IBM takes first 3D image of atomic bonds | Hacker News Reader

IBM takes first 3D image of atomic bonds

gizmodo.com

149 pointsjedliu49 comments

WOW! this is a big breakthrough. I have friends working in my collaborators group using STM and AFM at UHV (Ultra High Vacuum) and ULT (Ultra Low Temperatures), and know second hand how difficult/near to impossible it is.

How is the picture 3D? Also shouldn't we see electrons in pi clouds above the aromatic rings?

I'd say it's 3D in the sense that it's a height map rather than a cross section. (We've been able to see cross-sectional images of bonds for some time using transmission electron microscopy, I think). It's not a full three-dimensional structure though, and it'd only work on flattish molecules like this.

It should be noted that this sort of resolution has been attainable for some time using scanning tunneling microscopy, but I'm pretty sure this is a first for atomic force microscopy. STM doesn't give you a very good image of bonds -- in fact bonds are generally the thing you _don't_ see, since STM works by pulling electrons in/out and bonds are stable places where electrons really don't want to come out of or go into. AFM, on the other hand, shows bonds very nicely.

You can sorta make out where the aromatic rings are. I'm not sure why it's so bright at the ends -- any organic chemists out there who can explain that?

about the brightness at the ends - I'm pretty sure that is due to the fact that this is a pi-conjugated system; that is, the pi-bonded electrons can jump around the whole molecule. This, together with the fact that the molecule is finite in size, means that the pi electrons are confined to a rectangle of lower potential energy, and when you solve the quantum mechanics (similarly to the quantum harmonic oscillator) you'll find higher electron density at the edges of the confining potential.

I'm totally willing to trust the word of someone called "graphene" on this one.

Those "clouds" are probability clouds. It means that the electron should be in the vicinity of the cloud at any given time.

Also, consider that an electron is 1/1000 the size of a proton.

actually, if you consider that afm is directly detecting charges, I guess we're talking about more than probability here - that picture ought to be a (rough) record of where the charges in that molecule were as the AFM needle passed over the molecule in that 20hr period

Electrons in an atom don't have a [specific] location. It's not a concept that exists for them. So, yes, it's a probability.

Despite the common image, electrons don't orbit the nucleus like planets around the sun. They sort of exist around the entire thing in all locations at the same time (in 3D, not in a ring, but a shell).

Are the samples cooled to near zero when scanning like this? As far as I understand, even slight temperatures cause molecules to move at ridiculous speeds.

They said it was a 20-hour scan, at 5K, with the AFM tip 0.5 nanometers from the pentacene molecule. The molecule itself is 1.4 nm long, so they were only about 30% of its length away from it in the vertical direction.

Yes, given the resolution of the image, I am guessing it must have been performed at UHV, ULT and vibration free room.

great comment on the page: "trivia: molecules have no color" They don't? Then where does color come from? Why wouldn't gold atoms be golden?

i'm hoping the guy was being sarcastic but...

Color is the wave length of light you can see. Red is one wavelength, blue another, infra red and ultra violet yet another. But you can't see those last two.

Molecules have no color because they are smaller then the shortest length wave of light you and I can see.

Think about dropping a stone in a quiet pond. Think of the waves that are created. If they bump into a large obstacle they are reflected back. If they hit a tiny one, like a thin blade of grass sticking out of the water, they just flow around.

Gold is golden because a whole lot of gold atoms bunched together reflect a yellowish range of light. Gold the material is gold colored. A single gold atom does not have color.

So if I'm a gold atom, and I absorb some photons, a bunch pass through me, and some get reflected - and the photons that are reflected from me over a period of time happen to be average out to something a cone cell in the retina would interpret as gold- couldn't I say that I'm gold-colored? In other words, replacing the billion-atom aggregation with a simple time series?

It seems to me it's an argument about semantics, not physics.

that's not the case, the physics in fact is very different for a single atom than for a lump of metal.

