Except that atoms are not homogenous entities.
Even assuming you'd somehow manage to produce and combine atoms to a spec, there's positively no way of obtaining that spec.
Even assuming you'd somehow manage to produce and combine atoms to a spec, there's positively no way of obtaining that spec.
If it does, you don't need a spec of that state, since we know that it can emerge from something simpler (humans start out as a single cell, after all, and so in fact did all of humanity). You don't need the whole system, just the right initial conditions.
At that point you're growing a brain rather than engineering one, and maybe it takes you no closer to understanding the mechanics. But the point stands that it must be possible to construct a brain in principle, because it's already happened so many times before.