Thursday, May 30, 2013

Tracking Reactions? AFM FTW

Thanks to @slugnads at Wired for pointing out this story!
Update 5/31/13 - Derek's also got a great review going at Pipeline.

Remember 2009, when you gasped for a moment at the beautiful IBM structure of pentacene

Credit: BBC News | IBM | Science
In 2012, just in time for the 2012 London Olympics, the same team helped to image "olympicene."

Credit: BBC | IBM
And now, just 5 months into 2013, a team of researchers from UC-Berkeley / LBNL and several physics institutes in Spain have watched cyclizations occur on silver surfaces, using AFM tips to detect the ghostly products in stunning resolution:

Credit: Science | LBNL | UC-Berkeley | Wired

As if this couldn't sound any more amazing, the researchers were able to predict and visualize several products previously predicted by theory, but never directly observed (stabilized diradicals, anyone?). 

So, will this be a standard technique for the practicing chemist? I'm guessing not for quite a few years, since the hardware involved still isn't commonplace, and the technique probably works best at prohibitively high dilutions with flat molecules. Med chem? Sure, you could watch a Suzuki coupling occur, or watch a Cope rearrangement, but for "3D" molecules (read: alkaloids, vitamins, sugars, etc...) I think NMR and X-ray crystallography will still be your best bets. 

But to paraphrase the futurists, predictions ironically suffer from poor foresight - after all, just over a month ago, a Japanese group disclosed how to take on-demand crystal structures of just about anything. So, I'm sure someone will invent a "rugged" surface capable of guiding the AFM tip around points and curves to monitor, say, real-time Pictet-Spengler reactions. Can't wait!


  1. DANG. That's cool.

    Also, careful with that crystallography paper; every crystallographer in the department here is criticizing that paper. Their real achievement was carefully disguising its (apparently severe) limitations.

    1. Ooh, now you've piqued my tell!

  2. I think the description of "tracking reactions" feels a little off. It's "deposit reactant on surface, do AFM. Heat it up to have some chemistry occur, do AFM of the products." Given the various ways we've developed to monitor chemistry in real time over the years (albeit in not quite so visual a manner), this isn't quite what I would think of when I read "direct imaging of covalent bond structure in single-molecule chemical reactions."

    Then again, I'm probably cranky and jealous since none of my projects have progressed in quite a manner to give me time to do any single-molecule studies or neat chemical microscopy. I will be interested in seeing where this sort of work goes, though!

    1. Fair point, MJ. Would be cooler if, say, it could be done all at room temp, and constantly scanning to "watch" the reaction (like Ahmed Zewail's femtosecond arrays)

    2. I tend to think of, for example, femtosecond electron diffraction from the Miller group at Toronto when it comes to time-resolved atomic-scale monitoring of physical/chemical processes. Or if you want to follow the multiple species involved in the enzyme kinetics of a membrane bound kinase via NMR, you can do so.

      People do room-temperature AFM, and on even biochemical systems, but I think there are some trade-offs involved (e.g., giant messy macromolecules 'stick' better to the surface even at higher temperatures, and they're usually not going after such incredibly high spatial resolution in such studies). And - yet another sign that I am a physical chemist, heh - images are nice and all, but being able to examine the dynamics/fluctuations, and mechanical properties of systems, at the molecular level is also really cool, and can be done with AFM. Although such 'spectra' don't usually make for pretty press releases.

      I imagine we'll have to wait a while before some enterprising scientist figures out how to circumvent all of the above, as that's what we do in science!