To see a world in a grain of sand

May 30, 2013 6:03 PM

First-ever high-resolution images of a molecule as it breaks and reforms chemical bonds. Remember those college textbook diagrams of molecules? They're surprisingly accurate.
posted by bitmage (32 comments total)

I see Benzene rings.
posted by localroger at 6:09 PM on May 30, 2013

Guys, LIVING IN THE FUTURE is AMAZING
posted by DoctorFedora at 6:16 PM on May 30, 2013 [26 favorites]

I don't really have anything intelligent to say about this, but I did let out an audible and amazed: "Whoaaaaaa, coooool" upon seeing the pictures.
posted by asnider at 6:21 PM on May 30, 2013 [5 favorites]

Very cool.
posted by MrMoonPie at 6:21 PM on May 30, 2013

You can even see the bonds between the molecules!
posted by Alice Russel-Wallace at 6:22 PM on May 30, 2013

But the carbon atoms should be dancing.
posted by localroger at 6:32 PM on May 30, 2013

> "High Resolution"

The accuracy of this description is surreal. It is literally true by definition, yet the images are exactly the opposite of what is contained in the set of {High Definition Images} we are used to encountering in real life. The cognitive dissonance is delicious; Just what I expect from sub-newtonian physics!
posted by I-Write-Essays at 6:35 PM on May 30, 2013 [3 favorites]

Once, while thinking about the problem, Kekule nodded off and had a day-dream. In it he saw a snake coil up, and suddenly grab its own tail. It then struck him that benzene might be a 'ring'.

Unreal.
posted by Otherwise at 6:37 PM on May 30, 2013

Fanciful images.
posted by benzenedream at 6:42 PM on May 30, 2013

Here's what Wikipedia says is the first diagram of benzene rings, from 1865. We knew what these suckers looked like 150 years before we could see them. Awe-inspiring.
posted by jhc at 6:42 PM on May 30, 2013 [4 favorites]

Wow, cool. Dr. Fischer actually gave a seminar at my school on this topic (graphene) a few months ago, and his fiance taught my organic chemistry class. Interesting to see this on metafilter.

Anyway, the seminar was really interesting - one of the best ones I've been to. This guy is definitely someone to watch. I was hoping he would eventually "watch" a reaction happen in real-time. I'm glad he got into Science.
posted by o310362 at 7:06 PM on May 30, 2013

Previously, when the technique was first presented about four years ago. It looks like the new part here is that they imaged the molecule both before and after a reaction. But regardless, things like this are pretty amazing, and Atomic Force Microscopy is just an incredibly clever idea. (I talked about it a bit last time.)
posted by whatnotever at 7:56 PM on May 30, 2013

Once it's benzene, it cannot be unzene.
posted by GenjiandProust at 8:03 PM on May 30, 2013 [25 favorites]

I just used the info in this FPP plus my best Neil DeGrasse Tyson impression to blow my kids' minds.
posted by davejay at 8:47 PM on May 30, 2013

Does the brightness of the image correspond exclusively to electron density, or is there something else going on here? Also, what happens when you give it hexane, which isn't planar?
posted by Kid Charlemagne at 8:52 PM on May 30, 2013 [2 favorites]

I think it can only "see" (or feel, maybe) things on a plane. So it might only detect the hydrogen atoms on top of the hexane molecule.

These images are stunning! You can actually see the bonds.
posted by Kevin Street at 9:16 PM on May 30, 2013

Remember those college textbook diagrams of molecules? They're surprisingly accurate.

This coming as a surprise to anyone says very sad things as to the state of science education. Mathematical and conceptual models aside, we've been doing x-ray diffraction for roughly a hundred years.
posted by 7segment at 10:10 PM on May 30, 2013 [5 favorites]

Maybe I'm just tired, but this part too seems quite silly, particularly the framing in the first sentence and how it ties back to the last sentence:

A chemical bond is not as simple a concept as it may appear, however. From the dozens of possibilities, the starting molecule's reaction did not yield what had intuitively seemed to Fischer and his colleagues the most likely products. Instead, the reaction produced two different molecules. The flat silver surface had rendered the reaction visible but also shaped it in unexpected ways.

posted by lordaych at 1:55 AM on May 31, 2013

Pfft. I made the exact same image 20 years ago using Kai's Texture Explorer.

Oh...This is real? Daaaaaaaaamn...
posted by Thorzdad at 3:52 AM on May 31, 2013

Bohr-ring.
posted by RobotVoodooPower at 5:33 AM on May 31, 2013 [4 favorites]

it's a picture of an unseeable thing, sort of like the false-colors in the hubble pictures. you *can't* see the molecules, you are looking at a map of small-ish scale electrical forces.
posted by ennui.bz at 6:10 AM on May 31, 2013 [2 favorites]

you are looking at a map of small-ish scale electrical forces.

