Chemical makeup refers to the atoms the mineral is composed of. Diamond has the simplest chemical makeup, with carbon being the only element present. Corundum is composed of just two elements, aluminum and oxygen. Its chemistry is expressed as Al2O3, meaning there are two aluminum atoms and three oxygen atoms in a molecule of corundum. The chemistry of other gems can get a lot more complicated.
Molecular structure refers to how the molecules attach to each other.
While you can t see the individual atoms, you can see the result of how they attach to each other in whole crystals. Diamonds form crystals that look like two pyramids attached at their bases. Quartz forms elongated crystals with six sides. This is a result of the molecular structure. It s as if you had two sets of tiles to work with.