Here, in one place is all you need to make everyone's favorite molecule, caffeine. Caffeine is an interesting molecule chemically because it is made up of a 5-membered ring which is aromatic (a chemspeak term for a 5 or 6-membered ring which is planar and particularly stable) and a 6-membered ring which is almost but not quite aromatic (I'm not sure if this is more like almost dead or almost pregnant). And once you're done with that, you can also make theophylline (present in tea) and theobromine (present in chocolate). Lets get started.
You need to make:
10 Hydrogen1 in white (or another color of your choosing)
2 OxygenDB2 in red
3 Carbon6 in black
2 CarbonDB3 in black
1 Carbon5PH1 in black
1 Carbon56PH3 in black
2 NitrogenSP21 in blue
1 Nitrogen5PH1 in blue
1 Carbon5PH1 in blue (this one will be nitrogen)
24 Bond1 (color doesn't matter)
I've made STL files with all the atoms of each color if that helps.
The bonds take a bit of force to insert. The bond insertion tool helps with this. After the first end is in you should be able to snap on the second atom pretty easily. Make the 5-membered ring first. Connect the Nitrogen5PH1 and the black and blue Carbon5PH1s by the rectangular sockets. Put bonds in the free sockets. Then snap the three atoms to the Carbon56PH3 on the side with the shallower angle (you may have to flex the three-atom section a little). Put bonds in the free sockets of the Carbon56PH3. Then snap a CarbonDB3 to the top bond of the Carbon56PH3 by the round socket (the rectangular socket should be on the outside) and put a bond in the other round socket. Then snap the other CarbonDB3 between the two NItrogenSP21s by the round sockets (the NitrogenSP21s are symmetrical, but they look best if the face on the build platform is outside). Snap this 3-atom section to the rest of the molecule by the two already installed bonds. Now snap the two OxygenDB2s to the CarbonDB3s by the rectangular sockets. Make three methyl groups by bonding 3 Hydrogen1s to each of the three Carbon6s. Snap these to the exposed sockets of the nitrogens. Add the last hydrogen to the Carbon5PH1 and you're done. Some folks say the methyl groups on the 6-membered ring project a little above the plane while the oxygens project below it. If you're wondering which side is above the plane, it probably doesn't matter; they probably change sides frequently.
If you now have an uncontrollable desire to make more molecules, check out the starter set (http://www.thingiverse.com/thing:1720048), the carbon expansion set (http://www.thingiverse.com/thing:1730299), the aromatic expansion set (http://www.thingiverse.com/thing:1754393), halogen expansion set (http://www.thingiverse.com/thing:1730099), nitrogen expansion set (http://www.thingiverse.com/thing:1753583), and the sulfur and phosphorous expansion set (http://thingaverse.com/thing:2350618).
3 perimeters works well. I used ABS.