Slashdot Mirror


IBM Images a Single Molecule

chrb writes "New Scientist is reporting that researchers at IBM Zurich have managed to image a single molecule in detail for the first time. In the images of a pentacene molecule, the bonds between the carbon atoms are visible as five linked rings."

47 of 169 comments (clear)

  1. Cool, but... by sircastor · · Score: 5, Funny

    I guess I expected it to look a little less like a High-school textbook drawing of the bonds. The only thing that would make it moreso is if little Cs were set next to each atom.

    1. Re:Cool, but... by tecnico.hitos · · Score: 3, Funny
      ...The only thing that would make it moreso is if little Cs were set next to each atom.

      They are still working on it.

      --
      The good, the evil and the vacuum tubes.
    2. Re:Cool, but... by marcosdumay · · Score: 3, Insightful

      Well, TFA says they measured the repulsive force caused by Pauli exclusion principle. That means that their microscope was sensible to filled orbitals, not electrons.

      Anyway, you can't really take a picture of an electron bounded into an atom. The uncertainty principle makes it impossible so say exactly where around the atom the electron is. The only way to measure that is releasing the electron from its bound, and then, it says nothing about where it was just before you release it.

    3. Re:Cool, but... by electricprof · · Score: 5, Funny

      The little C's are there, but they are in 0.000000001 font. I think it's Arial.

    4. Re:Cool, but... by commodore64_love · · Score: 2, Informative

      The other reason you can't take a picture of an electron is because photons of light are larger than the thing you are trying to image. Also you misquoted the uncertainly principle. It says you CAN find the precise location of an electron, but not its momentum. Or vice-versa find its momentum, but not position.

      --
      "I disapprove of what you say, but I will defend to the death your right to say it." - historian Evelyn Beatrice Hall
    5. Re:Cool, but... by marcosdumay · · Score: 4, Informative

      Not exactly. If the electron is bounded, it has some specific momentum probabilities, and some specific position probabilities. You can't find its position with any different certainty unless you remove it from the bounded state.

      And that comes from the uncertainty principle. It is not just Dx * Dp >= h/(2 * pi). It is an statement that each state has some specific uncertanty, and that it isn't lower than that relation.

    6. Re:Cool, but... by An+ominous+Cow+art · · Score: 2, Funny

      True. Molecules are awfully small though. Maybe he just has to squint harder.

    7. Re:Cool, but... by Timmmm · · Score: 3, Informative

      Wrong again. The uncertainty principle is very badly named because it applies even if you know *everything* about the electrons and are uncertain about nothing.

      The problem is like trying to find the position and frequency of a wave packet. Both position and frequency are kind of macro quantities and it wouldn't make sense to fix them both at the same time. For example a wave with only one frequency must be the same everywhere and hence has no position. Conversely a delta function has an infinitely wide spectrum.

      http://en.wikipedia.org/wiki/Fourier_uncertainty_principle#Uncertainty_principle

  2. Next story: by Anonymous Coward · · Score: 5, Funny

    Next story: IBM is sued by the IOC.

  3. As expected... by Drakkenmensch · · Score: 4, Funny

    The molecule blinked right when the snapshot was taken.

  4. What Material Is the Pantacene Sitting On? by eldavojohn · · Score: 4, Interesting

    So if the Pantacene is made of Benzene and the Benzene is C6H6, what is that gray flat smooth material that the molecules are sitting on top of in the second picture? Is this simply due to a focus so incredibly tuned that you can't see past the Pentacene molecules? I would expect that to be a field of bumps and crazy random shapes because it has to be made of some molecule or atom, right? How would they finish the slide/table/surface of that so accurately? I'm used to seeing that when you see bacteria or viruses with an electron microscope, what is in effect here that we don't see an alien landscape back-dropping these molecules? I'm not calling into question the authenticity of the image, just curious if anyone knows.

