What Is a Molecule?

Atoms, elements, molecules… What’s the difference? This is part 3 in the Stated Clearly series: An Introduction to Chemistry. In it you will find a simplified definition of a molecule, you will learn how we model molecules, and you will see actual images of real molecules and their vibrational modes!

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In this video we describe a molecule as “a group of atoms stuck together, usually through chemical bonds”

This definition is great because it’s so easy to make sense of, but there are some problems with it. Biologists will sometimes consider a double stranded chain of DNA to be a “single molecule”, even though each half of the strand is bound to the other via non-chemical hydrogen bonds. The same is true for some protein complexes composed of multiple sub-units.

Alternatively, some crystals (such as quartz) are made of repeating patterns of atoms all chemically bound. Using our definition, you’d have to consider an entire quartz crystal to be a “single molecule”. Chemists don’t usually do this, instead they consider each repeating sub-unit to be a molecule. Pure metals have a similar issue.

Language is a living, evolving mess! Even in formal scientific fields where you might expect more consistency.

In this animation we show a hydrogen molecule forming in space via a collision of just two atoms. Normally, this reaction also requires some sort of dust or ice particle to trap atoms as they bind together.

To avoid distraction when teaching the basic concept of a molecule, we chose to ignore this technicality in the animation. You can read here about how hydrogen molecules normally form in space: https://www.sciencedirect.com/science/article/pii/S2405675817300271


Here is the molecular image by Leo Gross at IBM in 2009: https://www.researchgate.net/publication/26773422_The_Chemical_Structure_of_a_Molecule_Resolved_by_Atomic_Force_Microscopy

Here is the paper on molecular vibrations by Joonhee Lee in 2019: https://www.nature.com/articles/s41586-019-1059-9

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