The best replacement for atoms is molecules.

The best alternatives to atoms are rated as following:
★★★★★  molecules
★★★★  ions
★★★  elements
★★  cells
★  bits
  compounds
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  mole of gold atoms
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Speaking about atoms, one probably shouldn't forget about isotopes.

Other search terms related to atoms and their ratings are:
★★★★★ isotopes
★★★ electrons
★★ polar covalent bonds
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