, and that means the bee has to leave part of its digestive tract, muscles and nerves embedded in your skin. It’s death for the bee, but the act of stinging releases the pheromone, which signals other bees to attack, attack, attack.

One bee sting might not deter a large predator, but several stings will. Multiple bee stings can trigger a lethal anaphylactic reaction, known allergy or not. So although utilising their stingers causes the death of a few (almost certainly infertile) bees, the rest of the colony (including the fertile individuals) is more likely to survive. From an evolutionary perspective it’s worth it – genes survive to be passed on.

Isoamyl acetate

Isoamyl acetate is an ester that smells of bananas, and is an alarm pheremone for bees (image source)

Moving on, I obviously can’t write a whole blog post about bees and not mention honey! We take it for granted, but it’s amazingly complicated. It contains at least 181 different substances, and nothing human food scientists have been able to synthesise quite compares.

In terms of sugars, it’s mostly glucose and fructose. Now, I’ve written about sugars extensively before, so I won’t explain them yet again, but I will just reiterate my favourite soap-box point: your body ultimately doesn’t distinguish between “processed” sugars in foods and the sugars in honey. In fact, one might legitimately argue that honey is massively processed, just, you know, by bees. So, you want to cut down on your sugar intake for health reasons? Sorry, but honey needs to go, too.

Honey is actually a supersaturated solution. In very simple terms, this means there’s an excess of sugar dissolved in a small amount of water. One substance which bees use to achieve this bit of clever chemistry is the enzyme, invertase, which they produce in their salivary glands. Nectar contains sucrose (“table sugar”) and, after the bees collect nectar, invertase helps to break it down into the smaller molecules of glucose and fructose.

“Set” honey is honey that’s been crystallised in a controlled way.

That’s only the beginning, though. There are lots of other enzymes involved. Amylase breaks down another sugar, amylose, into glucose. And glucose oxidase breaks down glucose and helps to stabilise the honey’s pH. One of the molecules produced in the reaction with glucose oxidase produces is hydrogen peroxide, which yet another enzyme, catalase, further breaks down into water and oxygen.

Bees regurgitate and re-drink nectar (yes, I suggest you don’t overthink it) over a period of time, which both allows the sugar chemistry to happen and also reduces the water content. When it’s about one-fifth water, the honey is deposited in the honeycomb, and the bees fan it with their wings to speed up the evaporation process even further. They stop when it’s down to about one-sixth water.

As I said a moment ago, honey is a supersaturated solution, and that means it’s prone to crystallising. This isn’t necessarily bad, in fact, “set” honey (my personal favourite) is honey which has been crystallised in a controlled way, so as to produce fine crystals and a creamy (rather than grainy) product.

The formation of a new honeycomb.

The potential problem with crystallisation is that once the sugar crystals fall out of solution, the remaining liquid has a higher-than-ideal percentage of water. This can allow microorganisms to grow. In particular, yeasts can take hold, leading to fermentation. Honey left on the comb in the hive tends not to crystallise, but once it’s collected and stored, there’s a greater chance that some particle of something or other will get in there and trigger the process. It helps to store it somewhere above room temperature. And honey is naturally hygroscopic, which means it absorbs water. So store it somewhere dry. In short, never put honey in the fridge.

Speaking of yeast and heat, heating changes honey and makes it darker in colour, thanks to the Maillard reaction. Commercial honey is often pasteurized to kill any yeast, which improves its shelf life and produces a smoother product. Also, because honey is naturally slightly acidic (around pH 4), over time the amino acids within in start to break down and this also leads to a darkening of the colour.

One more important safety concern: honey, even when pasteurized, can contain bacteria that produce toxins in a baby’s intestines and lead to infant botulism. So, never give children under one honey. It’s not a risk for older children (and adults) thanks to their more mature digestive systems.

T

Back to Dad’s bees! They were collected in a transport box by two local experts, Sharon and Ian. The bees march into the box two-by-two, wafting Nazonov’s pheromone to signal that this is home. From there, they were safely transferred to a new, wooden hive.

There’s only one way to finish this post, I think, and that’s with one of my all-time favourite Granny Weatherwax moments:

‘Your bees,’ she went on, ‘is your mead, your wax, your bee gum, your honey. A wonderful thing is your bee. Ruled by a queen, too,’ she added, with a touch of approval.

‘Don’t they sting you?’ said Esk, standing back a little. Bees boiled out of the comb and overflowed the rough wooden sides of the box.

‘Hardly ever,’ said Granny. ‘You wanted magic. Watch.’

Happy World Bee Day, everyone and, as always, GNU Terry Pratchett.


* Dad was unsure about the label “horticulturist” but I pointed out that the definition is an expert in garden cultivation and management, particularly someone’s who’s paid for their work. All of which he is. He replied wryly that, “x is an unknown quantity, and a spurt is a long drip.” Love you, Dad x 😄


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

 

Vibrant Viburnum: the fascinating chemistry of fragrant flowers

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

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

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

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

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

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

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

Phew.

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

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

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

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

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

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

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

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

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

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

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

Take care and stay safe.


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


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

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2021. You may share or link to anything here, but you must reference this site if you do. If you enjoy reading my blog, and especially if you’re using information you’ve found here to write a piece for which you will be paid, please consider buying me a coffee through Ko-fi using the button below.
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Want something non-sciency to distract you from, well, everything? Why not check out my fiction blog: the fiction phial.

 

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.
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.

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.
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.