Description: Molecule set for Sodium chloride, Water, Ammonia, Methane, Carbonic acid and Ethanol. The source contains atom models with holes suitable for building simple molecular shapes. The most common shapes with up to 6 bonds are supported. See https://en.wikipedia.org/wiki/Molecular_geometry.

Source for OpenSCAD is provided.

Instructions: Common matchsticks are recommended as bonding material. It is important to trim the hole diameters before printing the full set. I recommend adjusting the hole diameters in the source instead of scaling the STL models. Start by printing carbon_4() and trim bottom hole for a perfect fit (parameter hole_d0). Also trim the hole diameter for the rest of the holes (parameter hole_d1). The reason for using two parameters is to compensate for deformation during printing. Holes not facing directly downwards usually becomes a bit larger (and slightly oval). When done, print the full set according to the list below. Mark matchsticks at 13mm interval, insert match and cut with a small wire cutter.

Brief user guide for OpenSCAD: Load the source and press F6. This will generate the model of carbon_4. To export the STL, select "File->Export as STL" and save. Slice, print and test the hole diameters with a match. Adjust parameters as needed. When done, uncomment and generate new STLs for each molecule located at the end if this file (one by one).

Example structures:

Sodium chloride(NaCl):
  1 Na grey   metal_1();
  1 Cl green  halogen_1();

Water(H2O):
  2 H  white  hydrogen_1();
  1 O  red    oxygen_2();

Ammonia(NH3):
  1 N  blue   nitrogen_3();
  3 H  white  hydrogen_1();

Methane(CH4):
  1 C  black  carbon_4();
  4 H  white  hydrogen_1();

Carbonic acid(H2CO3):
  2 H  white  hydrogen_1();
  1 C  black  carbon_3(); // Double bond
  2 O  red    oxygen_2();
  1 O  red    oxygen_1(); // Double bond

Ethanol(C2H5OH):
  2 C  black  carbon_4();
  6 H  white  hydrogen_1();
  1 O  red    oxygen_2();
  
Print list:
 17 H  white  hydrogen_1();
  4 O  red    oxygen_2();
  1 O  red    oxygen_1();
  3 C  black  carbon_4();
  1 C  black  carbon_3();
  1 N  blue   nitrogen_3();
  1 Na grey   metal_1();
  1 Cl green  halogen_1();