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Imaging Atoms

September 26, 2012

If there was anyone who was still skeptical of the atomic theory of matter at the end of the twentieth century, they should have been convinced by the mass of photographic evidence that started to appear at that time. Sure, Xray diffraction suggests that matter is made from atoms arrayed in space, but that's not an image of an actual atom. At the end of the century, scientists were able to image atoms, themselves.

Atoms have now been imaged for quite a few decades. Atoms of the heavy elements, such as tungsten and uranium, were the first to be imaged using electron microscopy. These were somewhat easy targets, since they're relatively large and packed full of electrons. The covalent radius of tungsten atoms is about 162 picometers (pm), and that of uranium atoms is 196 pm. The covalent radius of hydrogen atoms is just 31 pm.[1]

The invention of atomic force microscopy has simplified atomic imaging, so it's now common to see neat arrays of atoms, sometimes with highlighted defects, published in scientific journals. The following figure, selected more for its aesthetic appeal than anything else, is representative of the present state of the art in atomic imaging. Carbon is a low atomic weight element, but it's been imaged often because of its utility as its graphene allotrope.

Atomically-resolved scanning tunneling microscope image of graphene on Copper

Atomically-resolved scanning tunneling microscope image of graphene on copper.

The bright areas are the regions of highest electron density, where the carbon atoms are located. The planar hexagonal lattice, built from circles of six carbon atoms, is highlighted.

(Fig. S1(a) of ref. 2, via the arXiv Preprint Server.)[2)]

A team of scientists from the IBM Zurich Research Laboratory, the Universidade de Santiago de Compostela (Spain), and the French National Centre for Scientific Research (CNRS, Toulouse Cedex, France), have advanced the state of the art in atomic imaging by producing images of bits of graphene that have a resolution high enough to allow measurement of the different bond lengths that exist from from the center of the graphene patch to its edge (see figure).[3-6]

Figure caption

I always thought that carbon atoms were black.

An atomic force micrograph of a small piece of a graphene sheet.

The AFM tip was functionalized with a carbon monoxide molecule.

(IBM Research - Zurich image, used with permission))

The IBM members of this team were the first to image a single molecule in 2009.[4] The recently produced images have used the technique of frequency modulation atomic force microscopy (FM-AFM) with a functionalized AFM probe tip. The metal tip held a single carbon monoxide (CO) molecule at the tip to localize and amplify the signal.[4-5] The apparatus was cooled to -268 °C, otherwise the atomic vibrations would have blurred the images.[4]

Said IBM scientist Leo Gross, who was an author of the paper on this work which made the cover of the September 14, 2012, issue of Science,[6]
"We found two different contrast mechanisms to distinguish bonds. The first one is based on small differences in the force measured above the bonds. We expected this kind of contrast but it was a challenge to resolve... The second contrast mechanism really came as a surprise: Bonds appeared with different lengths in AFM measurements. With the help of ab initio calculations we found that the tilting of the carbon monoxide molecule at the tip apex is the cause of this contrast."[3]
The functionalized tip allowed a measurement of bond length to a precision of three picometers.[3] This is just 5% of the diameter of a hydrogen atom. The research team is set to investigate the performance of molecules other than CO.[4] I think that ammonia (NH3) might be a good candidate. Measurement of interatomic spacing from place to place on a surface could assist research in such areas as catalysis, photovoltaics, and molecular electronics.[5]

Now that we've covered the scientific aspects of atomic imaging, it's time to take off our lab coat, put on our philosopher's fez, and talk about whether or not we really are "seeing" atoms. I wrote an article on this topic many years ago for a general interest magazine.[7] In that article I used the example of the oil painting, The Treachery of Images (La trahison des images, 1928–1929), by Belgian surrealist artist, René Magritte.

This is a copyrighted work of art, presently at the Los Angeles County Museum of Art, so I can't show its image here; but a low resolution image is available at Wikipedia. The painting shows a smoker's pipe and the inscription, "Ceci n'est pas une pipe" ("This is not a pipe"). Magritte's point being that this is an image of a pipe, and not a pipe.

When you use an optical microscope to view a small object, you actually do see the object. The microscope acts as a magnifier for the light that reaches your eyes, but the vision process is the same as always. Atomic force microscopes are not magnifiers of anything that can be seen, so what appears on a computer display is a representation of atoms. There's no direct linkage to the human sense of sight, so we really aren't seeing atoms. Figure caption

This is not a pipe from the heating system of my house.

(Photo by the author)


  1. Covalent Radius 2008, Web Elements.
  2. Jifa Tian, Helin Cao, Wei Wu, Qingkai Yu and Yong P. Chen, "Direct Imaging of Graphene Edges: Atomic Structure and Electronic Scattering," arXiv Preprint Server, July 25, 2011.
  3. IBM Scientists First to Distinguish Individual Molecular Bonds, IBM Press Release, September 14, 2012.
  4. Jason Palmer, "Atomic bond types discernible in single-molecule images," BBC News, September 13, 2012.
  5. Ruben Perez, "Discriminating Chemical Bonds," Science, vol. 337, no. 6100 (September 14, 2012), pp. 1305-1306.
  6. L. Gross, F. Mohn, N. Moll, B. Schuler, A. Criado, E. Guitian, D. Pena, A. Gourdon and G. Meyer, "Bond-Order Discrimination by Atomic Force Microscopy," Science, vol. 337, no. 6100 (September 14, 2012), pp. 1326-1329.
  7. D.M. Gualtieri, Cyborgs and Atomic Microscopes, Phi Kappa Phi Forum, vol. 84, no. 2. pp. 6-7 (Spring 2004).

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