A few very useful features

As far as the inertia-based rotation, I think what you're looking for is if you flick the display you want the molecule to spin for a short duration after the flick, with the degree of rotation determined by the speed of the flick. This would be similar to the scrolling effect of the lists on the iPhone. Right now, rotation is determined by the instantaneous differences in position of your finger as it moves across the screen. To implement this suggestion, I'd need to differentiate between a slow and fast moving gesture, as well as one that stops before the finger is picked up or one where the finger leaves the surface as it is still moving. Then, I'd need to add a timing routine that moves the molecule at a set rotational velocity determined by the flick speed, and decelerating for a set period of time. This timing routine would need to be interruptible in case you wanted to stop the rotation before it was finished and move it a different direction.