    --
    My work here is dung.
    1. Re:What Material Is the Pantacene Sitting On? by Anonymous Coward · · Score: 5, Informative

      This image isn't from an electron microscope, it uses AFM (atomic force microscopy: http://en.wikipedia.org/wiki/Atomic_force_microscope), which actually touches the molecules with its tip. In this case though, they bonded a single carbon monoxoide molecule to the AFM cantilever so that it would only interact with the oxygen atoms on the pentacene molecule. I imagine it didn't image the substrate at all because of that

    2. Re:What Material Is the Pantacene Sitting On? by mastahYee · · Score: 5, Interesting

      This image isn't from an electron microscope, it uses AFM (atomic force microscopy: http://en.wikipedia.org/wiki/Atomic_force_microscope), which actually touches the molecules with its tip. In this case though, they bonded a single carbon monoxoide molecule to the AFM cantilever so that it would only interact with the oxygen atoms on the pentacene molecule. I imagine it didn't image the substrate at all because of that

      It doesn't actually touch the molecules, because weak force cancels out the attraction. That's kind of a key point here because touching it was too destructive to get these images in the first place.

    3. Re:What Material Is the Pantacene Sitting On? by UnHolier+than+ever · · Score: 5, Interesting

      An AFM image will often look like it has a shadow. In that case, the tip was probably scanning from the right, and it "bounced" after being raised by the pentacene. The shadow size is related to the tip speed as much as the molecule height.

    4. Re:What Material Is the Pantacene Sitting On? by Anonymous Coward · · Score: 5, Informative

      From the Science article http://www.sciencemag.org/cgi/content/full/325/5944/1110 (require subscription):

      " The asymmetry in the molecular imaging in (D) (showing a "shadow" only on the left side of the molecules) is probably caused by asymmetric adsorption geometry of the CO molecule at the tip apex. "

    5. Re:What Material Is the Pantacene Sitting On? by Sorny · · Score: 5, Informative

      You are correct. I get the chance to see AFM readouts at work (you see some really cool shit in a fab), and this is a bit higher resolution that I'm used to seeing, but the "shadow" is something you'll frequently see.

      I've never "seen" the substrate from AFM scans at work either.

      --
      OSX pwns.
    6. Re:What Material Is the Pantacene Sitting On? by MadAnalyst · · Score: 5, Interesting

      A lot of microscopy like this will be done using very carefully prepared atomically smooth surfaces. A good example would be Cu(111). I haven't' dug in, but they might also work with something akin to the "depth of field" in optical work to largely exclude the effect of the background.

    7. Re:What Material Is the Pantacene Sitting On? by Colonel+Korn · · Score: 4, Informative

      So if the Pantacene is made of Benzene and the Benzene is C6H6, what is that gray flat smooth material that the molecules are sitting on top of in the second picture? Is this simply due to a focus so incredibly tuned that you can't see past the Pentacene molecules? I would expect that to be a field of bumps and crazy random shapes because it has to be made of some molecule or atom, right? How would they finish the slide/table/surface of that so accurately? I'm used to seeing that when you see bacteria or viruses with an electron microscope, what is in effect here that we don't see an alien landscape back-dropping these molecules? I'm not calling into question the authenticity of the image, just curious if anyone knows.

      From the paper: "In this work, we present atomically resolved AFM measurements of pentacene both on a Cu(111) substrate and on a NaCl insulating film. For atomic resolution with the AFM, it is necessary to operate in the short-range regime of forces, where chemical interactions give substantial contributions."

      This was a scanning probe microscope, and the tip of the probe was a single carbon monoxide atom. Apparently the CO didn't interact with the Cu or NaCl in such a way that it saw contrast from atom to atom, but it had a finer interaction with the atoms in the pentacene.

      --
      "I zero-index my hamsters" - Willtor (147206)
    8. Re:What Material Is the Pantacene Sitting On? by Colonel+Korn · · Score: 4, Informative

      Sorry to reply to myself, but here's the most important reason for the lack of substrate heterogeneity in the image:

      "The AFM images (Fig. 1, C and D) were recorded in constant-height mode; that is, the tip was scanned without z feedback parallel to the surface while the frequency shift {Delta}f was being recorded (16). In this and all of the following measurements, the tip height z is always given with respect to the STM set point over the substrate."

