Can We See Atoms? Electron Microscopes and Scanning Tunnelling Microscopy

For most of history, atoms were a matter of inference. Chemists deduced their existence from the way elements combined, physicists from the behaviour of gases, and Einstein from the jittering of pollen grains in water. Nobody had seen one. Today, researchers routinely produce images in which individual atoms appear as neat rows of bumps, and they can even pick atoms up and place them one at a time. How did we get from inference to images?

Why an ordinary microscope can never do it

A light microscope forms an image by collecting light waves that bounce off or pass through a sample. Waves blur out any detail that is much smaller than their own wavelength. This is the diffraction limit: the finest detail a light microscope can separate is roughly half the wavelength of the light used.

Visible light has wavelengths from about 400 to 700 nm, so even a perfect light microscope struggles to resolve anything smaller than about 200 nm. A typical atom is around 0.1 to 0.5 nm across (see how small is an atom?). That’s roughly a thousand times too small. No amount of lens-polishing can fix this; it is a limit set by the nature of waves.

To see atoms, we need either waves with much shorter wavelengths or a completely different way of “looking”.

Electron microscopes: using shorter waves

In the 1920s, Louis de Broglie proposed that particles have wavelengths too. The faster an electron moves, the shorter its de Broglie wavelength. An electron accelerated through 200 kilovolts has a wavelength of about 2.5 picometres, around a hundred times smaller than an atom. In principle, a microscope using electrons instead of light could resolve atoms easily.

Ernst Ruska and Max Knoll built the first transmission electron microscope (TEM) in 1931. It works much like a slide projector:

• a beam of high-energy electrons passes through a very thin sample, often only tens of nanometres thick;
• magnetic lenses focus the electrons;
• the transmitted electrons form a magnified image on a detector.

For decades, imperfections in the magnetic lenses (called aberrations) stopped TEMs from reaching their theoretical resolution. That changed around the start of the 2000s with aberration correctors, complex sets of extra lenses that cancel the distortions. Modern aberration-corrected instruments can resolve features smaller than 0.1 nm, so columns of atoms in a crystal show up clearly. In the scanning version (STEM), a finely focused beam scans across the sample, and the brightness of each spot even reveals which element sits there, because heavier atoms scatter electrons more strongly.

Electron microscopy has one big catch: the sample must sit in a vacuum and survive a beam of energetic electrons. Delicate materials, such as biological molecules, can be damaged. Cryo-electron microscopy, which images frozen samples with low electron doses, got around much of this problem and earned a Nobel Prize in Chemistry in 2017.

The scanning tunnelling microscope: feeling atoms with a current

In 1981, Gerd Binnig and Heinrich Rohrer at IBM’s Zurich lab built something radically different: the scanning tunnelling microscope (STM). It doesn’t use lenses or waves to form an image. Instead, it “feels” the surface.

Here’s how it works:

1. An extremely sharp metal tip, ideally ending in a single atom, is brought to within about a nanometre of a conducting surface.
2. A small voltage is applied between the tip and the surface.
3. Even though the tip doesn’t touch the surface, electrons tunnel across the gap, a quantum effect with no classical equivalent. This produces a tiny current, typically around a nanoampere.
4. The tunnelling current is extraordinarily sensitive to distance: it changes by roughly a factor of ten for every 0.1 nm change in the gap.
5. The tip is scanned across the surface while a feedback loop moves it up and down to keep the current constant. The recorded up-and-down motion is a map of the surface’s height, precise enough to show individual atoms.

Tunnelling is the same quantum weirdness discussed in the quantum mechanical model: an electron has a small but real probability of appearing on the far side of a barrier it doesn’t classically have the energy to cross.

The STM’s first spectacular results included images of the surface of silicon showing its atoms rearranged into an intricate pattern. Binnig and Rohrer shared the 1986 Nobel Prize in Physics, together with Ernst Ruska for the electron microscope.

Strictly speaking, an STM image is a map of electron states near the surface rather than a photograph of atomic nuclei. But the bumps line up with atoms, and the images agree with what X-ray crystallography says about where atoms should be.

Moving atoms one at a time

The STM can do more than look. By lowering the tip and adjusting the voltage, researchers found they could drag individual atoms across a surface. In 1989, Don Eigler and Erhard Schweizer at IBM arranged 35 xenon atoms on a nickel surface, cooled to about 4 K, to spell out “IBM”. It was the first time humans had deliberately built a structure atom by atom.

Later experiments arranged iron atoms on copper into a circular “quantum corral”, whose interior showed ripples of electron waves, a direct picture of quantum behaviour. In 2013, IBM researchers even made a short stop-motion film, A Boy and His Atom, from thousands of images of carbon monoxide molecules moved one step at a time.

The atomic force microscope: works on insulators too

The STM has a limitation: it needs a current, so the sample must conduct electricity. In 1986, Binnig, Calvin Quate and Christoph Gerber introduced the atomic force microscope (AFM), which measures tiny forces instead of current.

An AFM tip sits on the end of a microscopic cantilever, a little like a diving board. As the tip scans over a surface, forces between the tip atoms and the surface atoms bend the cantilever, and a laser reflecting off its back records the movement. AFMs work on insulators, polymers and even living cells in liquid.

In 2009, a team at IBM Zurich used an AFM with a single carbon monoxide molecule on its tip to image a pentacene molecule (a chain of five fused benzene rings). The picture showed the molecule’s rings and bonds so clearly that it looked like a textbook structure diagram. Similar techniques have since been used to watch chemical reactions happen on surfaces, bond by bond.

Other ways of “seeing” atoms

• X-ray crystallography doesn’t produce a direct image, but by analysing how a crystal scatters X-rays, it reveals the positions of atoms with great precision. It is how we know the structures of DNA, proteins and most minerals.
• Field ion microscopy, developed by Erwin Müller in the 1950s, produced some of the first images in which individual atoms could be distinguished, at the tip of a sharp metal needle.
• Atom probe tomography evaporates a sample atom by atom and identifies each one by its mass, building up a 3D map of where every atom of each element sat.
• Trapped ions. In 2018, a long-exposure photograph showed a single strontium ion held in an electromagnetic trap as a tiny glowing dot, visible because it scattered laser light. The dot is much larger than the ion itself, but it is light from one single atom.

So do atoms really “look like” balls?

Not quite. The images show where electron density is concentrated, or how forces vary over a surface. Atoms appear as soft bumps because their electron clouds fade gradually rather than ending at a hard surface (see electron probability clouds). The colours in published images are added by software to make heights or intensities easier to read. What the images do confirm, beyond any doubt, is that matter is made of discrete atoms, arranged exactly as chemistry predicted.

Key takeaways

• Light microscopes can’t show atoms: visible light’s wavelength is about a thousand times bigger than an atom.
• Electron microscopes use electrons with picometre wavelengths. Modern aberration-corrected TEMs resolve atomic columns below 0.1 nm.
• The STM (1981) maps surfaces using a quantum tunnelling current that is extremely sensitive to distance, and it can move single atoms.
• The AFM (1986) measures tiny forces, works on non-conductors and can image the bonds inside molecules.
• The images show electron density and forces, so atoms appear as soft bumps. They still give direct visual confirmation of the atomic theory begun by Democritus and Dalton.