Benzene trap and butane on gold surface

These 3D simulations demonstrate the molecular dynamics simulations of a benzene molecule being trapped between two xeon atoms through the van der Waals forces at low temperature, and a butane molecule on a gold surface. While the simulations may not appear to be very fun, it demonstrates two key features of the 3D model container behind the scene: (1) the AMBER Force Fields that stablize the molecular structure (12 radial bonds, 12 angular bonds and 6 torsional bonds were constructed to maintain the structure of benzene, and more for butane); (2) the 3D Molecular Constructor that allows the user to sketch up a virtual molecular world from vacuum --- directly from the 3D view --- and then run molecular dynamics simulation to show how objects interact and move. The movie clips below do not show the process of how the molecules were created. (The butane molecule shown here does not have accurate structures, hence the simulation should be considered qualitative.)

The above clips are just animated gif files. Click the above button or this link to launch this interactive activity.

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