Chemical jigsaw puzzles: how do chemists identify molecules?

Front cover of Great ExplanationsA quick thing before I get into this month’s chemistry ramble: I’m guessing that you, lovely reader, enjoy reading about science stuff. Especially stuff written by an amazing crowd of hard-working science communicators, one of whom is yours truly. So, please consider spreading the word about this awesome book: Great Explanations. Or even better, pledge! There are some fabulous rewards at the different pledge levels. Either way, thank you x

Okay, back to it! Recently, a bit of an argument blew up on Twitter regarding what is, and isn’t, in covid vaccinations. The particular substance du jour being graphene oxide. The @TakeThatChem account pointed out that one of the sources being touted by some as ‘evidence’ for its presence (the article in question was by Robert O Young, remember him? Yes, the one that did actual jail time) didn’t describe the use of any sort of technique that could identify graphene oxide. Which, just to be clear, is absolutely not an ingredient in covid vaccinations.

The debate culminated with questions about how, exactly, scientists do identify substances on the molecular level. @TakeThatChem wondered if one of the users who had become embroiled in the debate even understood how a chemist might work out a molecule’s structure, and then posted an image.

Screenshot of tweet by @TakeThatChem showing an NMR spectrum (link in text)

This tweet illustrated a technique that can be used to identify molecules.

British students of chemistry first meet images like this somewhere around the age of 17–18, so although this is somewhat advanced, it’s still essentially school-level. Which means that for a chemist, it’s one of those things that’s so familiar that, half the time, we probably forget that the rest of the world will have absolutely no idea what it is.

But for those that have never studied A level chemistry or similar: what is it?

The answer is that it’s a proton NMR, or nuclear magnetic resonance, spectrum. Now, NMR is quite tricky. Bear with me, I’m about to try and explain it in a paragraph…

Here goes: you know magnets? And how, if you put one magnet near another magnet, it moves? Now imagine that certain types of atomic nuclei are basically tiny magnets. If you put them in a really powerful magnetic field, they sort of move. If you then alter that magnetic field, they move as the field varies. A computer records and analyses those changes, and spits out a graph that looks like that one back there – which chemists call a spectrum.

Photo of MRI equipment

Medical MRIs use essentially the same technology as the one used to generate the spectrum

Did I nail it? There’s a lot more to this, not surprisingly. In particular, radio waves are involved. My quick and dirty explanation is the equivalent of describing a car as a box on wheels – it’s broadly true from a distance if you squint a bit, but if you said it in the presence of a qualified mechanic they’d wince and start muttering words like ‘head gasket’ and ‘brake discs’ and ‘you do know this is a diesel engine, yes?’

Anyway, it’ll do for now. If you’re studying NMR at a more advanced level, take a look at this episode of Crash Course Organic Chemistry written by… someone called Kat Day. No idea who that is 😉

The same technique, by the way, is used in medicine – but there you know it as MRI, or magnetic resonance imaging. It turns out that if you shove a human (or pretty much anything that contains a lot of carbon-based molecules) into a powerful magnetic field, the atomic nuclei do their thing. You might imagine that having all your atoms do some sort of cha-cha would hurt, but no – as anyone who’s ever had an MRI will attest, it’s mostly just very loud and a bit dull. The end result is an image with different contrast for different types of tissue. Fatty tissue, for example, tends to show up as areas of brightness, while bone tends to look darker – so it’s useful for diagnosing all sorts of problems.

Photo of jigsaw pieces

Interpreting a proton NMR spectrum can be a bit like looking at a jigsaw pieces

But back to chemistry. Chemists, preferring a simpler life (haha), are often working with single substances. Or at least trying to. If we imagine a molecule as a picture, looking at a proton NMR spectrum is a bit like looking at a mixed-up jigsaw puzzle of that picture. Each individual piece – or peak – in the spectrum represents an atom or a group of atoms.

Each piece tells you something and, at the same time, it also tells you about the bits that are joined to it. In the same way that you might look at a jigsaw piece and think, ‘well, this has a sticky-out bit so the piece that goes next to it must have an inny-bit,’ chemists look at a spectrum and say, ‘well, this bit looks like this, so its carbon atom must be attached to group of atoms like that.’

Okay, so what do the pieces in the spectrum @TakeThatChem posted show us? Well, reading spectra takes practice but, like most things, if you do that practice, after a while you get into the habit of spotting things straight away.

