The goal of the game is that you get a set of molecules. Then you have to take them apart, move the atoms and parted molecules around, and bond them together again. To win the level you just have to provide a small number of the correct molecules to the exits.
Completing a level usually isn't too hard. But once you have a working design you can try to optimize it to solve the puzzle in the shortest time, with as little commands as possible, or with as little reactors as possible. Thats where you can spend weeks of your life trying to reach or even beat the highscore of the other players out there.
You can also download the demo from the developers website (
http://www.zachtronicsindustries.com/ or
http://www.spacechemthegame.com/ ).
The game is pretty much like "The Codex of Alchemical Engineering", which is a free browser game (in case you dont want to install games on your pc or dont want to play a demo for some reasons.
The main gameplay Difference to "The Codex of Alchemical Engineering" is, that in "SpaceChem" you have serveral Reactors, which you set up to manipulate 2 types of molecules and then connect those reactors. And additionally the storyline of SpaceChem is pretty insane.
I liked the game. I only played the demo, though. I got pretty tired of the optimization part after playing a lot of games like this.