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IBM Science

IBM Images a Single Molecule 169

Posted by kdawson from the blow-it-up dept.
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."
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IBM Images a Single Molecule More

IBM Images a Single Molecule

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  • Cool, but... (Score:5, Funny)

    by sircastor ( 1051070 ) on Friday August 28, 2009 @08:41AM (#29230045)
    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.

    • Re: (Score:3, Funny)

      by tecnico.hitos ( 1490201 )
      ...The only thing that would make it moreso is if little Cs were set next to each atom.

      They are still working on it.

    • Well, the textbook drawings are supposed to represent the underlying physical reality, so it would be disappointing if the drawings and the "photo" didn't resemble one another.

      • Re: (Score:2)

        by elrous0 ( 869638 ) *
        Yes but IIRC, textbook drawings of atoms usually look nothing like the physical reality (since simplified drawings never show the electrons forming a cloud around the nucleus and greatly shrink the scale of the distance between the electrons and nucleus for simplicity). So it's not surprising that we would expect the physical reality vs. the drawings of the molecules to be very different too.
    • I think the pictures were a little blurry. The guys at IBM probably didn't read the directions on the camera that says "Stand about 2-3 feet away from subject, then point, and shoot!"

  • 5 Rings? (Score:2, Funny)

    by idontgno ( 624372 )
    Miyamoto Musashi [wikipedia.org] would be intrigued.

  • Next story: (Score:5, Funny)

    by Anonymous Coward on Friday August 28, 2009 @08:42AM (#29230057)

    Next story: IBM is sued by the IOC.

  • As expected... (Score:5, Funny)

    by Drakkenmensch ( 1255800 ) on Friday August 28, 2009 @08:42AM (#29230061)
    The molecule blinked right when the snapshot was taken.
  • 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.

    • Re: (Score:2)

      by BobMcD ( 601576 )

      I caught that too, and I am calling it into question. Especially when combined with the fact that they seem to be casting a shadow. Why/how would a probe detect a shadow? Artist's rendition, perhaps?

      • 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.

      • Re:What Material Is the Pantacene Sitting On? (Score:5, Informative)

        by Anonymous Coward on Friday August 28, 2009 @09:10AM (#29230399)

        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. "

      • Re: (Score:2, Flamebait)

        by geekoid ( 135745 )

        Yes, I'm sure you PhD in molecular physics and your extensive experience with AFM allows you to make such propositions. Perhaps you should contact your colleges and let them in on your ground breaking realization~

    • Re:What Material Is the Pantacene Sitting On? (Score:5, Informative)

      by Anonymous Coward on Friday August 28, 2009 @08:53AM (#29230195)

      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

    • Re:What Material Is the Pantacene Sitting On? (Score:5, Interesting)

      by MadAnalyst ( 959778 ) on Friday August 28, 2009 @09:12AM (#29230421)
      A lot of microscopy like this will be done using very carefully prepared atomically smooth surfaces [omicron.de]. A good example would be Cu(111) [ibm.com]. 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.

    • Re:What Material Is the Pantacene Sitting On? (Score:5, Informative)

      by Colonel Korn ( 1258968 ) on Friday August 28, 2009 @09:15AM (#29230461)

      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.

      • Re:What Material Is the Pantacene Sitting On? (Score:5, Informative)

        by Colonel Korn ( 1258968 ) on Friday August 28, 2009 @09:21AM (#29230533)

        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.

        • Re:What Material Is the Pantacene Sitting On? (Score:5, Informative)

          by je ne sais quoi ( 987177 ) on Friday August 28, 2009 @09:45AM (#29230857)
          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.

      • Re: (Score:2)

        by 6031769 ( 829845 )

        This was a scanning probe microscope, and the tip of the probe was a single carbon monoxide atom.

        Er, no. It may have been a single carbon monoxide molecule, however.

    • Clearly this is a fraud perpretrated by a fanatical intro to chemistry teacher.

