I Can See Clar-ly Now

It's Monday, I don't feel like doing a lit review, nor have I found any good chem-related poop jokes, so it must be time for another unsolicited advice column.
One of the stranger tenets of aromatic chemistry, when first diving into it, is that not all molecules we'd call aromatic by definition are very stable. We learn as sophomores that benzene is remarkably stable, by nearly 30 kcal/mol, due to its 6π-electron, cyclic, conjugated system, and, if you were like me as a sophomore, you were entranced by the idea that a simple formulation such as that would impart such stability into a molecule. My fascination with organic chemistry started with benzene, and suffice it to say, that fascination hasn't gone away. Just check out the background.

But after benzene, things get kind of weird with aromatic molecule with more than one ring (polycyclic aromatic hydrocarbons, or PAH's). Naphthalene isn't as stable as benzene, as it'll react with conc. sulfuric acid at room temperature. Anthracene can react as a diene in Diels-Alder reactions. But they all conform to Hückel's 4n+2 rule, so what gives? In the middle 20th century, Eric Clar developed a theory of PAHs laid out in two now-classic books: The Aromatic Sextet and Polycyclic hydrocarbons. In them, he gives an explanation for the increased reactivity of those systems, which I'll briefly introduce here. In any case, The Aromatic Sextet, from 1972, is a quick read, complete with some ass-old NMRs for your amusement. His thesis is, put simply: Hückel's 4n+2 rule doesn't necessarily apply to PAH's, and a far more important factor in the stability of PAH's is the setup of their aromatic sextets.

Benzene contains what Clar defines as an aromatic sextet: that is, the six π electrons in benzene constitute a sextet. These sextets can be written as circles. Note, however, that only sextets can be written as circles: in naphthalene, there is only one sextet, and four other electrons, so writing two circles in for the electrons is wrong. It's something we teach sophomores to do, even though a lot of teachers and grad students get it wrong too:

Of course, since the two rings have equal electron density due to resonance, that sextet isn't on the one ring alone. Clar denotes that there is only one sextet in the molecule, although it is dispersed about the ring, with arrows.

An example of reactive non-sextets is phenanthrene. Phenanthrene has two sextets, shown here on the outside rings, that are in resonance with the middle ring, which contains a double bond. Even though there is resonance, the middle ring's double bond acts like a real double bond, and the outer rings have benzene-like stability.

With linear acenes, there is only one available sextet, and the longer the system, the more reactive the rings. Anthracene is reactive, tetracene is even more reactive, and the violet pentacene is so reactive that it'll dimerize and must be stored under nitrogen and in the dark.

In general, the more sextets that can be utilized to represent the pi-system of a PAH, the more "stable" it is. Molecules that can be represented with only sextets, called "fully-benzenoid" by Clar, are extremely stable. Triphenylene, isolated from coal tar, is very unreactive. peri-hexabenzocoronene (HBC), which I've blagged about before, is so stable that you can't use a mel-temp to find the melting point, because the glass will melt before the compound does.

This lil' introduction only scratches the surface of the large, rather diverse, and exceptionally pretty-colored field of arene chemistry. Next week, I'll share my award-winning* recipe for chicken parmesan.

*My mom likes it

THE TOP PIC: According to legend, Kekulé's discovery of benzene's ring structure was sparked by a day-dream of a snake biting its own tail. In ancient cultures, a snake or dragon biting its own tail is known as Ouroboros, representing the cyclic nature of the universe, among other things.


Kutti said...

This is a nice one! I like these kinds of posts very much although I always get an eyestrain when reading so much white text on a black background ;-)

milkshake said...

Somewhat Unrelated Question: Does azulene have any use in the kind of material science that you are doing? You know, it's blue.

Jan said...

There are so many interesting PAHs. Look up the mineral Karapartite. It is a natural occuring mineral of coronene!
Also the stability of the oxidation products of acenes can be estimated by the the numbers of electron sextets versus the numbers of cyclohexadiene rings. (e.g. 1,4-anthraquinone vs. 9,10-anthraquinone, 6,13-pentacenequinone vs. pentacene-5,7,12,14-tetraone).
Tried to synthesize pentacene from the scratch? never do it! The isolation is a major pain in the aßß. But if you want to try it choose this route: W. Ried, F. Anthöfer, Angew. Chem. 1953, 65, 601. for the synthesis of pentacenequinone followed by the reduction with LAH (Nathalie Vets, Mario Smet, Wim Dehaen, Tet. Lett. 2004, 45, 7287.). Have a gradient sublime ready and never use aluminium in cyclohexanol!!!

ElwoodCity said...

Thanks. That was awesome.

By the way, when I met my now-wife one of her opening flirtations had to do with the stability of benzene. That was certainly an attention getter.

Excimer said...

kutti, psi*psi and I are just the opposite. We prefer reading white text on black backgrounds for some reason.

Milkshake: I don't know of any uses for azulene, but that doesn't mean there are any. It is purty, though.

Jan: Wow, awesome. I don't ever plan on making pentacene but if I do... well I just hope I don't have to.

Ψ*Ψ said...

I might argue with you about pentacene storage. If it's in solution, keeping it in the dark and under nitrogen will not do a damn thing--it will still butterfly-dimerize like crazy. In the solid state, though, it's pretty much OK.
jan: The color change between 9,10-anthraquinone and 1,4-anthraquinone is pretty striking.
Does the text appear white? It looks blue to me!

