Quite hexagonal

I’m of the personal opinion that polycyclic aromatic hydrocarbon molecules, often known as PAHs, are one of the finest proofs that the Universe is beautiful. Carbon, at the molecular level, organises itself into geometrically perfect hexagons. It doesn’t even need any energy to do this. It does it all by itself, because this perfect hexagonal geometry is actually the lowest energy state of the atoms themselves. Just beautiful.

Though PAHs are generally rather badly understood, if I’m honest. I can understand astronomers making mistakes, but chemists I have a little less sympathy for. In fairness though, they’re difficult things to properly represent using only a pen and paper. It all started with a German chemist named Friedrich August Kekulé. While he was one of Europe’s most prominent chemists during his time, Kekulé (who never normally used his first name, preferring to go by the name August) is most famous for one thing. Benzene. In Kekulé’s work, benzene molecules were six membered carbon rings joined together with alternating single and double bonds. For his time, Kekulé’s work was brilliant.

But it wasn’t perfect. Organic chemists still like the “Kekulé structure” of benzene, because they can draw curly arrows and show how reaction mechanisms work…

These drawings showing double bonds moving are called resonance structures. And they’re a reasonably adequate description of how these things work. But… If you aren’t an organic chemist, you shouldn’t really like using Kekulé structures. They’re not really accurate. You see, spectroscopically, benzene doesn’t look like that. Those single and double bonds would vibrate at slightly different frequencies, but this isn’t what we see in the lab. Instead, we only see one vibration for carbon-carbon bonds. In other words, all the bonds are equal length. They share their electrons liberally, like a little carbonaceous hippy commune.

So the best way to depict a benzene ring is a hexagon to show the six carbon atoms, and a little circle in the middle to show that six electrons are being shared evenly between them. It’s almost adorable really, isn’t it? Because there are six electrons, and this causes aromaticity (a chemical property where delocalised electrons cause increased stability), it’s referred to as an “aromatic sextet”.

So that’s benzene, with one aromatic ring. And this is where people start to get PAHs wrong. Which is fair, I suppose, seeing as no one teaches you this stuff as an undergrad. The worst mistake is to draw a PAH molecule (this one is pyrene) with circles in every ring of atoms. This is wrong in a lot of ways, and frankly, it makes me twitch a bit. It causes the same discomfort I feel when a seminar speaker has slides written in Comic Sans. You see, each of those circles would denote six electrons. But that’s way more than should be in the drawing. For me, all those circles spell out Noooo!

So most people resort to using Kekulé-type structures for PAHs. But in PAHs these are inaccurate for different reasons. For a start, you need to be careful where you draw the bonds, or things are just messy and bleh. But if you draw them more tidily like this, you find something interesting. Like this, you can quite easily see that a couple of the rings in this pyrene molecule are basically the same as Kekulé benzene molecules. This same thing was noticed in the 50s by a Czech chemist named Erich Clar. Clar, sadly, isn’t particularly well known, but his work laid the foundations for most of what we know about the chemistry of PAH molecules.

The structures Clar devised (now known as Clar structures in honour of his work) involved drawing in these “benzene-like” regions as circles just like in benzene molecules, and filling in the remaining spaces with traditional double bond-type structures. Interestingly these structures make for a good prediction of how PAH molecules act, chemically speaking. Chemical reactions will typically occur at the sites which are shown as regular double bonds, and not on the aromatic sextets. Simply put, not all aromatic bonds are the same. When you have a lot of them together, some are more aromatic than others!

For instance, if you try drawing a few, you’ll notice that some structures can hold a lot more of these aromatic sextets than others. These long thin PAH molecules, for instance, are acenes.

Because acenes can only really hold a sextet on one of their end rings, those central carbon atoms are the most reactive. The longer the chain, the more the electrons tend to all clump together at the ends, and the more reactive the centre carbons are. This is why, if you oxidise anthracene, you get anthraquinone — which pretty much always has two oxygen atoms stuck to the central carbon atoms. Those atoms are simply more reactive. Interestingly, this prediction of Clar theory, made back in the 50s, was quite definitively proven correct just a few short years ago using atomic force microscopy. So basically, Clar made some pretty awesome predictions by deriving molecular structures in the same sort of way that mathematicians derive equations!

The other rather beautiful prediction in Clar theory is that certain molecules will consist entirely of interconnected benzene rings. Referred to as “fully benzenoid”, these molecules are highly resistant to chemical attack, because they’re as aromatic as can be. They also always tend to have lovely symmetric shapes, forming triangles and hexagons like triphenylene and hexabenzocoronene.

I love carbon chemistry. It makes such beautiful shapes!

I feel obliged to mention that those lovely people over at Carbon Based Curiosities were writing about Clar theory before it was cool.

A curious quirk I’ve noticed, which seems to be virtually unique to american scientists is to turn “PAH” into a word and say it in sentences as “paah”. I really can’t adjust to this for some reason. I’m probably too used to being like everyone else in the world and referring to one as a “pee ay haytch”.

About Invader Xan

Molecular astrophysicist, usually found writing frenziedly, staring at the sky, or drinking mojitos.
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