6 ms·

High-resolution images of a molecule as it breaks and reforms chemical bonds

174 points by samlittlewood 13y ago

ck2 13y ago
Fantastic. http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteverhig.jpg http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteve... Not sure how they "feel" the interactions without disturbing them but that's why they are the physicists.
- csense 13y ago
  > how they "feel" the interactions without disturbing them They can't. I don't know if there are quantum complications at that scale that change this picture, but my basic idea from classical physics is that Newton's Third Law says the probe can't have a force exerted on it by the sample (action) without also simultaneously itself exerting a force on the sample (reaction). > The single-atom moving finger of the nc-AFM The mass of the detector particle being deflected by the fields is small compared to the mass of the molecule being measured. So a force large enough to move the probe by a lot might still be small enough to only move the sample by a little. The bottom line is, you can't measure a sample without disturbing it, but as the ratio of probe mass to sample mass shrinks, the level of that disturbance also shrinks. In this case they're using a single atom probe to measure a large organic molecule, apparently the ratio is small enough. > Resulting movements of the stylus are detected by a laser beam I guess in order to engineer a system this small, you need a probe to measure the probe. Again I'm guessing the momentum of the photons from the laser that are used to measure the probe atom is small enough not to appreciably deflect the probe.
  - coldtea 13y ago
    >They can't. I don't know if there are quantum complications at that scale that change this picture, but my basic idea from classical physics is that Newton's Third Law says the probe can't have a force exerted on it by the sample (action) without also simultaneously itself exerting a force on the sample (reaction). Well, that goes without saying. The question is if that "force" used to measure had any, well, measurable impact.
  - sp332 13y ago
    Since the molecule is only heated momentarily to induce the reaction, it is cold before and after. The molecule might be effectively "stuck" to the silver surface it's resting on.
    - mtdewcmu 13y ago
      The molecules they were touching were perfectly flat, and must have been pretty well adhered to the silver surface. Now that I think about it, silver is used as a catalyst, and they had to heat it to 90C to cause the reaction. So it sounds like it was more of a problem of overcoming the inherent stability of the molecule to get it to do anything at all.
  - simcop2387 13y ago
    > > how they "feel" the interactions without disturbing them > They can't. I don't know if there are quantum complications at that scale that change this picture, but my basic idea from classical physics is that Newton's Third Law says the probe can't have a force exerted on it by the sample (action) without also simultaneously itself exerting a force on the sample (reaction). Best part about that line of reasoning is that it leads directly to the Heisenberg uncertainty principle which is definitely in play here. The act of them measuring the position of each of the atoms means that they can't know that the atoms aren't moving because of the force they exerted. On such small molecules they can likely be reasonably certain they haven't introduced any errors, but for a much larger sample they'll start to have issues where the act of measuring is going to change the outcome. What I'm waiting for is when someone figures out how to make diffraction gratings for things in the 5nm area so that you can actually image this stuff with photons rather than with an AFM, that should let them handle larger sheets of graphene, and possibly even look at doped graphene with semiconductor properties to get a really awesome understanding of how and why it works (or doesn't).
    - Dove 13y ago
      I think what you're describing is the observer effect[1], not Heisenberg uncertainty[2]. Heisenberg uncertainty is much stronger than not being able to observe a system without disturbing it. It's more like, at a physical level, making the probability distribution of a position tight makes the distribution of momentum wide. [1] http://en.wikipedia.org/wiki/Observer_effect_(physics) http://en.wikipedia.org/wiki/Observer_effect_(physics) [2] http://en.wikipedia.org/wiki/Heisenberg_uncertainty http://en.wikipedia.org/wiki/Heisenberg_uncertainty
  - Groxx 13y ago
    Nitpicking, but just going with classical physics and Newton's Third Law, yes, you can do such things. If the thing you're studying emits something, and you can infer the thing's state from what it emits, you can study the emissions without disturbing the thing. Similarly, looking at something doesn't change its state, since the light was already reflected / emitted. Obviously there are additional complications at such small scales, and it depends on what you're detecting (measuring / passing through magnetic fields does affect the source since it changes the field), and it depends on what you define as "change" and which quantum mechanics interpretation you subscribe to. I'm just pointing out that the thing being measured doesn't have to be the thing you're investigating, so that law in particular doesn't really imply anything.
  - gus_massa 13y ago
