These little circles are atoms. Those atoms indicate how often you can connect the molecule to an other molecule. When you connect a molecule with one atom, you're out of atoms with that molecule.
In the top you see a circle. In that circle there is a combination of molecules. If you make that combination, you'll get points.
This is the point of the game which makes this game unique. In this situation, you can make an other combination of molecules. If you make those, new molecules are falling down. With those new molecules, you can try to make the combination of molecules you want.
Connect molecules together to get points. You can only get points when you connect the right one.
In the circle you see which molecules you have to connect to get points. To get more combinations, simply swipe in the circle.
You can also connect more molecules than just two. Here you see an example with a molecule with two atoms and one atom.
In this mode you can connect all the molecules together. You'll get points for the number of atoms you have scored.