You won’t believe these pictures of molecules!

Well, I just wrote my first clickbait headline as a test to see if it attracts readers. I’m referring here to a 2.5-year-old paper that just came to my attention; I call it to yours because although the chemistry is complicated, the pictures are lovely. The work in question is by Dimas de Oteyza et al. and appeared online in Science Express in March of 2013 (reference at bottom; free download). There’s also a blurb at the campus news site at UC Berkeley, where the work was done.

The research was an attempt to synthesize large structures of “graphene“, a honeycomb of hexagonal carbon structures that has a lot of practical uses. But rather than detect the products of their reaction through chemical analysis, they decided to do it visually using non-contact atomic force microscopy (nc-AFM; see below). They started with reactant 1 below, heated it and chilled it on the visualization surface (this stops molecular motion cold), and looked at the products.

The figure below shows the outcome. The chemical structures are at the bottom, the top row gives the visualization from coarser scanning tunneling microscope (STM), which uses a fine metal tip that moves across the sample.

But look at the second row, which shows the improved resolution with nc-AFM. You can see the chemical bonds themselves and the hexagonal carbon structures with double bonds. When I was a kid, I used to say that all our evidence for atoms and molecules is indirect: based on prediction and observation on the macro level. It’s astounding to me that humans have now developed the technology (and I emphasize that all of this technology comes from raw elements and molecules found on Earth) to see individual atoms and molecules.


(From UC Berkeley figure): Non-contact atomic force microscope (nc-AFM) images (center) of a molecule before and after a reaction improve immensely over images (top) from a scanning tunneling microscope and look just like the classic molecular structure diagrams (bottom).

Here’s the amazing way they visualized these molecules: an nc-AFM appartus that scans the surface of the plate using a single carbon monoxide molecule as the probe, which moves back and forth over the molecule—not touching it—on the chilled plate. The CO molecule’s interaction with the big carbon molecules is detected by displacement of the plate, which is then converted into images by a laser hitting the plate, producing a readout of displacements in all three dimensions:


An atomic force microscope probes a molecule adsorbed onto a surface, using a carbon monoxide molecule at the tip for sensitivity.

Ain’t humans smart?

According to the authors, this isn’t just a neat trick, for they say they’ve gotten insight into the precise chemical mechanisms,induced by heat, that convert the molecule on the left to the three molecules on the right; and they give a detailed scenario (of interest only to chemists) of what has happened. For our purposes, we can just gape in awe at what we can see happening, and the fantastic apparatus that helps us see it.


Oteza, D. G. et al. 2013. Direct imaging of covalent bond structure in single-molecule chemical reactions. Science 340: 1434-1437


  1. GBJames
    Posted November 30, 2015 at 9:33 am | Permalink

    I clicked!

  2. Merilee
    Posted November 30, 2015 at 9:38 am | Permalink


  3. Ali
    Posted November 30, 2015 at 9:40 am | Permalink

    This is fantastic, extremely exciting stuff!
    I always dreamt of seeing molecules this way!
    This is what science can do. As for faith…

  4. BobTerrace
    Posted November 30, 2015 at 9:45 am | Permalink


  5. TJR
    Posted November 30, 2015 at 9:54 am | Permalink

    I think I can see Jesus in one of those pictures.

    • Posted November 30, 2015 at 10:27 am | Permalink

      And the Virgin Mary!

      • Adam M.
        Posted November 30, 2015 at 5:33 pm | Permalink

        Our Lady of Fatima guided the CO molecule from her heavenly repose… We must give thanks.

      • Newish Gnu
        Posted November 30, 2015 at 5:34 pm | Permalink

        And two(!) Kardashians

  6. Torbjörn Larsson
    Posted November 30, 2015 at 10:00 am | Permalink

    It is an image averaged over time (the volumes where bond electron visits are more ephemeral than they appear here), but fantastic details!

    I would argue that Einstein’s analysis of Brownian motion showed that we could see individual atoms or molecules back then, just fleetingly. My favorite example before being shown this treasure trove was individual ions remaining in slowly leaked ion traps, used for photon transmission visualization – ‘lighthouse’ ions.

  7. CRS
    Posted November 30, 2015 at 10:12 am | Permalink

    I took the bait, and I’m hooked. Wow.

  8. Joseph Stans
    Posted November 30, 2015 at 10:28 am | Permalink

    Are you trying to say that these images of molecules were developed outside the eye of God?

    Really, I have never heard of such a thing!

  9. Posted November 30, 2015 at 10:37 am | Permalink

    I am equally in awe of Row 3: Human intelligence correctly figured out the exact shapes of those carbon bonds in the 19h century, when very few clues were available. The correspondence between Row 2 and Row 3 is a beautiful testament not only to advancing technology but also to good old-fashioned 19th Century reasoning.