    Well, there are a lot of quantum complications in this scale, the structure of the bounds is totally a quantum effect. And there are some problems with the Newton's Third Law when you consider the electromagnetic field. Anyway the general idea of force-reaction still holds, so it's a good approximation for this experiment. If the tip "see" the molecule, then the molecule "see" the tip. The problem with your explanation is that the probe is much much bigger than 1 atom. It's a whole macroscopic tip, with a mass of a few grams. The tip of the tip use a single CO molecule, so the prove ends in a single atom, but the atom is attached to a big structure. If the tip were thicker, they would measure an average of the surface under the tip, with a very sharp tip they measure a small area. The molecules are attached to a silver surface, so they are relatively fixed. The O atom in the CO molecule in the tip is approached to measure the force at each point of the surface. I couldn't find the exact distance but Wikipedia says that in similar experiments the distance is between 10A and 100A. For comparison, a bound between two Carbons in a molecule is approximately 1.5A. So the CO molecule is far away and the force is very small (in the absolute and the relative sense), and the system must use an incredible amount of amplification. But the force in the sample molecule is also relatively small, so it isn't disturbed too much, and the data that you get are very similar to the data of the unperturbed molecule. I suppose that it's possible to tweak the setting to decrease the distance so the interaction between the molecule in the tip and the sample molecule is smaller. I suppose that it's possible to use this to make some reactions happen, but I don't remember an experiment with this phenomenon. Anyway a usual problem is to crash the tip against the surface. It's bad for the tip, you need to pick another CO molecule and if it hit the sample molecule it could be interesting. With a similar microscope that use the tunnel effect it's possible to move atoms from one place to another, so it's possible to do things on the surface using the correct settings. You can even do a movie! https://news.ycombinator.com/item?id=5637150 https://news.ycombinator.com/item?id=5637150
    - csense 13y ago
      > the probe is much much bigger than 1 atom I guess I didn't clearly state an additional assumption of my explanation. I assumed the oxygen atom has an electric charge, the rest of the probe structure is electrically neutral, and the electrostatic attraction/repulsion of charges is the mechanism by which the oxygen atom on the probe reacts to the sample [1]. So while the rest of the probe structure does exist, it's effectively [2] electrically neutral. [1] I think we can agree that the gravitational attraction of the probe and sample to each other is way too small to matter. [2] I think the large probe structure is close enough to neutral and/or far enough away from the sample to have an effect which is smaller than the effect of the oxygen atom. The structure may contribute some nontrivial amount of noise due to being neither exactly neutral nor infinitely far away, but not enough to totally drown out the signal from the oxygen atom.
- adlpz 13y ago
  Well, as far as I understand it, the interactions (joints) manifest themselves as a larger density of electrons. That's pretty trivial (heh) to detect, just measure electrostatic interaction with a needle, or do some deflection fun.
kumar_navneet 13y ago
Amazing stuff, feels really good to see that it is exactly the same as we read in textbooks.
- andy_ppp 13y ago
  When I looked at chemical symbols before seeing this I had always assumed them to be a sort of vague outline of what was really happening. It's amazing to think that the way chemicals bond is the same in reality as drawn in textbooks.
  - marcosdumay 13y ago
    They choosed a molecule that was similar to its diagram, but that's not always the case. the main difference is that the diagram is 2D, and molecules are usualy 3D.
    - jcrites 13y ago
      I think you can see some slight 3D effects in the picture: http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteverhig.jpg http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteve... In the two variants on the right, their edges seem to be curling upward making a bowl shape. Their edges are also brighter, which perhaps means they are closer to the probe than parts that are farther away. Additionally, the hexagons are also not all the same shape. I assume that's due to the curling. I would be interested to know if my interpretation of the image is correct, or if the molecule is really flat and what I'm seeing is an artifact.
      - Komodo9 13y ago
        To answer your question (flat vs. artifact) directly: It's flat. Sorta. Bear with me a moment. If this is confusing, please let me know, and i'll try to clarify. Molecular symmetry isn't my strong point, unfortunately. The trouble with all of this is the "picture" is not an actual picture-made-with-photons picture, but a visualization via computer. That isn't to say it's a poor reflection on reality, but that the limitations of the techniques should be accounted for. In this case, the electron density of the overall molecule is being measured. The brighter signals correspond to an increase in local electron density. In such chemical structures as these, the aromaticity [1] is the main force at play. Without getting too technical, the brighter regions are those with increased electron density. (See figure 4 at the IBM Zurich page on pentacene [2]) The hexagons (and square and pentagons) in fact do not have idealized geometry, but not due to any curling. The unique environment of each carbon is more at play. Symmetry plays a large role; imagine a symmetric vs. unsymmetrical tug-of-war between the carbons with the electrons as the rope. The left hand side and lower right have a dihedral mirror plane, simplifying the density somewhat, where the upper right has a more muddled situation. Getting back to the flatness, the target molecule is 'mounted' on a suitably uniform surface, such that only one side is being scanned/read by the probe. In a vacuum, the tug of war in the Z direction (into the plane) will cancel out between the +Z and -Z vectors, giving a 'flat' molecule. (Depending on your point of view, either because of this or due to this, each of these molecules has a mirror plane in the plane of the molecule, bisecting each atom.) Setting all that aside, the entire process is really #$%*& cool, particularly to a chemist. (Yes, those crazy textbook pictures are often reflected in reality. If only the different atoms were color coded, though!) [1] http://en.wikipedia.org/wiki/Aromaticity http://en.wikipedia.org/wiki/Aromaticity [2] http://www.zurich.ibm.com/st/atomic_manipulation/pentacene.html http://www.zurich.ibm.com/st/atomic_manipulation/pentacene.h...
alexholehouse 13y ago
Original paper here http://www.sciencemag.org/content/early/2013/05/29/science.1238187 http://www.sciencemag.org/content/early/2013/05/29/science.1...
da_n 13y ago
Incredible stuff, seems essentially (to a layman) like a stylus on vinyl records.

