You imply that atoms and molecules are elementary particles, which we already know to not be the case. It's possible that quantum effects, which seem to be probabilistic (depending on your interpretation), are vital for human intelligence. However, that seems fairly unlikely. While it's still mostly speculation, most experts tend to think that classical mechanics are sufficient to explain the functions of the human brain, which would imply that an identical arrangement of atoms/molecules would also be an intelligent system, and a good computer simulation (which is currently still unfeasible) of the atoms/molecules would also be an intelligent system.