Friday, August 28, 2009

Scientists finally image a single molecule (pentacene).

The most shared story on the BBC's excellent site right now is from the realms of chemistry - a subject that rarely gets a look-in these days.

It shows a remarkable "photograph" of a single molecule - obtained with a new gee-whizz imaging technique.

Here's the image (hope I'm not out-of-order here):

Pentacene molecule - in the flesh, so to speak

The molecule chosen for study is an aromatic hydrocarbon by the name of pentacene.  It's a relative of naphthalene (mothballs).  What's immediately clear from the piccy is that it's made from five fused six-carbon rings - benzene rings in fact. (Naphthalene by contrast has only two fused benzene rings).

The BBC's report draws attention to the fact that one can even see the bonds to hydrogen at the periphery of the molecule. However, that won't mean a lot to non-specialist readers if they are not familiar with pentacene's chemical structure.

Ay, but there's the rub - there are different ways of representing chemical molecules, depending on precisely which aspects one wishes to highlight.  A quick look at Google images will show what I mean:

Here's the most "realistic" model, so-called space-filling, in which the carbon atoms (black) and the hydrogen atoms(white) are shown in their correct relative sizes. The atoms merge with each other to represent strong chemical bonds. But the fused-ring aspect is now scarcely visible, the "hole' in the centre of each benzene ring being reduced to a mere white spot due to "crowding" of carbon atoms.

The conventional chemical shorthand strips out all non-essential detail, including the hydrogen atoms, and attempts to show the chemical bonding within the rings, as an alternation of single and double bonds (wrong, as it happens).

But that's another story: suffice it to say that chemists know it's wrong...

It took a bit of searching, but here's the representation that best complements, in my view, the BBC's image:

Ignore the second small molecule that hovers above pentacene. This structure shows clearly the five fused rings, and the hydrogen atoms. It is the bonds to the hydrogens at the two opposite ends of the molecule that are visible as bright areas in the BBC image. Don't ask me why the other C-H bonds are not easily visible.


ColinB ("sciencebod") said...

Tester: have just posted a comment to the New Scientist article on this topic.

ColinB ("sciencebod") said...

Am getting visitors from folk who have googled "pentacene photograph". Oh, those wonderful sitemeters.

Aficionados may be wondering why the ends of the molecule show up with brighter regions between C-H bonded atoms than the centre. This has been the subject of some interesting discussion on the New Scientist's write up. This link is to Page 1, but see Page 2 especially. The technique is apparently showing of regions that are electron-dense and electron-deficient, which correlate with the known chemical reactivity of the centre of the molecule.

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