174 points by samlittlewood 13y ago

ck2 13y ago

Fantastic. http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteverhig.jpg http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteve... Not sure how they "feel" the interactions without disturbing them but that's why they are the physicists.

csense 13y ago
> how they "feel" the interactions without disturbing them They can't. I don't know if there are quantum complications at that scale that change this picture, but my basic idea from classical physics is that Newton's Third Law says the probe can't have a force exerted on it by the sample (action) without also simultaneously itself exerting a force on the sample (reaction). > The single-atom moving finger of the nc-AFM The mass of the detector particle being deflected by the fields is small compared to the mass of the molecule being measured. So a force large enough to move the probe by a lot might still be small enough to only move the sample by a little. The bottom line is, you can't measure a sample without disturbing it, but as the ratio of probe mass to sample mass shrinks, the level of that disturbance also shrinks. In this case they're using a single atom probe to measure a large organic molecule, apparently the ratio is small enough. > Resulting movements of the stylus are detected by a laser beam I guess in order to engineer a system this small, you need a probe to measure the probe. Again I'm guessing the momentum of the photons from the laser that are used to measure the probe atom is small enough not to appreciably deflect the probe.
- coldtea 13y ago
  >They can't. I don't know if there are quantum complications at that scale that change this picture, but my basic idea from classical physics is that Newton's Third Law says the probe can't have a force exerted on it by the sample (action) without also simultaneously itself exerting a force on the sample (reaction). Well, that goes without saying. The question is if that "force" used to measure had any, well, measurable impact.
- sp332 13y ago
  Since the molecule is only heated momentarily to induce the reaction, it is cold before and after. The molecule might be effectively "stuck" to the silver surface it's resting on.
  - mtdewcmu 13y ago
    The molecules they were touching were perfectly flat, and must have been pretty well adhered to the silver surface. Now that I think about it, silver is used as a catalyst, and they had to heat it to 90C to cause the reaction. So it sounds like it was more of a problem of overcoming the inherent stability of the molecule to get it to do anything at all.
- simcop2387 13y ago
  > > how they "feel" the interactions without disturbing them > They can't. I don't know if there are quantum complications at that scale that change this picture, but my basic idea from classical physics is that Newton's Third Law says the probe can't have a force exerted on it by the sample (action) without also simultaneously itself exerting a force on the sample (reaction). Best part about that line of reasoning is that it leads directly to the Heisenberg uncertainty principle which is definitely in play here. The act of them measuring the position of each of the atoms means that they can't know that the atoms aren't moving because of the force they exerted. On such small molecules they can likely be reasonably certain they haven't introduced any errors, but for a much larger sample they'll start to have issues where the act of measuring is going to change the outcome. What I'm waiting for is when someone figures out how to make diffraction gratings for things in the 5nm area so that you can actually image this stuff with photons rather than with an AFM, that should let them handle larger sheets of graphene, and possibly even look at doped graphene with semiconductor properties to get a really awesome understanding of how and why it works (or doesn't).
  - Dove 13y ago
    I think what you're describing is the observer effect[1], not Heisenberg uncertainty[2]. Heisenberg uncertainty is much stronger than not being able to observe a system without disturbing it. It's more like, at a physical level, making the probability distribution of a position tight makes the distribution of momentum wide. [1] http://en.wikipedia.org/wiki/Observer_effect_(physics) http://en.wikipedia.org/wiki/Observer_effect_(physics) [2] http://en.wikipedia.org/wiki/Heisenberg_uncertainty http://en.wikipedia.org/wiki/Heisenberg_uncertainty