      Seriously though, maybe they cleaned up the background noise or maybe the tip (which they modified with carbon monoxide so it was "tuned") was extremely selective in how it responded to the substrate material.

    • Atomic force microscopes can be very selective to "height" (being height the dimension perpendicular to the smple).

    • Re: (Score:3, Funny)

      by jeffb (2.718) ( 1189693 )

      Scrith.

  • 5 linked rings (Score:5, Funny)

    by russotto ( 537200 ) on Friday August 28, 2009 @08:47AM (#29230123) Journal

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

  • Impressive (Score:5, Insightful)

    by ballpoint ( 192660 ) on Friday August 28, 2009 @08:51AM (#29230179)
    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.

    • 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.

  • link to journal abstract (Score:5, Informative)

    by jschen ( 1249578 ) on Friday August 28, 2009 @08:53AM (#29230197)
    For anyone who wants the original paper, published in Science today, it may be found here [sciencemag.org]. The abstract is free.

    • Re: (Score:3, Informative)

      by Jim Hall ( 2985 )

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

      • The pic, here [flickr.com], with the foil on the microscope made me smile. The whole damn thing is cool but that there is foil too I felt like if I just could get a glimpse of some duct tape somewhere we could even show this to non-geeks and make them smile too.

  • Polymers are molecules too (Score:3, Informative)

    by Colonel Korn ( 1258968 ) on Friday August 28, 2009 @09:09AM (#29230387)

    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.

    • Re: (Score:2, Interesting)

      by caffiend666 ( 598633 )

      Don't forget, a good diamond is basically one big carbon molecule. A diamond's not only imageable, but you can feel/hold/interact with it.

    • The images are stunning and I congratulate IBM for their efforts.

    • For example with 3D electron microscopy. It requires multiple copies of the same molecule on a chilled plate, take a progressive electron microscopy scan of the plate, and the 3D image is reconstructed from the multiple images. Individual atoms can often be identified by relative size. It's been awhile since I've looked at this but I can only assume the field has progressed since then.
  • So, does this mean for all those years when we see a modelled structure of a molecule, it has been theory as one has never been observed? So now, theory has been proven and is now science as it has now been observed?

    • Re: (Score:2)

      by Myopic ( 18616 )

      We've been observing molecules in lots of ways for a long time. This is just the first time we've made a certain kind of picture.

  • What do you do with 5 rings chained together?

  • The picture is marked in units of HERTZ and AMPS?

    • Re:What the hell... (Score:4, Informative)

      by Jack Malmostoso ( 899729 ) on Friday August 28, 2009 @09:38AM (#29230751)
      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.

    • ...and what in God's name are negative hertz supposed to represent?

      • Re: (Score:2)

        by ceoyoyo ( 59147 )

        Do a Fourier transform of a time signal. You get positive and negative frequencies.

        • Symmetrical, IIRC... but I don't think that has much to do with this. Geekoid's thinking is more along my line of reasoning, esp. after some of the explanations people have given of how AFM scanning works.

          • Re: (Score:2)

            by ceoyoyo ( 59147 )

            Hermitian symmetric, for a real-valued input, which means anti-symmetric for a 1D real-valued input. For a complex-valued input, the negative frequencies are not simply related to the positive.

            Not sure what Geekoid said, but I suspect the measurement is relative to a reference frequency, which is why there are negatives.

            There are plenty of imaging modalities where it would be valid to label an axis in frequency units, with negatives though. Any form of interferometry or synthetic aperture radar technique

            • Not sure what Geekoid said, but I suspect the measurement is relative to a reference frequency, which is why there are negatives.

              This, and yeah:

              Maybe it's based on a base line? so, for examples, if your baseling was 10Hz, -1Hz would be 9.

      • Re: (Score:2)

        by geekoid ( 135745 )

        I don't know; however that won't keep me from speculating...

        Maybe it's based on a base line? so, for examples, if your baseling was 10Hz, -1Hz would be 9.

