Full Idea
Even if we claim that it is really isotopes not atoms that are the natural kinds (thus divorcing chemistry from ordinary language), atoms are said to differ with respect to such features as energy levels of the electrons.
Gist of Idea
Even atoms of an element differ, in the energy levels of their electrons
Source
John Dupré (The Disorder of Things [1993], 2)
Book Reference
Dupré,John: 'The Disorder of Things' [Harvard 1995], p.39
A Reaction
So we can't just pick out the features of one atom, and say that is the essence. Essence always involves some selection. I say the essence arises from the explanation of the atom's behaviour.