So that’s what pentacene looks like
August 28th, 2009 by excimerThis has been blogged everywhere already, but Sam at Everyday Scientist gets the credit for exposing me to this paper in Science by Gross et al. at IBM Research Zurich, where they, uh, take a picture of a molecule- namely, pentacene.
Imaging to the atomic level is possible with one technique, scanning tunneling microscopy, which images molecules based on the densities of electronic states of the molecule relative to the surface it’s on. (That’s the technique used for all those “holy crap” single-atom images IBM Almaden is famous for.) However, getting atomic resolution with STM for organic molecules is a little tricky, and most of the time all you see are blurry-ish hexagons.
The authors in this paper, instead, use atomic force microscopy to image single molecules of pentacene on Cu(111) and Cu(111) with an insulating NaCl at temperatures of 5K under ultrahigh vacuum. Consider all the things that have to go right for this kind of imaging to work correctly. For one thing, you have to make sure that pentcene aligns with your surface correctly- namely, flat. This isn’t always the case. Fortunately, pentacene does lay flat on most metal surfaces. Then you have to make sure you have the right kind of probe. The probe is the really interesting part of this paper- they use a CO-terminated Cu probe tip to enhance the resolution of the AFM. Atomic imaging of this kind basically means you have to use a single-molecule probe, and that molecule can’t be too big, either. CO seems to work rather well to that effect. (Check out the SI to see how they make the probe, it’s ridiculous. They basically pick up the CO from another Cu surface with a little electrochemistry.)
Sometimes a picture is worth a thousand words. Though I hate to put on my douchey skeptical scientist hat on here, in papers like these where the crux of the paper is a pretty picture, those thousand words are mostly bullshit. They, at least, do some nice calculations to deconvolute the nature of the relevant forces in these images, I hope that this paper is vindicated further by others using this technique to image other molecules, like nanoqueers.
They also interviewed the authors of the paper in this video.
So you put on the douchey scientists pants because they published “just a picture” or because they felt they had to try and justify the pic with a bunch of other calculations?
I think this is pretty awesome from a proof of concept approach, as when people never though one would be able to image individual atoms. Now you can do it with a “toy” STM.
Well, normally I’d put the douchey science hat for papers without other supporting information and just a pretty picture (ie. the majority of papers which rely on AFM). But from my limited knowledge of the inner workings of AFM they do a nice job in this paper.
While this has been done before, here’s what I see as one of the next frontiers; determining stereochemistry by STM/AFM without having to do x-tal or NMR
The thing is, it hasn’t really been done before- not for organic molecules, not with this kind of resolution, and not with AFM.
A number of people have looked into stereochemistry of 2D networks (Colin Nuckolls comes to mind)- it’s an interesting idea, that some “flat” molecules are chiral when forced into two dimensions.
STM has been used to determine stereochemistry of single molecules before, although rather crudely and not with this kind of resolution.
There was a Nature paper a couple of years back about determining stereochemistry of hydrogenation products of alkenes which I am too lazy to dig up right now. There’s also George Flynn from Columbia who I believe has done some related stuff, albeit in most of his cases he ascertains single mol. stereochemistry by looking at monolayers. I will look up Colin Nuckoll’s work.
I love it — nice resolution! You can draw and explain structures and back the explanation up with all kinds of data, but a picture really is worth a lot to show Organic 101 students that the molecules really do have the expected shape!
this pentacene should be in Always adds
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