Two models of phenolphthalein, one in its 0-8.4 pH form and its 8.4-10.0 pH form.
MolView (http://molview.org/) and Jmol (http://www.jmol.org/), both open source pieces of software, were used to create this model.
How to generate any molecule:
Note: for cases where you need a structure that is common (eg. caffeine) you can skip the first two steps and open it in Jmol by clicking file->get MOL and typing the name.
Now there will be two files, [NAME].obj and [NAME].mtl in your home directory which you can use for whatever you want.