Molecule construction and visualization website

For a couple of months now, I've been at work on a website for constructing and visualizing molecules. In-browser molecular dynamics are done with a molecular mechanics modeler based on Norman Allinger's MM2 as described in Eric Drexler's Nanosystems. This is the same set of mathematics I used in an earlier effort in the same vein called NanoCAD in 1997. Unfortunately my knowledge of chemistry and molecular modeling hasn't grown very quickly in that time. I know a bit more from my time with Nanorex, where molecular modeling was mixed with gadgets to supply external forces ("jigs" in the parlance of our program), an idea that I believe is crucial to nanotechnology design software and also to scaling molecular simulations to much larger scales. I hope to use the code from this website as a starting point for working in that area.

I have expenses like everybody else, and I'm trying to think of ways to use this website to make a little money without tarnishing its educational potential or scientific credibility. I want the website to be readily available for use in schools and universities. If I end up putting ads on the website, I hope to make them tastefully small and out-of-the-way. I've noticed that the HTML5 canvas I'm relying upon for graphics doesn't work on iPhones, iPads, or Android phones, so there's an opportunity to sell mobile apps for those platforms, using their native graphics canvases. I'm very open to ideas to bring in a little revenue without being tacky. I've put a lot of work into this, and plan a lot more.

Longer term plans include adding jigs as discussed above, maybe an interface for a force-feedback joystick so that you can find out what Brownian motion feels like, using the website to get access to much better and faster simulators, and storing your own private library of molecules. This stuff started out as Java code with the website's JavaScript being co-developed, but at some point the JavaScript development took off and I didn't make time to keep the Java up to date. So I need to do that, and then the JAR file can become a useful computational chemistry tool.