https://en.wikipedia.org/wiki/Chirality
What you your intuiting/sensing is correct
Natural and synthetically made chemicals aren't 'the same' despite being having the same components and relationships the difference is due to chirality.
For whatever reason it's rarely discussed unless you are a chemist and I only know about it as my dad did a degree in chemistry.
Nature seems to produce homochirality aka spins in one direction. Synthetic molecule creation produces a 50/50 split in either direction. Imagine these molecule coming into contact with proteins in a living system like your self or a plant and you can start to see why the effects are different.
