There are essentially two main elements on the screen that are used for game play. The Playfield is the large area in the middle of the screen, and the Vial runs along the right side of the Playfield.
You place atoms in the playfield by clicking anywhere within using your mouse. The bottom atom in the Vial will be placed where you have clicked. Using this method, you need to place atoms in such a way (depending on which atoms you get, they fall into the Vial randomly) that you build a complete, satisfied molecule.
Other elements you will see when playing are the Schzapp indicator, Score box and Bonus box. A schzapp is similar to an extra life. It will clear the Vial of atoms in the event it overflows. If you have no Schzapps and the Vial overflows, you loose the game. The Schzapp indicator will also tell you how many molecules you need to build to complete the level.