      In school, when I ran AFM I allow feedback from the tip to adjust the height of the probe so that it maintains contact with the thing I'm imaging, regardless of topography. Here, they had a very smooth substrate and then set the height of their probe to a fixed position above it.

      --
      "I zero-index my hamsters" - Willtor (147206)
    9. Re:What Material Is the Pantacene Sitting On? by je+ne+sais+quoi · · Score: 4, Informative

      Also the physioelectronic structure of the cu(111) is diffuse enough such that you can't easily resolve individual atoms. Each copper atom is so heavily bonded to it's neighbor that there is very little difference from one atom to the next. If you think about it, that makes sense since copper is a conductor, so the electrons must be able to move from one atom to the next easily. Graphite on the other hand (polymerized carbon like the pentacene here) is an insulator -- much less overlap between the orbitals of neighboring atoms.

      --
      Gentlemen! You can't fight in here, this is the war room!
    10. Re:What Material Is the Pantacene Sitting On? by Bob-taro · · Score: 4, Insightful

      It doesn't actually touch the molecules, because weak force cancels out the attraction.

      At this scale the meaning of words like "touch" gets a little fuzzy.

      --
      Prov 9:8 Do not rebuke mockers or they will hate you; rebuke the wise and they will love you.
    11. Re:What Material Is the Pantacene Sitting On? by jeffb+(2.718) · · Score: 2, Funny

      Scrith.

    12. Re:What Material Is the Pantacene Sitting On? by Myopic · · Score: 3, Informative

      I think he wants you to check the surety of your conclusions. You stated that you "called into question" the results, and supported that with an observation, but the observation was easily explained by someone with basic knowledge of the thing you were questioning. So, since you knew that you were ignorant of this topic, but went ahead and drew a wrong conclusion, and did in fact question the veracity of the results, the person responded to you with mockery.

      Sure, you are allowed to use your eyes and draw conclusions. And when your conclusions are proffered with gusto, and are totally wrong, and based on ignorance, then you are open for a little criticism.

  5. Re:Molecules are made of atoms, right? by epiphani · · Score: 5, Informative

    Good job reading the article.

    FTA:

    Thanks to specialised microscopes, we have long been able to see the beauty of single atoms. But strange though it might seem, imaging larger molecules at the same level of detail has not been possible â" atoms are robust enough to withstand existing tools, but the structures of molecules are not. Now researchers at IBM have come up with a way to do it.

    emphasis mine.

    --
    .
  6. 5 linked rings by russotto · · Score: 4, Funny

    4 calling birds
    3 french hens
    2 turtle doves
    and a partridge in a pair tree?

    1. Re:5 linked rings by Shrike82 · · Score: 5, Funny

      You should have gone with:

      5 linked rings
      4 carbon bonds
      3 electrons
      2 tiny dots
      and a grainy image on my PC...

      --
      You can advertise in this sig from as little as £99.99 a month!
    2. Re:5 linked rings by TimeTraveler1884 · · Score: 2, Funny

      Ah ha ha ha! It's like the original joke never happened!
      (Much like the 2003 Hulk movie)

  7. Impressive by ballpoint · · Score: 5, Insightful

    This is a very impressive image that's in the same league as the famous Hubble deep field image. Both images confirm what was already known, but in a more direct and visual way.

    --
    Flourescent (adj): smelling like ground wheat.
    1. Re:Impressive by mapsjanhere · · Score: 2, Informative

      I fail to see the novelty of this, it's another little incremental improvement in AFM resulution. They were able to image benzene rings with AFM 20 years ago; I remember in grad school one of the guys showing a video of them actually making a lot of substituted rings rearrange their layers on command, like a row of soldiers.

      --
      I'm aging rapidly, I bought a new game and had no idea if my machine was good for it.
  8. link to journal abstract by jschen · · Score: 5, Informative

    For anyone who wants the original paper, published in Science today, it may be found here. The abstract is free.

