Most organic molecules consists of a "backbone" with some branches tacked on, they resemble a central chokepoint, with some almost one dimensional corridors leading to it. That doesn't sound like a very interesting battle.
I did find a possible candidate though, [vitamin B12](http://en.wikipedia.org/wiki/Vitamin_B12
) ([alternative illustration](http://www.jonesken.com/vitaminX.png
)). On the top half, sure all those CNOH2 branches will be a little boring, but the centre looks interesting. And the bottom half at least has two connections to the top half (not much, but a lot better than the single connection in most organic molecules).
If you look at inorganic compounds, molecules tend to be rather small, which also makes them unsuitable for a map.
@Richard Sharpe, Moros:
Caffeine and glucose could work, but only for a two player map I think. My reasoning is for "multi" player maps.