    • Jim Knight
      Posted November 30, 2015 at 11:15 am | Permalink

      …and an awesome example of the various correct interpretations of science spread over so many years. I don’t think this is in Revelations…!

      • Mark Sturtevant
        Posted November 30, 2015 at 12:50 pm | Permalink

        Clearly, these structures are revealed to us, if one but read holy scripture with enlightened eyes. B/c Lo:

        “And six branches shall come out of the sides of it; three branches of the candlestick out of the one side, and three branches of the candlestick out of the other side:
        –Exodus 25:32

        • infiniteimprobabilit
          Posted November 30, 2015 at 3:46 pm | Permalink

          Now I remember why I decided the Bible was too pompous and long-winded to bother with.
          You could replace the entire second clause with just “three each side”, with no change at all in meaning and a vast saving in word count.


    • Adam M.
      Posted November 30, 2015 at 5:35 pm | Permalink

      I’m pretty sure Row 3 was drawn to match the pictures, but it’s still very neat.

      • HaggisForBrains
        Posted December 1, 2015 at 4:12 am | Permalink

        No, row three definitely came first, and as Lou says, has been the standard way of illustrating these carbon bonds for ages. To me, it’s amazing to see a “photograph” of these molecules, which exactly matches the way we’ve been drawing them. My mind is truly boggled.

  10. Saul Sorrell-Till
    Posted November 30, 2015 at 10:40 am | Permalink

    How long before someone else runs with your idea Jerry?…

    ’20 Molecules That Interact To Form Kim Kardashian’s Boobs(Number 11 Will Make You QUESTION Reality!!!!)’

  11. Matti K.
    Posted November 30, 2015 at 10:43 am | Permalink

    Well, obiously, molecules are not just a therory. 🙂

  12. Ken Kukec
    Posted November 30, 2015 at 10:59 am | Permalink

    Might be your first clickbait headline, but that screenshot of the cultish Muslimahs yesterday had the look of clickbait material.

  13. Posted November 30, 2015 at 11:00 am | Permalink

    I now believe in chemistry! Another nail in the coffin of instrumentalism.

  14. frankschmidtmissouri
    Posted November 30, 2015 at 11:02 am | Permalink

    The most remarkable thing to me is that the visualized reaction pathways conform to what was previously inferred from the properties and structures of the products and reactants.

    In a way, it’s very like evolution. Darwin and many others could observe mutation and selection on an organismal level and it was confirmed by analysis of DNA sequences, which was generally regarded as impossible until the 80s and 90s.

    • BobTerrace
      Posted November 30, 2015 at 12:13 pm | Permalink

      Nice analogy.

    • Diane G.
      Posted November 30, 2015 at 9:27 pm | Permalink

      And like Alfred Wegener’s hypothesis about continental drift, which was not fully accepted until evidence supporting plate tectonics theory was observed.

  15. Paul D.
    Posted November 30, 2015 at 11:06 am | Permalink

    This entry reminded me of a very interesting medchem blog I read: “In The Pipeline”, by Derek Lowe. He’s talked about this AFM work before, with a similar tone.

    The blog has recently moved to Science, but all the archives were ported over.

    • infiniteimprobabilit
      Posted November 30, 2015 at 5:18 pm | Permalink

      Many of us know Derek Lowe’s blog, though I suspect for most of us it’s through his highly entertaining ‘Things I won’t work with’ thread.

      Most famously, ‘Sand won’t save you this time’ about the spectacularly reactive chlorine trifluoride. But there are many other delightful chemical freaks in there too.


  16. Scott Draper
    Posted November 30, 2015 at 11:20 am | Permalink

    I used to say that all our evidence for atoms and molecules is indirect: based on prediction and observation on the macro level.

    I think this is still true. The images are very theory-laden; sensory data is translated to visuals based on our indirect understanding of atomic theory.

  17. Posted November 30, 2015 at 12:12 pm | Permalink

    I remember hearing about this, I think in C&E News, when it came out. Still wonderful stuff! And shows the weakness of positivism; one should be a realist about molecular shapes! 🙂

  18. Vaal
    Posted November 30, 2015 at 12:14 pm | Permalink

    Absolutely amazing.

    As for actually managing to capture the images, I’m constantly reminded of the role ingenuity plays in science.

    Whenever someone says “X is something that can’t be established scientifically” my reply is “you just aren’t thinking like a scientist.” At one point or another, almost everything science has been able to test and investigate was beyond the limits of science.
    Never say never.

