Tag Archives: spectrum

Chemical jigsaw puzzles: how do chemists identify molecules?

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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.

Support the Great Explanations book here!

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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Five science facts we learned at school?

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This week a post called ‘Five Science ‘Facts’ We Learnt At School That Are Plain Wrong‘ popped into my Facebook feed from a few different sources.

It led to more than one argument, and the unearthing of some interesting titbits. Most of these facts aren’t directly about chemistry, but hey, still interesting. Let’s have a look:

We’re taught we only have five senses: smell, sight, hearing, touch and taste
True enough that there are more than five, but I clearly remember being told in school that balance and pain were also senses, so I’m fairly sure biology teachers have been quietly trying to dispel this one for decades.

plastic paperclips

Non-magnetic paper-clips. Ha!

Which of the following are magnetic: a tomato, you, paper-clips? (Answer: all of the above)
I think this is a misleading question. What do you mean when you say ‘magnetic’? I think most people understand that to mean something that’s capable of being magnetised or at least is attracted to your everyday fridge magnet. In other words, the ferromagnetic materials: iron, nickel, cobalt and most of their alloys. True enough tomatoes and people interact with magnetic fields (this is the basis behind MRI scanners – check out these beautiful images) but does that make them magnetic? We-ell….technically…. (there are lots of types of magnetism) but it seems a bit mean to criticise an assumption by asking a less-than-clear question about it. Besides, if you’re going to be pedantic about it, what’s that paper-clip made of hmm? Plastic and aluminium (both generally considered to be completely non-magnetic) paper-clips exist. Bad question. Next!

CMYKThe true primary colours for paints and pigments are cyan, magenta and yellow
Broadly fair enough, look at your printer cartridge. Although we really ought to include black as well (which the original article didn’t mention; it’s the K in the CMYK model). You can make something pretty close to black by mixing the others, but it’s not the nice, crisp, blackest black that people want for text and outlines. All that said, to actually get red from a mixture of magenta and yellow you have to have pretty pure pigments. Grab a paint box and try mixing something that looks like magenta with something that looks like yellow, and you’ll actually get something that looks like orangey-pink (serious artists agree that if you want really bright red, you’re better off just buying some red pigment). Whereas if you mix blue paint with yellow paint you will, fairly reliably, get green of one shade or another. I just worry that attempting to clear this one up is going to cause a lot of children to mess up their paintings. That’s all I’m saying.

A little addition here: this question then led to a debate about the colour spectrum of visible light. How many colours are there, exactly? It’s commonly held that Newton invented the colour indigo because he felt, possibly for superstitious reasons, that there ought to be seven colours. As a result, some people will tell you the spectrum actually consists of six colours rather than seven: red, orange, yellow, green, blue and violet. But hang on. Look at a spectrum (here’s one):

600px-Spectrum

What’s that colour in between blue and green there? You might say turquoise, but in a return to the original question it’s more accurately named cyan. That band is pretty obvious. I’d argue that if you’re going to include orange in the spectrum, then you ought to include cyan. And, in fact, some people think that’s exactly what Newton was doing. Except he didn’t call it cyan, he simply called it blue. The bit we think of as blue is what he named indigo. In other words, the spectrum is, in fact: red, orange, yellow, green, cyan, blue, violet. Still seven colours, they just don’t quite fit with the whole Richard Of York Gave Battle In Vain thing.

Of course, those of us in the know are aware that there are actually eight colours. But you need to have octagonal cells in your eyes to see the other one. Or be a cat.

pzg3m9pk-1414136926

Debunked in 1974. Still hanging around like a bad smell or, er, taste.

Tongue taste maps are nonsense
Yep. This one is unambiguous: there aren’t regions for sweet, salt, bitter etc. on your tongue. This was debunked back in 1974, but it’s still hanging around for some reason.

There are more states of matter than just solid, liquid and gas
Ah-ha, a chemistry one! Again, this is true. The strict states of solid, liquid and gas are fine when you’re talking about elements and pure, fairly simple, compounds (water, for example), but matter can indeed take other forms. There are ‘liquid crystals‘ – you’re probably reading this right now using some – and yes, there’s plasma. Once you get into mixtures all bets are off (no, you can’t melt wood, sorry). And colloids are a whole other kettle of fish.

But I think this is one of those times where you have to ask yourself why are we bothering to talk about solids, liquids and gases in the first place? Is it purely so that students can memorise three words? No. It’s so that they can go on to understand the concepts of melting and boiling, and their partners freezing and condensing. These ideas are critical to understanding ideas of measuring temperature as solid liquid gaswell as what happens to particles when they warm up (or cool down). Adding other technical terms in at this early stage is just likely to cause confusion. I don’t think that learning about the transition from solid to liquid to gas precludes later learning about liquid crystals, colloids and the like (hey, it’s how I did it). You’re just adding more information to a simple model, and someone studying A-level sciences and beyond ought to be capable of dealing with that. No harm, no foul, I say.

So there we have it: less “Five Science ‘Facts’ We Learnt At School That Are Plain Wrong”, and more one thing your teacher probably tried to correct you on, one misleading question, one thing you might have learned incorrectly at school, and a couple that might be technically untrue but it doesn’t really matter that much in the long run. But I suppose that IS less of a snappy title for an article.

Truth, Justice, Freedom, Reasonably Priced Love, and a Hard-Boiled Egg.