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As long as the problem does say you can use either atoms OR molecules as the unit, I'm sure they are interchangeable depending on context. Of course, if it specifies one rather than the other, then use that unit instead.
Although atoms and molecules are different, you convert them from moles in the same way. For both atoms and molecules, you would use Avogadro's number. Therefore, for every 1 mole of a compound or substance there are 6.022x10^23 atoms or molecules. Whatever the problem specifies, you would use that as your units.
Like said above, pay attention to the what the problem is asking for. A question can ask for the atoms of H in the molecule H2O for example, in which you would have to use Avogadro's number and then multiply by two to account for the two hydrogen atoms for every molecule of H2O.
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