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Seeing Atomic Bonds Before and After Reactions

Soulskill posted about a year ago | from the bond.-atomic-bond. dept.

Science 47

Necroloth sends this quote from an article at Wired: "For the first time, scientists have visually captured a molecule at single-atom resolution in the act of rearranging its bonds. Until now, scientists were only able to infer molecular structures. Using atomic force microscopy (abstract), the individual atomic bonds that connect the carbon molecule's 26 carbon and 14 hydrogen atoms are clearly visible and look startlingly similar to the stick diagrams in chemistry textbooks."

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first post (-1, Offtopic)

thisisnotreal (888437) | about a year ago | (#43873175)

just like how i saw it in my mind's eye!

Re:first post (-1, Offtopic)

magic maverick (2615475) | about a year ago | (#43876993)

You're an ugly fucker and you smell funny. Also, I think you really should have that rash looked at.
PS You're going to die alone and lonely.

Amazing To Actually "See" it (5, Interesting)

Striikerr (798526) | about a year ago | (#43873401)

I remember so many years of visualizing the molecule structures in school and learning how and why the atoms arrange themselves in molecules. The diagrams drawn and the physical models helped but always the thought of (Camelot)"It's just a model." (/Camelot) was there. Seeing the images created of these molecules by something actually measuring them was pretty damn cool and shows us just how accurate those models are. The technology which allows us to obtain these images is always pretty amazing too. To obtain these images .. "Non-contact atomic force microscopy uses a very fine, sharp point to read the electrical forces produced by molecules; as the tip is moved near a molecule’s surface, it’s deflected by different charges, producing an image of how the atoms and bonds are aligned."

So, it's in a way, similar to old record players where the stylus drags across the surface of an album and through the physical interactions with the play surface, converts the grooves and ridges to sound.. The stylus used in the article to measure the layout of the atomic forces is one atom thick at the end and is deflected by the forces which allows the generation of an image (it never physically touches anything).. All very cool stuff.

Re:Amazing To Actually "See" it (1)

Hoi Polloi (522990) | about a year ago | (#43874005)

I'm just very impressed that people were able to infer the structures of these molecules indirectly without ever being to see them directly.

Re:Amazing To Actually "See" it (1)

SnarfQuest (469614) | about a year ago | (#43876131)

Interesting tidbit: The first periodic table predates knowledge of the atomic structure.

Re:Amazing To Actually "See" it (2)

Saethan (2725367) | about a year ago | (#43874143)

Just imagine a scientist going "nobody move! I've dropped the stylus"

Re:Amazing To Actually "See" it (1)

rwa2 (4391) | about a year ago | (#43874337)

I imagine the scientist comforting the molecules... "don't worry, you're just going to feel a tiny prick!"

J/K, I'm sure all the researches have big brass ones. Bravo!

Re:Amazing To Actually "See" it (2)

kermidge (2221646) | about a year ago | (#43875439)

Very neat stuff, indeed. I recall chem classes in early '60s where we were introduced to trying to calculate bonding energies in single and double bonds, then on to forces in crystals. Along the way, many of us thought "gee, wouldn't in be neat if we could not only see the bonds but measure them as well?" To see this, and the work leading up to it over the years, has amazed me.

Given the number of times I played some of my LPs, would have been good to have had a no-contact stylus.

Re:Amazing To Actually "See" it (1)

drkim (1559875) | about a year ago | (#43881393)

Given the number of times I played some of my LPs, would have been good to have had a no-contact stylus.

That would be awesome! Maybe you could use a laser to read the music data off the spinning disk. I guess instead of grooves, you could encode the music with little 'dots' to represent...
oh, never mind...

Re:Amazing To Actually "See" it (1)

kermidge (2221646) | about a year ago | (#43882837)

Gotcha, and the wry sarcasm, and got a nice laugh; I thank you. I wonder, tho, if there's a nifty way to read old LPs with no contact. I might have missed it. Do you know?

Re:Amazing To Actually "See" it (1)

monkeyhybrid (1677192) | about a year ago | (#43883243)

You could get a ELP Laser Turntable [elpj.com] but it would probably be cheaper to get the original artists to reform and perform live in your home.

Re:Amazing To Actually "See" it (1)

kermidge (2221646) | about a year ago | (#43893087)

Wow, that's one fine piece of equipment! Also twice my annual income. Thanks for finding it.

"cheaper to get the original artists to reform and perform live in your home."

Um, no, especially when you add in transpo, accomodations, consumables. For a lot of it, it wouldn't work anyway, too many of 'em are indisposed or dead.

