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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: Twitter: Dereklowe

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September 17, 2012

Another One of Those Startling Molecular Images

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Posted by Derek

There's a paper out in Science from a team led by the IBM-Z├╝rich folks, who have been pushing the capabilities of atomic-force microscopy for some time now. These are the people who published the paper in 2009 with those images of pentacene, and now they're back with even higher resolution.
One of their images is shown here. This is a big polycyclic aromatic hydrocarbon, hexabenzocoronene. One of the things that students note when they first try drawing such things is where the "holes" are. Aromatic benzene rings are special (different electron densities, different bond lengths), and if you connect one to another by a single bond (biphenyl), that connecting bond is of ordinary length. But a structure like this one - is it six benzene rings connected by a network of those ordinary bonds? Or are the electrons spread out over the whole surface in a great big delocalized cloud? Or something in between?

Calculations suggest that "in between, but still different" is the right answer, with some of the bonds having more double-bond character than others. And that's what this paper has determined by reaching down and feeling the bonds with an AFM tip. There's a single CO molecule at the end of the probe, and they've gotten to the point where they can see that they get greater sensitivity if that carbon monoxide molecule is tilted over rather than pointing straight down. I am not making that up. Running this single-molecule finger over the surface of hexabenzocoronene gives you the images shown.

"A" is the structure of the molecule, with the two different kinds of bond (i-bonds and j-bonds) noted. "B" is an AFM image at a constant height of 0.35 angstrom, which is really putting your atomic thumb down. The dark parts of the image correspond to attractive forces (van der Waals), and the light parts correspond to repulsive push-back. In this case, the pushback is due to the Pauli exclusion principle - those electrons cannot occupy the same quantum states, and they are quite adamant about that when you try to force them together. The electron density is highest around the outer part of the structure, but you can clearly see the bonds all the way through the internal structure as well. Take a look at the central aromatic ring - its bonds show up more more clearly than the bonds leading out from it, reflecting the greater electron density in there. "C" is an AFM image at 3.5A height in a "pseudo-3d representation", and "D" is the calculated electron density in between these two heights (at 2.5A above the molecule). Note that the two different kinds of bonds are also apparent in panel C, where some of them are brighter and shorter.

This kind of thing continues to give me a funny feeling when I read about it. Actually using things like Pauli repulsion to make pictures of molecules, well. . .maybe I am living in someone's science fiction novel, at that.

Comments (16) + TrackBacks (0) | Category: Chemical News


1. Ludwig Boltzmann on September 17, 2012 9:03 AM writes...

I was right, damn you Mach.

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2. TeddyZ on September 17, 2012 9:19 AM writes...

Someone should update the Nobel Prize odds. If I were a betting man, this would get my money for a win in the next few years.

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3. Curious Wavefunction on September 17, 2012 9:28 AM writes...

What's interesting is that Don Eigler from IBM who was the first one to arrange atoms in fantastic shapes using a STM and who created the first quantum corrals and logic gates using carbon monoxide atoms never got the Nobel. Maybe it's still not too late to team him up with other atom viewers.

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4. svi on September 17, 2012 9:41 AM writes...

this is crazy. Can something like this only work for flat molecules?

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5. cdn_chemist on September 17, 2012 10:09 AM writes...

@ 4. svi

In the paper they actually show some measurements taken on buckministerfullerene (60), which is not planar. However they do mention that only C-C bonds parallel to the sample surface were investigated, to ensure that, amongst other things, variations in the distance between the sample and tip are negligible.

This is really fascinating work!

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6. cdn_chemist on September 17, 2012 10:11 AM writes...


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7. Morten G on September 17, 2012 10:12 AM writes...

So this is an image only of the pi-bonds, correct?

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8. David Formerly Known as a Chemist on September 17, 2012 10:32 AM writes...

Wow, this is the kind of stuff that drew me into science all those years ago!

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9. MIMD on September 17, 2012 12:01 PM writes...


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10. nitrosonium on September 17, 2012 2:25 PM writes...

how do they determine there is one CO molecule on an AFM tip?? how do you know where to tap/drag and AFM tip on a surface where there is only one molecule???

i did not read the paper. i am a synthetic chemist with a scorching case of ADD...i don't read papers this far outside synthesis and drug design.

from the lab next door....i just have a strange metallic taste in my mouth when it comes to AFM and interpretation of data. I guess these guys are at IBM and they have pretty pictures. at least they are not interpreting some "blip" on a force-extension-curve as a single, specific H-bond breaking. total hog wash when you see that published!!

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11. Sisyphus on September 17, 2012 8:19 PM writes...

Neo: I thought it wasn't real.
Morpheus: Your mind makes it real.

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12. Brooks Moses on September 18, 2012 1:37 AM writes...

nitrosonium @10: I assume they put a bunch of hexabenzocoronene molecules down on the surface (with a density that doesn't lead to too many overlaps) and then just scan until they find one.

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13. NJBiologist on September 18, 2012 11:30 AM writes...

How is it that these guys have management's support in doing this research while drawing a paycheck from IBM, while drug companies can't even sustain drug development research?

That's not a rant against the work or against IBM; I think the work is really cool, and I think it's great that IBM supports it.

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14. Structure Fetishist on September 19, 2012 3:46 AM writes...

@10 and @12:
I haven't had the chance to read the paper yet, though will do soon. Great science.

It's usually done in a way, that you spread your molecules on a flat, clean surface, say Mica sheets. You will have to find a way to deposit your molecules, so that there's not too much overlap. Then you go scanning on a defined area of the surface.

The images you see are processed heavily. The mask around the molecule tells you, that they are a) certainly averaged and b) they are 6-fold rotationally symmetrized as well.

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15. Carl 'SAI' Mitchell on September 21, 2012 4:54 AM writes...

@13, IBM will probably use this for chip design/evaluation. The current smallest transistor that I know of is a FinFET 3nm across (30 Angstroms, about twice the size of the molecule above) and Intel expects to have 5nm feature size by about 2020 in consumer chips. Finding ways to evaluate the operation of such small features is quite important, this research is likely a part of that.

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16. GianpaoloR on September 25, 2012 7:17 AM writes...

Interesting. Just wondering what is the major bottleneck beyond a future use of this tech for single-cell DNA sequencing. Is a question that makes sense?

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