For example, it’s fairly obvious to me that whatever-it-is it probably has a carboxylic acid (COOH) group, and it definitely has a benzene ring. I can also see that the benzene ring has things bonded to opposite points, in other words, if you numbered the carbons in the ring from 1 to 6, it has things attached at carbon 1 and carbon 4. There’s a chain of carbons, which is branched, and there’s another CH3 group somewhere. To get more precise I’d have to look more carefully at the integrals (the differently-sized ∫ symbols over the peaks), hunt for a data sheet and study the scale on the horizontal axis along the bottom.

Photo of white pills

The spectrum is of a common drug substance, but which one…

My brain got as far as ‘hm, maybe it’s aspirin, oh no, it can’t be, because…’ before I came across the already-posted answer. I won’t give it away – spoilers, sweetie – but let’s just say it’s a molecule not a million miles different from aspirin.

So yes, chemists do have the means to identify individual molecules, but it requires a fair bit of knowledge and training to both carry out the techniques and to interpret the results. Despite what Hollywood might have us believe, we don’t (yet) have a machine that intones ‘this material is approximately 40% isobutylphenylpropionic acid, captain’ when you plop a sample into it.

The fact that real chemistry (and science in general) is not simple is precisely why pseudoscience peddled by the likes of Robert O Young is so appealing: it’s nice and easy, it follows a sort of ‘common sense’ narrative, it’s not swathed in all sorts of technical language. Anyone can read it and, without any other training, feel as if they understand it perfectly.

None of us knows what we don’t know. If someone comes along with an easy explanation, it’s tempting to believe it – particularly if they go on to play into our anxieties and tell us what we were hoping to hear.

Which brings me to a thread by the lovely Dr Ben Janaway, one tweet of which said, extremely eloquently:

Please do not harass [people protesting covid vaccines]. Please do not blame them. My education is a privilege they have not been afforded. They do not lack intelligence, they lack being taught how to make sense of very complicated things, most of it hidden. What can we do, listen and talk.

Photo of a facemask, syringe and vaccine vials

Please get vaccinated

His point is a good one. All we can do is keep spreading the word as clearly as possible and just hope that, maybe, it will change one mind somewhere. Because maybe that mind will change another, and maybe sense will spread.

Take care, stay safe, and get vaccinated. Get your flu jab, too, if it’s that time of year in your part of the world.


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

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The Chronicles of the Chronicle Flask: 2017

We’ve made it! Not only to 2018 (which was starting to look doubtful earlier in the year), but also to the Chronicle Flask’s 100th post. Which doesn’t seem that many, really, but since posts on here frequently run to 1500 words, that adds up to a rather more impressive-sounding 150,000 words or so. I mean, that’s like… half a Brandon Sanderson novel. Oh.

Anyway, it’s time for a yearly round-up. Here goes!

Last January I began with a post about acrylamide. We’d all been enjoying lots of lovely crispy food over Christmas; it was time to tell us about the terrible dangers of such reckless indulgence. The newspapers were covered with pictures of delicious-looking chips, toast and roast potatoes alongside scary headlines such as:  “Crunchy toast could give you cancer, FSA warns”. The truth was not quite so dramatic. Acrylamide does form when foods are cooked to crispiness, and it is potentially harmful, but the quantities which form in food are tiny, and very unlikely to cause you any serious harm unless you literally live on nothing but burnt toast. The FSA (Food Standards Agency) hadn’t significantly revised their guidelines, it turned out, but were in fact only suggesting that the food industry should be mindful of acrylamide levels in food and seek to reduce them as much as possible. That wouldn’t have made for quite such a good “your food is going to killllll you!” story though, I suppose.

In February the spikey topic of vaccination came up. Again. Vaccines are awesome. They protect us from deadly diseases. No, I don’t want to hear any nonsense about “Big Pharma“, and I definitely don’t want to hear how “natural immunity” is better. It’s not. At best, it might provide a similar level of protection (but not in every case), but it comes with having to suffer through a horrible, dangerous disease, whereas vaccination doesn’t. It ought to be a no-brainer. Just vaccinate your kids. And yourself.

It was Red Nose Day in the UK in March, which brought some chemistry jokes. Turns out all the best ones aren’t gone, after all. Did you hear about the PhD student who accidentally cooled herself to absolute zero? She’s 0K now.

April brought a post which ought to have been an April Fool’s joke, but wasn’t. Sceptics often point out that homeopathy is just sugar and water, but the trouble is, sometimes, it’s not. There’s virtually no regulation of homeopathy. As far as I’ve been able to establish, no one tests homeopathic products; no one checks the dilutions. Since a lot of the starting materials are dangerously toxic substances such as arsenic, belladona, lead and hemlock, this ought to worry people more than it does. There has been more than one accidental poisoning (perhaps most shockingly, one involving baby teething products). It really is time this stuff was banned, maybe 2018 will be the year.