Re:Amazing To Actually "See" it (0)

Anonymous Coward | about a year ago | (#43888779)

There are projects that let you used a scanned image of the LP to recover the audio from the image. It doesn't require too extreme of a scanner, but still needs some quality. In theory 1200 dpi would be enough... but in practice probably need more.

Re:Amazing To Actually "See" it (1)

kermidge (2221646) | about a year ago | (#43893143)

That's an interesting approach; neat idea.

Re:Amazing To Actually "See" it (0)

Anonymous Coward | about a year ago | (#43876147)

and is deflected by the forces which allows the generation of an image (it never physically touches anything)

*Facepalm*

What do you think "touching" means? Hm?

deflected by the forces

In the case of electromagnetic forces, that is exactly what we mean with "touches"!

FAIL!

Re:Amazing To Actually "See" it (1)

Anonymous Coward | about a year ago | (#43877315)

There are multiple modes of atomic force microscopy, including both contact and non-contact versions.

In the case of electromagnetic forces, that is exactly what we mean with "touches"!

In such a context, contact is usually consider the case where a repulsive force is dominating, preventing the probe from getting any closer without more force applied to it. You can still be closer to the sample, without being in this repulsive regime, and for example have an attractive van der Waals force. This isn't "touching" because if you let go of the probe, it will move closer, as opposed to the case of it not being able to move closer without pushing harder. Frequently, in non-contact mode, the probe can be a couple nanometers above the surface, which would be a factor of 5-10 times larger than the length of bonds in the molecule.

Re:Amazing To Actually "See" it (0)

Anonymous Coward | about a year ago | (#43876185)

My understanding of this sort of thing was that, in an ultimately absolute and real way, nothing ever physically touches anything anyway...

not "visually captured" (4, Informative)

girlinatrainingbra (2738457) | about a year ago | (#43873419)

Atomic Force Microscopy [wikipedia.org] does not visually capture anything. It measures atomic forces with a finer resolution that goes beyond the optical diffraction limit for wavelengths of light visible to the unaided eye.

The rendered images are derived from the force measurements and thus these really are "inferred images" or visual renderings of force measurements. These are definitely not "visual capture" images. These are visual renderings.

Re:not "visually captured" (2)

sensei moreh (868829) | about a year ago | (#43873501)

It still very cool stuff!

Re:not "visually captured" (0)

Anonymous Coward | about a year ago | (#43873901)

But it makes the fact that the bonds look similar to stick figures in books "not startling at all'

Re:not "visually captured" (0)

Anonymous Coward | about a year ago | (#43874245)

The fact it is not a direct visual image doesn't change whether it is surprising or not that the images look like stick figure. It is not like AFM image consist of them finding the atoms, and then connecting the dots in an artificial post processing, instead it directly measures the electron structure of the molecule. If you were not surprised that it looks like the stick figures because you knew the stick figures were already a simple representation of electron structure and that the actual bonds are typically kind of stick shaped anyways, you wouldn't have been surprised regardless of it being a direct image or not.

Re:not "visually captured" (1)

rwa2 (4391) | about a year ago | (#43874323)

Are you trying to say that you can't "see" braille?

Re:not "visually captured" (1)

VortexCortex (1117377) | about a year ago | (#43875659)

No, I'm BLIND you insensitive clod!

Re:not "visually captured" (1)

rwa2 (4391) | about a year ago | (#43877163)

You don't have to SHOUT; I'm hard of hearing!

Re:not "visually captured" (2)

Striikerr (798526) | about a year ago | (#43875631)

Correct. I never indicated that they were taking pictures but were able to "generate an image" based upon the stylus' deflection from the forces in the atomic bonds (it's why I used the record player analogy). I recall first hearing about this when scientists used this method of visualizing atoms when they arranged some atoms to form the acronym IBM. See this article: http://en.wikipedia.org/wiki/IBM_(atoms) [wikipedia.org] and This for information on the Scanning Tunneling Microscope they used http://en.wikipedia.org/wiki/IBM_(atoms) [wikipedia.org]

Absolutely cool, relatively meh (4, Funny)

Just Some Guy (3352) | about a year ago | (#43873539)

That's awesome, but a little bit of a letdown after I'd misread "bonds" as "bombs".

Re:Absolutely cool, relatively meh (1)

Anonymous Coward | about a year ago | (#43873759)

I didn't think there'd be much of an atomic bomb left to see after a reaction.

Re:Absolutely cool, relatively meh (1)

sconeu (64226) | about a year ago | (#43874183)

[AOL] Me Too! [/AOL]

On the other hand... "My name is Bonds... Atomic Bonds..."