A single atom has very specific set of electron energies as a consequence of the electrons being confined to the area around the nucleus. This means that it can only absorb or emit photons with energies corresponding to the spacings between any two energy levels (and the absorption/emission must be accompanied by a jump/fall of an electron between corresponding energy levels. Any type of atom will thus have a secific pattern of absorption/emission peaks, this is incidentally how we can tell the composition of stars and dust clouds in distant galaxies.

For a lump of metal, a good approximation is to consider the electrons as being able to freely roam throughout the entire crystal. As a consequence, when they are excited by an incoming photon (of any energy), they immediately relax back to their original state, emitting the photon again at the same energy. This is why metal films act as mirrors and why metals in general are shiny. As for the goldish color of Gold, that has to do with some relativistic effects which I don't understand (yet ;-) ). I believe the same is true for Copper.

I think there is some terminology confusion. The image is not a "photo" - it is not a recording of emitted light. Hence the colors used to display the image for us have nothing to do with the color (reflected wavelengths) of the molecules.

Ah but protons aren't particles... except some times they are, other times they are a waves. The bottom line is individual atoms don't reflect protons.

Did you mean photons?

Embarrassingly, yes. Obviously I can neither type nor spell well.

Molecular absorption and emission of photons is one mechanism by which color is created. For example, the color of water is caused by molecular absorption.

Judging by how big of a feat this is to image a molecule, how on earth do we know how things like cellular respiration work? How do we know cells use ATP, etc without being able to watch?

(I may make this question a separate post to HN, it's been bothering me for a while.)

Biochemists use easily hundreds of different techniques to elucidate, logically or probabilistically, details about cellular processes. They take serious advantage of techniques like optical properties of solutions and selective targeting of fluorescent tags to visualize effects. Moreover, they tend to abuse the very nanomachine proteins they're trying to study in order to study them further.

A simple example (the names are removed to make this easier to digest, but if you're curious it's the action of Glyceraldehyde-3-Phosphate Dehydrogenase in glycolysis) involves a protein which is known to play a part in the breakdown of glucose. This protein catalyzes the addition of a "high energy" phosphate to our compound so we can break it down further while also pulling off a reactive hydrogen (and adding it to NAD+ to make NADH) so the cell can use that later (another kind of energy like ATP).

Biochemists, assuming they can already purify the compound and know the overall reaction, investigated the action of the enzyme by mixing in a highly reactive fluorescent-tagged molecule that looks similar to the product of the reaction. This molecule bound permanently to the inside of the enzyme which was then denatured and sequenced, looking for whatever amino acid showed the fluorescent tag (cysteine). Then the inserted modified reagents which contained radioactive hydrogen and phosphate to figure out where exactly those molecules ended up. In this way they learned where the enzyme added the phosphate to the product and exactly which hydrogen was removed from the initial compound to make that NADH.

Biochemistry is a really fascinating story of minute triumphs of discovery. Unfortunately, like any part of science like that, it means that the day-to-day life of a biochemist is backbreaking and tedious. Regardless, if you're interesting, there is a lot of fun stuff to study.

Oh, and as far as imaging goes, it's simply amazing what has been done with X-ray crystallography.

I second that. My s.o. works in that field. Tiny discoveries mixed with frustration. Still it's fun.

Not a biologist, but I've been in bio labs and it is _meticulous_ work. Very, very clever processes for detecting molecules as they pass through (or don't pass through) certain organelles, a good dose of math, some inference, and sometimes luck.

Not being able to see (and as the toothpick -> truck of floss poster mentioned above, this isn't going to help with biological systems much at this point) does mean there are significant gaps in what biologists know. On the other hand, biologists have been visualizing larger structures for some time (even proteins via xray etc.)

They have to crystalize the proteins to make the xray-technique work.

That is fucking awesome.

It's depressing to consider the fact that it would probably get downvoted on the science subreddit.

Second that. Picture of the year as far as I'm concerned. Simply unbelievable. What a time to be alive.

So, now that we can 'see' the 3D arrangement in a manner of speaking is there any way we could feed known protein structure in to neural networks by imaging them in quantity and take some of the sting out of protein folding by identifying likely candidate ways to do the folding ?

Or is that too big of a leap ?