Some of my best friends are made of small-ish scale electrical forces!
posted by Kid Charlemagne at 7:01 AM on May 31, 2013 [1 favorite]

Huh, I always assumed those diagrams were abstractions. Cool.
posted by benbenson at 7:06 AM on May 31, 2013

The collaborators then turned to a technique called noncontact atomic force microscopy (nc-AFM), which probes the surface with a sharp tip. The tip is mechanically deflected by electronic forces very close to the sample, moving like a phonograph needle in a groove.

A sharp tip might be the understatement of the year; it's a single oxygen atom.

Also how cool is it that we live at a time when noncontact atomic force microscopy is a thing.
posted by Mitheral at 7:46 AM on May 31, 2013 [1 favorite]

HOLY SHIT! I just made a PDF of that article and showed it to 3 of our scientists, one of our QC chemists and the regulatory manager. There is a little nerdgasm occurring right here at my desk!

I work at a pharma manufacturing site, so this article is like, the BEST THING EVAR
posted by lonefrontranger at 7:47 AM on May 31, 2013

My gosh, this is really cool. My take on organic chemistry and biochemistry was that in organic chemistry you learn the very clean, abstract diagrams like they present, but then in biochemistry you get into some of the exceptions to these interactions, which turn out to be really important. Things like "such and such carbon should act this way, but because it's next to this other stuff it actually acts in a slightly different way." It feels like you're constantly bending the rules - the local environment of an atom or amino acid or whatever causes it to behave slightly differently than the idealized model. THAT'S what blows my mind about this picture - you can see it! Look at the way that the carbon rings in the original 3-ring structure are more-or-less perfect hexagons, but then they become warped slightly as other rings are added in, elongating some sides and shortening others. Man. Neat.
posted by Buckt at 8:21 AM on May 31, 2013

I was just thinking more about that. I didn't read the paper - does anyone know whether that distortion I was seeing actually is distortion in the shape of the ring, or perhaps it could be that the whole molecule has started to form a more 3-dimensional, with a bulge in the middle, and that's what makes it look distorted?
posted by Buckt at 8:36 AM on May 31, 2013

The authors think the distortions in bond lengths were a measurement problem. From an article of last year from the same group: "With the help of ab initio calculations we found that the tilting of the carbon monoxide molecule at the tip apex is the cause of this contrast."

In other words, the tip of their needle bent over the course of the scan. I'm sure this will get better as they improve their technique.

The evolution of nc-AFM has been great to watch, and the IBM Zurich lab has always been at the tip of the field. They're not so serious all of the time. Bonus movie.
posted by bonehead at 9:04 AM on May 31, 2013 [1 favorite]

Mathematical and conceptual models aside, we've been doing x-ray diffraction for roughly a hundred years.

Indeed: The atomic structure of the benzene ring was first measured by Katherine Lonsdale, in 1929 (paywall, but first page for free).

This, however, is electronic structure. AFM measures electron densities buy using the Pauli-exclusion principle. This is amazing because the electronic structure is so close to what Huckel predicted in 1931 (paywall, first two pages are free, German).

This is so exciting because atomic nuclei are mostly spectators in chemistry (at least for light elements). To understand reactions, the electronic densities are overwhelmingly important. XRD is a great tool for understanding molecular geometry, but doesn't say anything about bond shapes. It's like trying to infer how dinosaurs behaved from their fossilized skeletons. NC-AFM allows us, for the first time, to see molecules in their full electronic glory roaming silver surfaces, rather than their nuclei frozen in crystals.
posted by bonehead at 9:30 AM on May 31, 2013 [2 favorites]

The authors think the distortions in bond lengths were a measurement problem. From an article of last year from the same group...

My mistake, I've confused the Berkley and Zurich groups. That's from the IBM Zurich group from a similar measurement last year. The work in the post is from the group at Berkley. I think the comments from the Zurich paper however still hold.
posted by bonehead at 10:21 AM on May 31, 2013

Thanks for the information!
posted by Buckt at 1:11 PM on May 31, 2013

What's getting me about this is that the technology used to create the image was introduced a few years after Kekulé died, the Victrola.

My folks own one and I used to marvel at how awesome it was that you could plop in a fresh needle, and it would transmit the vibrations from those tiny wavers in the grooves of the record to a glass plate, where it would go through a trombone's worth of funnel and come out of the box loud enough to dance to. That's pretty much what they've got going on here once you abstract it a little bit and shrink it a whole bunch.
posted by mcrandello at 1:12 AM on June 1, 2013