- Groxx 13y ago
  Nitpicking, but just going with classical physics and Newton's Third Law, yes, you can do such things. If the thing you're studying emits something, and you can infer the thing's state from what it emits, you can study the emissions without disturbing the thing. Similarly, looking at something doesn't change its state, since the light was already reflected / emitted. Obviously there are additional complications at such small scales, and it depends on what you're detecting (measuring / passing through magnetic fields does affect the source since it changes the field), and it depends on what you define as "change" and which quantum mechanics interpretation you subscribe to. I'm just pointing out that the thing being measured doesn't have to be the thing you're investigating, so that law in particular doesn't really imply anything.
- gus_massa 13y ago
  Well, there are a lot of quantum complications in this scale, the structure of the bounds is totally a quantum effect. And there are some problems with the Newton's Third Law when you consider the electromagnetic field. Anyway the general idea of force-reaction still holds, so it's a good approximation for this experiment. If the tip "see" the molecule, then the molecule "see" the tip. The problem with your explanation is that the probe is much much bigger than 1 atom. It's a whole macroscopic tip, with a mass of a few grams. The tip of the tip use a single CO molecule, so the prove ends in a single atom, but the atom is attached to a big structure. If the tip were thicker, they would measure an average of the surface under the tip, with a very sharp tip they measure a small area. The molecules are attached to a silver surface, so they are relatively fixed. The O atom in the CO molecule in the tip is approached to measure the force at each point of the surface. I couldn't find the exact distance but Wikipedia says that in similar experiments the distance is between 10A and 100A. For comparison, a bound between two Carbons in a molecule is approximately 1.5A. So the CO molecule is far away and the force is very small (in the absolute and the relative sense), and the system must use an incredible amount of amplification. But the force in the sample molecule is also relatively small, so it isn't disturbed too much, and the data that you get are very similar to the data of the unperturbed molecule. I suppose that it's possible to tweak the setting to decrease the distance so the interaction between the molecule in the tip and the sample molecule is smaller. I suppose that it's possible to use this to make some reactions happen, but I don't remember an experiment with this phenomenon. Anyway a usual problem is to crash the tip against the surface. It's bad for the tip, you need to pick another CO molecule and if it hit the sample molecule it could be interesting. With a similar microscope that use the tunnel effect it's possible to move atoms from one place to another, so it's possible to do things on the surface using the correct settings. You can even do a movie! https://news.ycombinator.com/item?id=5637150 https://news.ycombinator.com/item?id=5637150
  - csense 13y ago
    > the probe is much much bigger than 1 atom I guess I didn't clearly state an additional assumption of my explanation. I assumed the oxygen atom has an electric charge, the rest of the probe structure is electrically neutral, and the electrostatic attraction/repulsion of charges is the mechanism by which the oxygen atom on the probe reacts to the sample [1]. So while the rest of the probe structure does exist, it's effectively [2] electrically neutral. [1] I think we can agree that the gravitational attraction of the probe and sample to each other is way too small to matter. [2] I think the large probe structure is close enough to neutral and/or far enough away from the sample to have an effect which is smaller than the effect of the oxygen atom. The structure may contribute some nontrivial amount of noise due to being neither exactly neutral nor infinitely far away, but not enough to totally drown out the signal from the oxygen atom.
adlpz 13y ago
Well, as far as I understand it, the interactions (joints) manifest themselves as a larger density of electrons. That's pretty trivial (heh) to detect, just measure electrostatic interaction with a needle, or do some deflection fun.

