« Chemistry in the Quantum Vacuum. No, Really. |
| Pharma Sales Corruption in India. And How. »
September 17, 2012
Another One of Those Startling Molecular Images
There's a paper out in Science from a team led by the IBM-Zürich 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.
+ TrackBacks (0) | Category: Chemical News
POST A COMMENT
- RELATED ENTRIES
- Scripps Update
- What If Drug Patents Were Written Like Software Patents?
- Stem Cells: The Center of "Right to Try"
- Speaking of Polyphenols. . .
- Dark Biology And Small Molecules
- How Polyphenols Work, Perhaps?
- More On Automated Medicinal Chemistry
- Scripps Merging With USC?