Atom + Atom = Molecule

Share this post:

IBM Research scientists Susanne Baumann and Ileana Rau explain how atoms form molecules, and why they used carbon monoxide in the film A Boy and His Atom.

What properties attract atoms to connect and form molecules?

Susanne Baumann

Atoms contain charged particles such as electrons and protons. The protons reside in the nucleus, while the electrons orbit around it. When you put atoms together, some of their electrons get shared between the atoms. This binds the atoms together, and they may form a molecule or a more complex structure such as a crystal.

Atoms can also interact (connect) via electrostatic forces (attraction or repulsion between charged particles), which can also lead to the formation of a bond between atoms. Depending on the details, such as what kind of atoms you use, you can have ionic bonds, covalent bonds, hydrogen bonds, or others.

Traditionally, physical chemists study the bonds between different atoms.

Why were carbon monoxide molecules used to film “A Boy and His Atom”?

Ileana Rau

First, the atoms that make up the surface (for the movie shoot) are all the same kind — copper (but silver and aluminum are also used). They are arranged in a periodic pattern called a crystal lattice. As a result, these atoms are tightly stuck together. Now, depending on what kind of atom we put on top of this surface, the bond between this atom and the copper surface can be weak (the atom just slips around the surface easily), strong (the atom is stuck to the atoms in the surface) or somewhere in between.

To make the movie, we used carbon monoxide because the bond between its carbon atom and the copper are well balanced. The oxygen atom also must bind with the tip of the scanning tunneling microscope so that we could move the entire molecule.

We also need the carbon atom to bind with the copper surface tightly enough to hold still while acquiring the image. It turns out that carbon monoxide on copper has just the right balance of these bonds between the atoms of the surface, the atoms of the tip, and the oxygen atom to be arranged on top of the surface (although we can also slide single atoms such as iron, cobalt, manganese, sodium, cesium, and iodine on a copper surface).

The carbon atom in the molecule attaches to a copper atom in the surface, while the oxygen atom sticks out. The atoms in the STM tip pull the oxygen atom around. The oxygen atom then pulls the carbon along with it.

We don’t see the atoms that make up the copper surface — we’re actually “seeing” their electrons. Inside the copper crystal, the conduction electrons are shared among all atoms, which forms a uniform background at the resolution that we used (a magnification of 100 million). You see these electrons as a cloud or waves that appear around the individual structures we built out of carbon monoxide — that make up the frames of the movie.

Feeling an Atom


More stories

A new supercomputing-powered weather model may ready us for Exascale

In the U.S. alone, extreme weather caused some 297 deaths and $53.5 billion in economic damage in 2016. Globally, natural disasters caused $175 billion in damage. It’s essential for governments, business and people to receive advance warning of wild weather in order to minimize its impact, yet today the information we get is limited. Current […]

Continue reading

DREAM Challenge results: Can machine learning help improve accuracy in breast cancer screening?

        Breast Cancer is the most common cancer in women. It is estimated that one out of eight women will be diagnosed with breast cancer in their lifetime. The good news is that 99 percent of women whose breast cancer was detected early (stage 1 or 0) survive beyond five years after […]

Continue reading

Computational Neuroscience

New Issue of the IBM Journal of Research and Development   Understanding the brain’s dynamics is of central importance to neuroscience. Our ability to observe, model, and infer from neuroscientific data the principles and mechanisms of brain dynamics determines our ability to understand the brain’s unusual cognitive and behavioral capabilities. Our guest editors, James Kozloski, […]

Continue reading