I think there would be major issues getting folded protein to 5K. Plus proteins "live" in 300K and the oscillations are probably very important for the function (perhaps even more than a single arbitrary structure you would get from a picture like this).

Yes to all of the above. Not to mention that we've long been able to visualize protein molecular structure using X-rays and NMR. This probably isn't very useful to anything related to proteins.

Regardless of what the headline says about "3D", this only works on flattish molecules. Using it to study a protein would be like a blind man determining the structure of a truckload of candy floss using a chopstick.

XFEL is probably going to be a better way to look at biological macromolecules (though I'm not sure if the resolution would be high enough to see atom-sized details).

It's a kind of the opposite approach: instead of slowly collecting information from extremely static scene they will blast the sample with very powerful X-ray laser, taking snapshot before shattering it to pieces.

http://www.xfel.eu/en/research-examples/structure-of-biomole...

we've had 3D atomic level detail for molecules - especially horrendously more complex ones than this - for a long, long long time. NMR and X-Ray crystallography in all its guises are the two main candidates here. NMR even gives you that info in real time, and (if you so desire) in more realistic conditions (vital to learn about folding and activity).

Not to piss on a parade, but I don't see this as major breakthrough. It's a technical achievement with an established technology, of primary benefit to material scientists and nanotechnologists, both of whom already have imaging techniques at this level, but lack easy, cheap and instant ones, and face most of their hurdles at the design and synthesis side, not imaging/proof of construct

From a biochemist's point of view, if it was anywhere near real-time, THAT would be awesome.

What a time to be alive.

What he said. This is amazing.

Don't be depressed, it's the top link on science reddit. Though, sadly, the top comment is grammar correction :/

Funny -- last time I checked the science subreddit (just before I unsubscribed), the front page was entirely flooded with ridiculous sensationalism that had little or nothing to do with actual science, while some actually science-focused articles I was watching on the new submissions page were getting downvoted to about -1 or -2 then ignored.

I guess the fact this book comes with pictures probably gives it an edge there.

If that's true, IBM is probably making history (again)

Wow this blew me away! Nothing beats visual confirmation from an emotional perspective ;-)

Where's the URL to the original IBM press release / article? I would rather read the news from the source, than from those gizmodo subhuman morons any day...

Some links closer to the point of origin:

Pentacene on flickr - http://www.flickr.com/photos/ibm_research_zurich/3839799374/

IBM Research Zurich (pix of lab) - http://www.flickr.com/photos/ibm_research_zurich/

Article in MIT Tech Review - http://www.technologyreview.com/blog/editors/24040/

"The imaging work is described today in the journal Science."

Fun search result on www.sciencemag.org for ibm+zurich

Science 10 July 1987 - 'IBM's Zurich Lab Is "Flower" in Europe: Two major discoveries—the scanning tunneling microscope and superconducting ceramics—highlight IBM Zurich lab's success in tapping Europe's scientific talent'

Thanks for the links. Much appreciated.

"I would rather read the news from the source, than from those gizmodo subhuman morons"

Cut them some slack. At least they're watching/trying. Their article is a news item here, after all.

Loftus and Matt Buchanan are quite good. I hope they'e getting paid a lot, because being associated with the likes of Jesus Diaz is not what I'd call a career- or even life-enhancing.

Have you read the comments on gizmodo?

They're trying? Trying what? What they usually do is copy-paste from the source. That does not add much value. Hence, I ask again: where's the URL to the original press release? I don't want to read such great news from a website that allows comments from retards who know nothing about Physics...

I have an easy win for you. Stop reading the comments! They are almost universally awful.

True. But would it be too far-fetched to claim that the quality of a website / blog can be indirectly measured by the quality of its comments? A quality blog should not tolerate certain comments which are more appropriate for YouTube.

Sigh, when you find the answer to that question, let me know ...

They will never sell Chanel No. 5 in gas stations because it would cheapen it. Likewise, a blog that tolerates retarded trollish comments looks cheap. If I were one of the IBM scientists who worked on that project, I would hate to have my work publicized by a blog as distasteful as Gizmodo.

Call me elitist if you will. BTW, my question was rhetorical.

If you're elitist, it's in a good way. I agree.

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