        Now that doesn't seem to make sens at the number sI am using, but when dealing with the number you would be using to do this, it makes more sens the a 8 decimal place number.
        Also, it my be a standard defined unit, not 1 Hz.
        So a uit might by in .00001 Hz.
        or 12345423 Hz.

  • The summary and the linked article are misleading. This is not the "first time a single molecule has been imaged." It's the first time a single molecule has been imaged using AFM. Scanning tunneling microscopy (STM) has been used for about a decade now to image single molecules. Just a simple google image search [google.com] will show you lots of them. My favorite is this guy [jmtour.com] who is imaging something he's calling "nanocars" which are single molecules. These finding are in no way less impressive due to resolution th

    • Those are a series of nanotubes, not a molecule on jmtour.com
      I saw no picture of a single molecule on your google link, either.

  • For some reason... (Score:3, Funny)

    by Myria ( 562655 ) on Friday August 28, 2009 @09:35AM (#29230723)

    Why do I have the sudden urge to play Arkanoid?

  • I'm inpressed by the chemists who deduced ... (Score:5, Insightful)

    by Anonymous Coward on Friday August 28, 2009 @09:37AM (#29230745)

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

    Now, that's genius!

  • Wow, this is amazing. It looks much like what I'd expect from high school chemistry all those years ago :)

    Watson and Crick wouldn't have had that much trouble with DNA if they had these tools... will the IBM scientists be able to do this for more complex molecules? As a complete layman in Chemistry, I think I recall that there are lots of work that involve the spatial geometry of molecules.

    • As a complete layman in Chemistry, I think I recall that there are lots of work that involve the spatial geometry of molecules.

      Yes, such as Folding at Home.

      • Re: (Score:2)

        by Acer500 ( 846698 )
        Thanks for pointing that one out, I had forgotten about it (not that I have that many spare cycles to donate :) ).

    • Re: (Score:3, Interesting)

      by PCM2 ( 4486 )

      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.

  • Simply Awesome (Score:5, Interesting)

    by gpronger ( 1142181 ) on Friday August 28, 2009 @09:49AM (#29230927) Journal
    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.

  • IBM has their faults, but it's good to see a company doing cutting edge RnD and producing results.

  • I am not a nuclear physicist so maybe my question is understandable...

    I thought that when you get to the molecular level The uncertainty principle would start to take effect. Very large molecules like DNA might be observable but what about smaller molecules? At what size scale would the uncertainty principle make observation impossible?

    • Re: (Score:2)

      by 6031769 ( 829845 )

      The Heisenberg uncertainty principle applies at the quantum level and its effect becomes more pronounced as the sizes of the objects and systems decrease. However, this alone imposes no limit on observability.

      Put simply, the principle states that the more precisely you know the position of a particle the less precisely you can know its momentum (and therefore velocity). At the quantum level the observation necessarily perturbs the system being observed.

  • The picture is all very impressive, but is there some practical application for this technique?

  • But... (Score:3, Funny)

    by SnarfQuest ( 469614 ) on Friday August 28, 2009 @12:34PM (#29233259)

    Can it be used to create biodiesel?

  • In other news, the International Olympic Committee has filed a trademark infringement suit against IBM and God, showing that pentacine resembles the trademarked "interlocking five ring [fredlaw.com]" design of the Olympic Games.

  • Compare those pics with 45nm chip design. (Score:3, Interesting)

    by deathcow ( 455995 ) * on Friday August 28, 2009 @01:35PM (#29234139)

    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

  • But what are the "STICKS" connecting the BALLS? (Score:4, Interesting)

    by Vitriol+Angst ( 458300 ) on Friday August 28, 2009 @02:39PM (#29235073)

    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.

    • Re: (Score:3, Interesting)

      by Chris Burke ( 6130 )

      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 chemist

  • Single Molecule (Score:3, Funny)

    by hidannik ( 1085061 ) on Friday August 28, 2009 @05:09PM (#29236951) Homepage
    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."

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