Avogadro

Avogadro is a multi-platform, open source application that allows three-dimensional, interactive molecular designs to be seen from almost any angle, and has multiple options for you to work with.

One of them, called Label, allows information to be placed on each molecule such as: the names and symbols of each element that composes it, the number of atoms, its partial load, the unique identifier, and so on. In all there are 17 different such options.

To add the chemical elements is easy. Just select them from the dropdown box in the Draw menu. If it is not listed in the menu, just click 'Other' to display the periodic tabl. The fragment library allows you to quickly insert a variety of chemical compounds.

Avogadro is compatible with GAUSSIAN, GAMESS, MOPAC and Q-Chem, and can export the models to EPS graphics formats, SVP, POV-Ray, PNG, JPG and BMP.