    1. Re:link to journal abstract by Jim+Hall · · Score: 2, Informative

      And if anyone wants to see more images from the IBM team, they have a flickr photostream. It's really impressive.

  9. Polymers are molecules too by Colonel+Korn · · Score: 2, Informative

    Single strands of synthetic polymers and DNA have been imageable for many years. I imagine many of us on slashdot have personally acquired images of these single molecules before.

    --
    "I zero-index my hamsters" - Willtor (147206)
  10. Re:Molecules are made of atoms, right? by KraftDinner · · Score: 2, Informative

    It's not that the molecule itself needs to be big enough, it's the structure of it. The stuff holding it together. The stuff holding the molecule together could not withstand the instruments, but now they've developed a way to do it.

  11. The photo is of the electric field. by Futurepower(R) · · Score: 5, Informative

    Atoms are mostly empty space. The photo is of the electric field caused by the electrons.

    This photo is better. The article says it is a 20-hour time exposure. The photo was available through a Reddit story yesterday.

  12. Re:5 Rings? by mfnickster · · Score: 2, Funny

    Miyamoto Musashi would be intrigued.

    So would the International Olympic Committee!

    --
    "Slow down, Cowboy! It has been 3 years, 7 months and 26 days since you last successfully posted a comment."
  13. For some reason... by Myria · · Score: 2, Funny

    Why do I have the sudden urge to play Arkanoid?

    --
    "Screw Sun, cross-platform will never work. Let's move on and steal the Java language." - Visual J++ Product Manager
  14. I'm inpressed by the chemists who deduced ... by Anonymous Coward · · Score: 5, Insightful

    the structures of the molecule with such accuracy - without actually seeing it!

    Now, that's genius!

    1. Re:I'm inpressed by the chemists who deduced ... by MadTinfoilHatter · · Score: 4, Informative

      The funny thing is that the first person to deduce this (Friedrich August Kekulé von Stradonitz) realized the solution to the problem of structure, after having a dream in which a snake bit its own tail.

  15. Re:What the hell... by Jack+Malmostoso · · Score: 4, Informative

    The marking in Hz is most probably referred to the vibration of the cantilever (see how an AFM works), while the other unit is not Amps but Angstrom (1Å = 0.1nm). The pentacene molecule is long roughly 17Å. This stuff is on another planet of cool.

  16. Simply Awesome by gpronger · · Score: 5, Interesting

    I likely would have had this post up about 20 earlier, but I've just managed to pick myself off the floor after taking a look at the photo. As a chemist, I personally find the verification of theory a significant milestone in our understanding. It's one thing to have a theory, and then through somewhat serendipitous means, verify the theory, but to have an actual photo, brings it to a new level.

    Greg

    Yes, I do have a life outside the lab, but maybe not as much of one as I once thought.

  17. But... by SnarfQuest · · Score: 2, Funny

    Can it be used to create biodiesel?

    --
    Who would win this election: Andrew Weiner vs Andrew Weiner's weiner.
  18. Compare those pics with 45nm chip design. by deathcow · · Score: 2, Interesting

    45nm is 450 angstrom, so you can see by the 20 angstrom ruler in one of the pictures that chip design is getting pretty small. In fact, you can see the atoms lined up in the traces of chips!
    http://i.zdnet.com/blogs/afm-bpm-e-beam.jpg

  19. Re:Wow, this is amazing by PCM2 · · Score: 2, Interesting

    I think I recall that there are lots of work that involve the spatial geometry of molecules.

    Yes. Elementary chemistry is pretty much just what is stuck to what, but once you get into organic chemistry, spatial geometry is pretty much half the class.

    --
    Breakfast served all day!
  20. But what are the "STICKS" connecting the BALLS? by Vitriol+Angst · · Score: 3, Interesting

    We take this model for granted. It's one thing for a handy, convenient model to hold Balls in place with sticks and the you connect your large blue Oxygen balls to the tiny Red hydrogen balls and call it a model.

    It's quite another that it's the actual, physical representation of it.

    We look at atoms and imagine electron shells -- that's really a domain that electrons spend their time in.

