Your idea does sound somewhat like an archetype, as used to be used in biology (not so much now).
It was used as something like a body plan (physically ill-defined) for a group of animals, in development and in evolution (it was something ancient determining how things grow/evolve).
In some cases its used as an abstract pattern, which the body plans of those groups tend to assume.
It is not a functionally well defined concept (mechanisms and causal chains of effect underlying how it works are not discussed).
It seems to me to have been used as a kind of hand waving to bridge over processes and intellectual gaps (like development or genetics, involving many microscopic cellular and molecular mechanisms) which could not at the time be explained.
Now things are different, mechanisms determining development are better understood and the concept is rarely used.
WRT molecules, they are made of atoms and will assemble in a variety of ways limited by the rules of molecular physics.
The molecules are a higher level of organization for the atoms.
The different ways these molecules might assemble at still higher organizational levels (like membranes, or polymeric things like proteins or amino acids, multi-molecular assemblies), allows a lot potential variety (a huge multi-dimensional space of different possible combinations).
This seems to be the level you are talking about.
You seem to want the way the molecules assemble, at larger scale higher organizational levels, to be determined by this archetype influence.
Its not clear how some disembodied psychic force could change how these molecules work beyond to develop these emergent properties.
This sounds like emergent properties (as mentioned by
@mjc123 ) of the molecules in large numbers.
Emergent properties could do the same thing.
The emergence of certain properties (determined in part by the molecules physics and that of their surroundings) in large numbers of molecules is not surprising.
The self-assembly of two layer lipid membranes into micells and vesicles from solution in water of lipids with a charge on one end, is a good example.
But since its a story, if you need the psychic force for the story, you could find some way to subtly influence how the physical forces drive molecules to come together, with your psychic force.
Maybe the physics force can set up some vibration which would favor (via some kind of resonance with molecular bonds) certain molecular assemblies.
This would be more like riding the emergent properties by directing the precis manner in which they are manifested.