Molecules that have been made are. Molecules that I investigate havent been made yet. They're drawn in jmol by hand and need to have their structures optimized otherwise you can't accurately calculate those molecules' properties. Eg. Raman spectra, strength of interactions between them and other molecules or ions, what the orbitals look like i.e how the molecule is actually held together or in the case of plane wave calculations and with the assistance of other software, you can design and build new materials with interesting properties. Eg. Stronger materials, materials that exhibit linearity in transistors (nanotubes are an example of this but so far various issues with their manufacture has not lead to strong evidence of this in experiments for a number of reasons)

New materials, catalysts to speed up reactions, new drugs, this sort of work has a lot of useful applications but its also just interesting to see what can be built just for the hell of it.