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The Journal of Chemical Education provides some Quicktime movies available on a CD that could provide what you are looking for.
There are also some nonprofit organizations that provide satellite-based video-on-demand and other movie-type media that have good educational content for chemistry training.
I applaud you for your innovative thinking in this area.
With respect to intellectual property (IP) protection issues, you'll note (if you run a few search engine queries), this is a robust market sector with companies beginning to recognize the utility of 3D tools for teaching complex concepts. Of course, as companies, their go-to-market strategy is what will help them protect their IP.
Flash movie developers take note. Opportunity knocks.