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Molecular models are a great tool for visualizing a molecule in three-dimensional space. These models even appear on the web (practically every chemical's Wikipedia page), and there is a very specific color coding for atoms. After some searching I found that it was called the CPK coloring system. It seems rather intuitive for some elements, like for $\text{carbon}$, $\color{\green}{\text{fluorine}}$, and $\color{\yellow}{\text{sulfur}}$, which use the colors for the elemental forms of these atoms (diamonds aside).

On what basis, though, did Robert Corey and Linus Pauling choose the colors for $\color{\red}{\text{oxygen}}$, $\color{\turquoise}{\text{nitrogen}}$, and hydrogen (I'm not going to do white on white). Were these arbitrary choices that had to be made for these colorless elements, or is there some reasoning behind them?

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There's an interesting article here - Illustrating Atoms and Molecules - that discusses atom colors:

In 1865, the chemist August Hoffman gave a Friday Evening Discourse at London’s Royal Institution on the “Combining Power of Atoms.” In order to demonstrate chemical bonding of atoms, he drilled holes in croquet balls and connected them with metal pipes (Figure 2). His choices were limited by the available colors of croquet balls and he relied on many of the same color conventions that had been adopted centuries earlier

These colors are listed as :

  • Carbon is colored black because it’s the color of charcoal.
  • Oxygen is red because it’s necessary for combustion.
  • Nitrogen is blue because it’s the most abundant element in the Earth’s atmosphere and the sky appears blue.
  • Hydrogen is white because it forms a colorless gas.
  • Chlorine is green because it forms a greenish gas.
  • Sulfur is yellow because that’s its color in mineral form.
  • Phosphorus is orange because it glows orange in a flame.
  • Iron is reddish brown because it rusts.

Which is interesting, but I've no idea where this list comes from...

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    $\begingroup$ It is interesting that it goes back so far (like quite a few decades before modern molecular structures were fully understood). But it is essentially arbitrary. But with a few links that make memorising the scheme slightly easier (nitrogen has nothing to do with the sky being blue but you are likely to remember the association because of the link). $\endgroup$ – matt_black Apr 19 '16 at 21:01

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