In May I turned to something which was to become a bit of a theme for 2017: alkaline water. It’s not so much that it doesn’t do anything (although it really doesn’t), more the fact that someone is charging a premium for a product which you could literally make yourself for pennies. It’s only a matter of dissolving a pinch of baking soda (sodium bicarbonate) in some water.

June brought a selection of periodic tables because, well, why not? This is a chemistry blog, after all! And now we’ve finally filled up period seven they do have a rather elegant completness. 2019, by the way, has just been announced as the International Year of the Periodic Table of Chemical Elements, to coincide with IUPAC’s 100th anniversary and the 150th anniversary of Mendeelev’s discovery of periodicity (his presentation, The Dependence Between the Properties of of the Atomic Weights of the Elements, was made on 6th March 1869). Looks like 2019 will be an exciting year for chemists!

In July it was back to the nonsense of alkaline diets again, when Robert O. Young was finally sentenced to 3 years, 8 months in custody for conning vulnerable cancer patients into giving him large sums of money for ineffective and dangerous treatments. Good. Moving on.

August brought me back to a post that I’d actually started earlier in the year when I went to a March for Science event in April. It was all about slime, and August seemed like a good time to finally finish it, with the school holidays in full swing – what could be more fun on a rainy day at home than making slime? Slime was a bit of a 2017 craze, and there have been a few stories featuring children with severely irritated skin. But is this likely to be caused by borax? Not really. Turns out it’s actually very safe. Laundry detergents in general, not so much. In short, if you want to make slime the traditional way with PVA glue and borax, fill your boots. (Not really – your parents will be uninpressed.)

In September it was back to quackery: black salve. A nasty, corrosive concoction which is sold as a cancer cure. It won’t cure your cancer. It will burn a nasty great big hole in your skin. Do not mess with this stuff.

October carried on in a similar vein, literally. This time with a piece about naturopaths recommending hydrogen peroxide IVs as a treatment for lots of things, not least – you guessed it – cancer. Yes, hydrogen peroxide. The stuff you used to bleach hair. Intraveneously. Argh.

The puking pumpkin!

The end of the month featured a far better use for hydrogen peroxide, that of the puking pumpkin. Definitely one to roll out if, for any reason, you ever find yourself having to demonstrate catalysis.

November brought us, somewhat unseasonally, to tomatoes. Where is the best place to store them? Fridge or windowsill? Turns out the answer involves more chemistry than you might have imagined.

And then, finally, December. Looking for a last-minute Christmas gift? Why not buy a case of blk water? I mean, other than it’s an exorbitantly priced bottle of mysterious black stuff which doesn’t do any of the things it claims to do, and might actually get its colour from coal deposits, that is.

And that, dear friends and followers, is it for 2017! Happy New Year! Remember to be sceptical when the inevitable “deadly food” story appears in a few weeks….


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Absurd alkaline ideas – history, horror and jail time

I’ve written about the absurdity of alkaline diets before, and found myself embroiled in more than one argument about the idea.

To sum up quickly, it’s the notion that our bodies are somehow “acidic”, and if only we could make them “alkaline” all our health problems – cancer included – would disappear. The way you make your body “alkaline” is, mainly, by eating lots of vegetables and some fruits (particularly citrus fruits – yes, I know, I know).

The eating fruit and vegetables bit aside (they’re good for you, you should eat them), it’s all patent nonsense. Our bodies aren’t acidic – well, other than where they’re supposed to be acidic (like our stomachs) – and absolutely nothing we eat or drink can have any sort of effect on blood pH, which is kept firmly between 7.35-7.45 by (mainly) our lungs and kidneys. And if your kidneys or lungs are failing, you need something a little stronger in terms of medical intervention than a slice of lemon.

But who first came up with this crazy idea?

Claude Bernard carried out experiments on rabbits.

Actually, we can probably blame a nineteenth century French biologist and physiologist, Claude Bernard, for kicking the whole thing off, when he noticed that if he changed the diet of rabbits from largely plant-based to largely animal-based (i.e. from herbivorous to carnivorous) their urine became more acidic.

This observation, followed by a lot of speculation by nutritionists and some really quite impressively dodgy leaps of reasoning (by others, I should stress – not Bernard himself), has lead us to where we are now: umpty-million websites and books telling anyone who will listen that humans need to cut out all animal products to avoid becoming “acidic” and thus ill.

Bernard’s rabbits were, it seems, quite hungry when he got them – quite possibly they hadn’t been fed – and he immediately gave them boiled beef and nothing else. Meat contains the amino acids cysteine and methionine, both of which can produce acid when they’re metabolised (something Bernard didn’t know at the time). The rabbits excreted this in their urine, which probably explains why it became acidic.