    • Posted December 1, 2015 at 11:28 am | Permalink

      An amusing (though sad) example is A. Comte’s (the world’s first “sociologist”) prediction that the composition of the stars would never be known, because they are so far away and we’d never get there. This was pronounced with a lifetime of those working on spectroscopy and such. Oops.

  19. Ben
    Posted November 30, 2015 at 1:53 pm | Permalink

    So after I observed one of the pictures, I heard something collapse and then this cat in a box started yeowling. Great stuff!

  20. Posted November 30, 2015 at 2:35 pm | Permalink

    My brain doesn’t do chemistry! So sad. I’m not able to visualize the words well enough to not experience more frustration than pleasure. But I liked this post.

  21. Steve Pollard
    Posted November 30, 2015 at 3:19 pm | Permalink

    Wonderful images! I wish this technique had been available when I was an active chemist about 100 years ago. I guess however that these molecules are basically 2-D. Imaging molecules or reactions in the third dimension will be a different challenge. Next year maybe?!

  22. Posted November 30, 2015 at 4:10 pm | Permalink

    Took the bait, awesome* stuff!

    IBM Research made a “stop motion” movie with what seems to be similar technology. Very neat.

    *I think the use of the word is well deserved here.

    • Diane G.
      Posted November 30, 2015 at 9:32 pm | Permalink

      “*I think the use of the word is well deserved here.”

      I was going to post the same sentiment but in regard to “amazing.”

      If this isn’t amazing work, I don’t know what is!

  23. pjie2
    Posted November 30, 2015 at 4:49 pm | Permalink

    Actually, we can even beat that. Back in 2009 some mad geniuses actually managed to visualise the s and p orbitals of electrons in a single carbon atom.

    That’s _subatomic_ resolution right there.

    • Dave
      Posted November 30, 2015 at 7:51 pm | Permalink

      Now THAT is cool! I had not seen that before. To think that those shapes and the structures shown on the AFM pics had all been sussed out by indirect and theoretical means long before they were actually “seen.” And yet, there they, just as predicted. Yes, humans are smart. Except for Lamar Smith.

  24. Adam M.
    Posted November 30, 2015 at 5:38 pm | Permalink

    Very cool, except for the clickbait headline. 😉

  25. Ken Pidcock
    Posted November 30, 2015 at 6:50 pm | Permalink

    First time I saw this, I was astonished. Molecules – molecules – look just like how we’ve long seen them. I guess chemists have always expected this, but I’d always assumed that their structures were just useful fabrications.

    • Dave
      Posted November 30, 2015 at 7:53 pm | Permalink

      Not by a long shot, except for the ‘useful’ part. They had to be that way based on theory and various observations.

    • Posted December 1, 2015 at 11:31 am | Permalink

      A colleague of mine from UBC for a semester (an undergraduate) went on to do an MA in philosophy paper elsewhere on whether we should be realists about molecular shape, defending the “yes”. (He had been a chemist.) In my view the best argument is catenanes – they seem to literally chainlike- you can thread them through and so on.

      • Diane G.
        Posted December 1, 2015 at 7:49 pm | Permalink

        I didn’t know there was a counter-argument.

        • Posted December 2, 2015 at 11:35 am | Permalink

          There are, like van Fraassen’s stuff about limiting realism to “observables” (and here he does not mean the physics sense, but literally what you can see, hear, etc.) I don’t know if I find any of the arguments other than wrongheaded, though.

          (I have the feeling, but it is just gossip, that the antirealists in philosophy of science tend to be religious or religiously sympathetic. Being an antirealist allows them to “have” divine intervention, non-materialism, etc.)

          • Diane G.
            Posted December 2, 2015 at 2:11 pm | Permalink

            “…(and here he does not mean the physics sense, but literally what you can see, hear, etc.)”

            He must then have a hard time explaining how anything works. Like, say, electricity. Or air, for that matter.

            I like your hypothesis in your second paragraph.

  26. Diana MacPherson
    Posted November 30, 2015 at 7:10 pm | Permalink

    Wow! I would have looked even without the hilarious click bait title.

    • Posted November 30, 2015 at 7:59 pm | Permalink

      Ya, the clickbait title was clever 🙂

      Kind of like girls gone wild or molecules misbehaving.

      And I didn’t know clickbait was a word. Kudos to the person who came up with it: great image.

  27. Shwell Thanksh
    Posted November 30, 2015 at 9:50 pm | Permalink

    Wow! Those AFM shots are mind boggling!

    I can only imagine how Kekulé would swoon at seeing his dreams revealed so clearly in front of his waking eyes.

  28. Posted November 30, 2015 at 10:27 pm | Permalink

    That’s amazing. As for click bait headlines, maybe next time try – “Four pictures of molecules. You won’t believe #3!”

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