Before and After -- not "during the act" (2)

cruff (171569) | about a year ago | (#43873659)

The article says the pictures are from before the reaction (by heating), and after showing various reaction products, including ones not expected. The AFM is too slow to capture the bond rearrangements.

Re:Before and After -- not "during the act" (0)

Anonymous Coward | about a year ago | (#43874303)

You are one of those that "likes to watch", aren't you?

Bonding rules (1)

EmperorOfCanada (1332175) | about a year ago | (#43873679)

I can't wait until some new rules derived from first principles are wrung out of this data.

No surprise really (1)

interval1066 (668936) | about a year ago | (#43873717)

...look startlingly similar to the stick diagrams in chemistry textbooks.

Yeah, well, applied physics has a history of looking very much as we imagined it would in almost every case where there have been questions. Begging the question; "Are we really looking at reality, or stuff we want to see?"

Re:No surprise really (-1)

Anonymous Coward | about a year ago | (#43873861)

That's not 'begging the question', that's 'raising the question'.

Re:No surprise really (1, Funny)

magic maverick (2615475) | about a year ago | (#43877257)

Which begs the question, are you really truly a gigantic dick, or are you just a turd?

atomic bombs (1)

schneidafunk (795759) | about a year ago | (#43873845)

Did anyone else misread the title and think of melting faces?

Fascinating (2)

PPH (736903) | about a year ago | (#43873923)

Extend this technology to 3D and it will have some interesting uses for things like protein folding.

Re:Fascinating (0)

Anonymous Coward | about a year ago | (#43874127)

It is already moving in 3D to map the force surface. The targets are kept in high vacuum on clean surfaces. I don't think there's much to be gained over protein crystallography, since the protein is subjected to extreme conditions to get it into the AFM in the first place. The technique won't work in vivo as it were. Higher dimension NMR might be a better area to investigate folding if it became sophisticated enough.

Re:Fascinating (0)

Anonymous Coward | about a year ago | (#43877541)

X-Ray Crystallography has been used to measure electron density (and thus chemical bonds) in 3D for decades.

http://en.wikipedia.org/wiki/X_ray_crystallography

Re: Fascinating (1)

Rostin (691447) | about a year ago | (#43880521)

Good luck examining the structure of a single molecule using crystallographic techniques.

just 2d? (1)

someone1234 (830754) | about a year ago | (#43873943)

I wonder if the same imaging is possible in 3d, that would be really awesome in research.

What about X-ray diffraction and spectroscopy (0)

Anonymous Coward | about a year ago | (#43874069)

This is an inferred image too in a sense, obtained from force measurements. Just because it looks like a photograph doesn't make it a photograph. Scientists have been able to make "photographs" of molecules with even better resolution for a long time based on other types of measurements, such as X-ray diffraction and microwave spectroscopy.

What is good about atomic force microscopy is that it is more intuitively understandable by the layman.

Re:What about X-ray diffraction and spectroscopy (0)

Anonymous Coward | about a year ago | (#43874207)

What is good about atomic force microscopy is that it is more intuitively understandable by the layman.

That, and its ability to give easier higher resolution images of individual molecules as opposed to a bulk crystal, in an environment where some processes can be watched as they happen, and in some cases facilitates direct manipulation of individual atoms...

Re:What about X-ray diffraction and spectroscopy (1)

NatasRevol (731260) | about a year ago | (#43874523)

They're all single Angstrom resolution.

Medical applications? (0)

Anonymous Coward | about a year ago | (#43874481)

Why don't they use this to see where viruses inject bad DNA?

Halos of Darkness (1)

darenw (74015) | about a year ago | (#43876103)

Reminds me of old-time television cameras, from the 1950s and early 1960s, with the bright objects surrounded by a halo of dark.

Huh? (2)

minkwe (222331) | about a year ago | (#43878449)

We've been seeing things like and many orders of magnitude more complex that this using Crystallography for more than a hundred years. Google "electron density maps" and check out some of the pictures in 3D. Then head over to the Protein Data Bank to see atomic resolution molecular structures determined using crystallography for more than 80,000 protein, nucleic acids (DNA, RNA) and carbohydrates. Even the Ribosome structure has been determined all in 3D. What they have here is a force map which is even more indirect than the electron density and these molecules are "nano-dwarfed" by the sheer complexity and size of molecules whose structures are already available by crystallography.

Atomic Bond == Financial WMD (0)

Anonymous Coward | about a year ago | (#43879311)

Is this another term for CDO (Collateralized_debt_obligation)?

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