About the communication tools, same here.
For the libraries, it depends on how the apps works, I think. One of the simplest idea is to build an apps to interactively generate 3D structure of the molecules. Here, JSME to sketch the 2D graph, then generate 3D by rdkit or pybel, and later show the structure with 3DMol, pymol, Or NGL, as you and @ea42gh had discussed before.