Felix said...

One has to say that the typical 4n+2 rule only applies to monocyclic systems (and has a pretty mathematical derivation there). you can apparently also generally solve Hückel's theory for linear polyacenes but it's not a general rule that applies to any system, just look at pyrene and biphenyle

Uncle Al said...

So much of organic - certainly pharma - is flat. 3-D with trypticene! One might go double trippy with 9,9'-bianthracene for starters. What fantastic fun from 10,10'-dibromo-9,9-bianthracene, to the alpha,omega Br-terminated trypticene dimer, then... wait for it... pursue the Wurtz possible product. Rigid rods, anybody?

David Eaton said...

I have always been fascinated by benzene, too. I flip-flop between liking the smell of benzene vs toluene. I like them both, really.

When I was a kid, I read Asimov's Guide to Science and got the great idea that I would try to distill something out of coal, precisely because of the stories about coal tar and oil. I made this ridiculous "vacuum system" out of dry ice and a refrigerator compressor and about all the spare glassware I could *ahem* borrow from the middle school.

To get some high heat, I made a discharge tube with coathanger wire and rubber stoppers and a condensor. I threw a spark using a neon sign transformer, and with a bit of ground coal, made a really cool explosion. The thing that made the most impression on me was a shard of screaming hot glass landing on my leg.

My parents never said a thing about the experiments I did in their garage. A lot of the shit was completely ill thought out and half-baked, but some of it worked. I still prefer making my own instrumentation and apparatus. And some of it still goes up on me. God damn, I love being a scientist.

Azulene in molecular electronics:

I just glanced at it. It's in my 'to read' pile.

I hear there are some simple, stable and readily accessible pentacene derivatives, but who knows?

Ψ*Ψ said...

If I see the structure of said soluble, stable, super-awesome pentacenes again, I think my head might explode.
Doesn't help that I used one of those as the crystal for my x-ray final.

Mike said...

According to legend, Kekulé's discovery of benzene's ring structure was sparked by a day-dream of a snake biting its own tail. In ancient cultures, a snake or dragon biting its own tail is known as Ouroboros, representing the cyclic nature of the universe, among other things.
I bet he just look a bit too deep into Loschmidt's notes.

GMC2007 said...

These effects also determine regioselectivity of electophilic aromatic substitution of naphthalene. Attack at C1 tends to localise the insult in one ring without excessive disruption of the aromaticity of the other. Attack at C2 results in two bits of pi-system that can only 'communicate' thru the other ring. Similarly, pyrrole undergoes electrophilic attack at C2 (vinylogy, separate topic) but indole takes the hit at C3. The effect of an amino group on pKa of isoquinoline can be seen in a similar light. At C1 it pushes pKa up by about 2 units but has practically no effect when placed at C3. Curious indeed.

Mitch said...

Is heat of formation the best way to measure "stability".


Excimer said...

Mitch- I'm not getting into an argument of semantics over this so I'll just say "in solution, yes." Do you know better? Sure. Do I care? Not really.

Mitch said...

Stability and inertness/lack-of-reactivity are often used interchangeably for whatever reason. Apparently, this isn't the place to discuss it though.


Charles Abrams said...

Just curious, what would Clar say about the pentalene dianinon? Katz made this and the double ferrocene sandwich too.

Excimer said...

Mitch- my issue with it is people tend to treat what is little more than a issue with terminology as a lack of conceptual understanding. This is something which I butt heads with edu-folk a lot over, and I can see where they're coming from- as I've stated in a previous post, the terminology is there for a reason, but it seems to be abused by people who wish to make the "I'm right" point in lieu of something deeper. It annoys me, y'know?

Is the "chemical inertness" of benzene determined by its heat of formation/ heat of hydrogenation/ etc. compared to analogous systems? Yes, it can- but there are other methods, and they all give about the same value: 30 kcal/mol compared to cyclohexatriene. Dare I say chemical intertness is the same as stability? From an organic chemist's perspective, sure- if it's stable under particular conditions, it won't react. From a strict semantic perspective, no- it's indefinitely stable under ambient conditions AND chemically inert. This lack of clarity, I suppose, has never bothered me, but it seems to bother a lot of other people, for whatever reason.

Also, I had about the worst day ever yesterday, and I needed someone to go off on (ask Ψ*Ψ). You were the lucky winner. Sorry about that.

mitch said...

Although, I admit, I do like to be right as much as the next chemist. Open ended questions, probably shouldn't be shot down so readily.

However, terminology is important. Hearing terms not used correctly is always a bit grating. Whether or not you know what it means, and whether or not all parties involve know what you mean. Vernacular laziness is not something you should excuse in yourself as a chemist.


Mitch said...

Oh, and sorry for the bad day that you had. Although, it may be prudent for you to look into other avenues of releasing pent up stress than the comments section of your shared blog.

Okay, I swear no more lectures from my end. :p


Excimer said...

psh, where's your sense of adventure, mitch? If I can't yell at people on my blag, where can i? Besides everywhere else, I mean.

While I agree with you about the terminology being important, my concern for it ends well before most chemists, I think. Does that make me a bad chemist? ...probably. *shrug*

Mitch said...

There is no one thing that will make you a bad chemist, but there are many things that we all need to work on to become better chemists. :)


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