Now, many of you will have noticed several problems here. Firstly, rabbits are herbivores by nature (they do not usually eat meat in the wild). Humans aren’t herbivores. Humans are omnivores, and we have quite different digestive processes as a result. It’s not reasonable to extrapolate from rabbits to humans when it comes to diet. Plus, even the most ardent meat-lover probably doesn’t only eat boiled beef – at the very least people usually squeeze in a battered onion ring or a bit of coleslaw along the way. Most critically of all, urine pH has no direct relationship with blood pH. It tells us nothing about the pH of “the body” (whatever we understand that to mean).

The notion that a plant-based diet is somehow “alkaline” should really have stayed in the 19th century where it belonged, and at the very least not limped its way out of the twentieth. Unfortunately, somewhere in the early 2000s, a man called Robert O Young got hold of the idea and ran with it.

Young’s books – which are still available for sale at the time of writing – describe him as “PhD”, even though he has no accredited qualification.

Boy, did he run with it. In 2002 he published a book called The pH Miracle, followed by The pH Miracle for Diabetes (2004), The pH Miracle for Weight Loss (2005) and The pH Miracle Revised (2010).

All of these books describe him either as “Dr Robert O Young” or refer to him as “PhD”. But he has neither a medical qualification nor a PhD, other than one he bought from a diploma mill – a business that offers degrees for money.

The books all talk about “an alkaline environment” and state that so-called acidic foods and drinks (coffee, tea, dried fruit, anything made with yeast, meat and dairy, amongst other foodstuffs) should be avoided if not entirely eliminated.

Anyone paying attention will quickly note that an “alkaline” diet is basically a very restrictive vegan diet. Most carbohydrate-based foods are restricted, and lots of fruits and nuts fall into the “moderately” and “mildly” acidic categories. Whilst a vegan diet can be extremely healthy, vegans do need to be careful that they get the nutrients they need. Restricting nuts, pulses, rice and grains as well as removing meat and dairy could, potentially, lead to nutritional deficiencies.

Young also believes in something called pleomorphism, which is a whole other level of bonkers. Essentially, he thinks that viruses and bacteria aren’t the cause of illnesses – rather, the things we think are viruses and bacteria are actually our own cells which have changed in response to our “acidic environments”. In Young’s mind, we are making ourselves sick – there is one illness (acidosis) and one cure (his alkaline diet).

It’s bad enough that he’s asserting such tosh and being taken seriously by quite a lot of people. It’s even worse that he has been treating patients at his ranch in California, claiming that he could “cure” them of anything and everything, including cancer.

One of his treatments involved intravenous injections of solutions of sodium hydrogen carbonate, otherwise known as sodium bicarbonate or baking soda. This common cookery ingredient does produce an alkaline solution (about pH 8.5) when dissolved in water, but remember when I said blood pH was hard to shift?

Screenshot from a BBC article, see http://www.bbc.co.uk/news/magazine-38650739

Well, it is, and for good reason. If blood pH moves above the range of 7.35-7.45 it causes a condition called alkalosis. This can result in low blood potassium which in turn leads to muscle weakness, pain, and muscle cramps and spasms. It can also cause low blood calcium, which can ultimately result in a type of seizure. Putting an alkaline solution directly into somone’s blood is genuinely dangerous.

And this is before we even start to consider the fact that someone who was not a medical professional was recommending, and even administering, intravenous drips. Which, by the way, he was reportedly charging his patients $550 a pop to receive.

Young came to the attention of the authorities several times, but always managed to wriggle out of trouble. That is, until 2014, when he was arrested and charged with practising medicine without a license and fraud. In February last year, he was found guilty, but a hung jury caused complications when they voted 11-1 to convict on the two medical charges, but deadlocked 8-4 on fraud charges.

Finally, at the end of June 2017, he was sentenced. He was given three years, eight months in custody, but due to the time he’s already spent in custody and under house arrest, he’s likely to actually serve five months in jail.

He admitted that he illegally treated patients at his luxury Valley Center ranch without any medical or scientific training. Perhaps best of all, he was also made to publicly declare that he is not microbiologist, hematologist, medical doctor or trained scientist, and that he has no post-highschool educational degrees from any accredited school.

Prosecuting Deputy District Attorney Gina Darvas called Young the “Wizard of pHraud”, which is rather apt. Perhaps the titles on his books could be edited to read “Robert O Young, pHraud”?


Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. All content is © Kat Day 2017. You may share or link to anything here, including the images, but you must reference this site if you do.


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