    However, physicists currently have this model of particles being particles. Now if a solid, frozen substance under the head of a pin, however, is detecting the structures of "most common region of covalent bonding" as actual "stick like" structures -- when in all rights, the interference of the probe should be pushing the electron around it -- then maybe we need to rethink this concept of particles.

    >> My own belief, and I'm likely to get slammed for this on Slashdot by folks who think about physics and chemistry all day -- is that EVERYTHING is a field. Particles are fields with pinpoint connections to other dimensions and that exhibit mass. But what you would expect, from a field, touching a field, is that the "domains" of the electron bonding, would appear solid.

    If you really think about it, the electron and proton in these pictures are so small, that the distance from the electron is as far from the proton vs. its size, that it would be like a period on this sentence on a football field.

    THAT any of these molecules is solid, means that the potential fields where the electron COULD BE, have some disruption on space, and that the patterns of force of the probe, interfere with the patterns of force on the studied atom.

    If Atoms were really very tiny particles, we would SOMETIMES see a structure and sometimes not -- because the probe's electron and the sampled atom's electron would not be occupying the same location most of the time.

    >> It's a bit like asking the basic question: Why are things opaque and why are they solid? Fields themselves are the only things that could be stopping the probe. And if physics recognizes the "strong and weak force" -- are those really propagated by particles, or is it a disturbance in space itself. I'm one of the anachronisms who still believes in the aether, I suppose -- think of Dark Matter, as the New Aether.

    --
    >>"ad space available -- low rates!!!"
    1. Re:But what are the "STICKS" connecting the BALLS? by Chris+Burke · · Score: 2, Interesting

      However, physicists currently have this model of particles being particles. Now if a solid, frozen substance under the head of a pin, however, is detecting the structures of "most common region of covalent bonding" as actual "stick like" structures -- when in all rights, the interference of the probe should be pushing the electron around it -- then maybe we need to rethink this concept of particles.

      My own belief, and I'm likely to get slammed for this on Slashdot by folks who think about physics and chemistry all day -- is that EVERYTHING is a field. Particles are fields with pinpoint connections to other dimensions and that exhibit mass. But what you would expect, from a field, touching a field, is that the "domains" of the electron bonding, would appear solid.

      If Atoms were really very tiny particles, we would SOMETIMES see a structure and sometimes not -- because the probe's electron and the sampled atom's electron would not be occupying the same location most of the time.

      I'm not going to tell you your belief isn't true. I mean, protons seem to have a "size" but they're made of quarks and who knows what smaller particles quarks may be made of and what binds them together. All I know is that matter is energy, so maybe "matter" is just some energy contained in a field that makes it act like a particle.

      The thing is, this image really doesn't help us distinguish. What we do know is that electrons and protons emit electric fields due to their charge, and it's the electrostatic force that the AFM is measuring. So the results are still consistent with a tiny particle that's flying around another particle, as is the van der Waals forces problem they had to work around. The force created when the probe's electron and the atom's electron are far away is enough to destroy the sample if they don't try to compensate for it, but at the same time the instrument isn't precise enough to measure that force occurring for the instant that it does. The average force over the interval that the probe is sensitive to looks like that in the photo, and as expected has a bright region of high probability of electron presence that fades off to less. So, this is not the proof you're looking for.

      --

      The enemies of Democracy are
  21. Single Molecule by hidannik · · Score: 2, Funny

    In a follow-up session, the Zurich researchers announced that by this time next year, they hope to have imaged two molecules. "We won't stop there," said one scientist, "We plan to image ten, then a thousand, and so on until we are able to image an entire piece of, say, fairy-cake."

  22. Look at the higher intesity at the ends by Chemisor · · Score: 2, Insightful

    It's interesting to see how the electrons bunch up at the ends. The aromatic delocalization clearly equalizes the energy levels of the bonds, making the entire molecule behave like a conductor, and concentrate charge at the extremes. Just as in a metal, electrons loosely float in the conduction band, it looks they do the same in pentacene, illustrating why graphite is such a good conductor.