Mathematica is a useful tool for analyzing chemical data, understanding chemical processes and visualizing chemical species.

The curated datasets ChemicalData, ElementData and IsotopeData have lots of useful information that some users want to access while not online and others want to display in graphical format. Graphical visualization of chemical systems such as finding lattice planes of solid state structures or merely viewing them appropriately are appropriate for this tag.

Mathematica can read a variety of molecular formats, although some require a bit of spelunking to use properly.

Also, although this particular question is not tagged with Chemistry, it demonstrates how one can explore the kinetics of fairly complex reactions using Mathematica.

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