kumar_navneet 13y ago

Amazing stuff, feels really good to see that it is exactly the same as we read in textbooks.

andy_ppp 13y ago
When I looked at chemical symbols before seeing this I had always assumed them to be a sort of vague outline of what was really happening. It's amazing to think that the way chemicals bond is the same in reality as drawn in textbooks.
- marcosdumay 13y ago
  They choosed a molecule that was similar to its diagram, but that's not always the case. the main difference is that the diagram is 2D, and molecules are usualy 3D.
  - jcrites 13y ago
    I think you can see some slight 3D effects in the picture: http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteverhig.jpg http://cdn.physorg.com/newman/gfx/news/hires/2013/2-firsteve... In the two variants on the right, their edges seem to be curling upward making a bowl shape. Their edges are also brighter, which perhaps means they are closer to the probe than parts that are farther away. Additionally, the hexagons are also not all the same shape. I assume that's due to the curling. I would be interested to know if my interpretation of the image is correct, or if the molecule is really flat and what I'm seeing is an artifact.
    - Komodo9 13y ago
      To answer your question (flat vs. artifact) directly: It's flat. Sorta. Bear with me a moment. If this is confusing, please let me know, and i'll try to clarify. Molecular symmetry isn't my strong point, unfortunately. The trouble with all of this is the "picture" is not an actual picture-made-with-photons picture, but a visualization via computer. That isn't to say it's a poor reflection on reality, but that the limitations of the techniques should be accounted for. In this case, the electron density of the overall molecule is being measured. The brighter signals correspond to an increase in local electron density. In such chemical structures as these, the aromaticity [1] is the main force at play. Without getting too technical, the brighter regions are those with increased electron density. (See figure 4 at the IBM Zurich page on pentacene [2]) The hexagons (and square and pentagons) in fact do not have idealized geometry, but not due to any curling. The unique environment of each carbon is more at play. Symmetry plays a large role; imagine a symmetric vs. unsymmetrical tug-of-war between the carbons with the electrons as the rope. The left hand side and lower right have a dihedral mirror plane, simplifying the density somewhat, where the upper right has a more muddled situation. Getting back to the flatness, the target molecule is 'mounted' on a suitably uniform surface, such that only one side is being scanned/read by the probe. In a vacuum, the tug of war in the Z direction (into the plane) will cancel out between the +Z and -Z vectors, giving a 'flat' molecule. (Depending on your point of view, either because of this or due to this, each of these molecules has a mirror plane in the plane of the molecule, bisecting each atom.) Setting all that aside, the entire process is really #$%*& cool, particularly to a chemist. (Yes, those crazy textbook pictures are often reflected in reality. If only the different atoms were color coded, though!) [1] http://en.wikipedia.org/wiki/Aromaticity http://en.wikipedia.org/wiki/Aromaticity [2] http://www.zurich.ibm.com/st/atomic_manipulation/pentacene.html http://www.zurich.ibm.com/st/atomic_manipulation/pentacene.h...

alexholehouse 13y ago

Original paper here http://www.sciencemag.org/content/early/2013/05/29/science.1238187 http://www.sciencemag.org/content/early/2013/05/29/science.1...

da_n 13y ago

Incredible stuff, seems essentially (to a layman) like a stylus on vinyl records.