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3D Printed Atoms to Build Molecule Structures

Written by ロナルド on . Posted in .

I was asked by a good friend if I could make 3D printed atoms on my printers to create molecule structures. I said to him: There must be plenty of kits for sale everywhere on line. The issue he has is that the existing kits are not really representative and most of the are kits with sticks and spheres, or some of them have spheres with one or more flat surfaces. He wanted just spheres with some kind of connection.

First we decided on a scale. We are using atoms with covalent radii in Ångstroms (10-10 m) based on data from Cambridge Crystallographic Database and scale them up. Here are some atoms with the sizes and colours that we print them in:

Notation Name Radius in Å Printed Diameter in mm Colour
H Hydrogen 0.31 9.3 white
O Oxygen 0.66 19.8 red
C Carbon 0.76 22.8 black

So, an atom with a radius of one Ångström (diameter of two Ångström) will become a printed sphere with a diameter of thirty mm in our case. This is a magnification of 150 million. We call this scale-3. Very soon the 3D printed spheres will be available in my webshop, so that you can build your own structures. Mainly in scale-3, but custom requests can be printed too.

3D Printing spheres

3D printing spheres is a bit tricky. Because the angle of the first few layers is too big for the layers to adhere to each other, you need to print them with supports. So the surface of the bottom part of the sphere is not perfect. You could also print 2 halve spheres and connect them to each other, but this is only necessary if you print larger spheres. The largest one I’ve printed so far is Silicium and this sphere has a diameter of 33.3mm.

Below are some pictures of the printing process. All spheres need to be printed with a brim to be sure that the prints don’t detach from the printer bed while printing. It happened only once so far. I am also using a glue stick to print almost all of my prints. Since I discovered this stick, I almost don’t have failed prints. The stuff is called Magigoo.

Printing spheres with the Ender 3

3D printed Hydrogen Atoms

3D printed atoms

variation of 3D printed Atoms

Connecting the atoms

Connecting the atoms is a bit of a puzzle to find the best option. It all depends on the use. If you are going to build structures once and display them as an ornament, 3mm sticks and glue would be ok. The holes are 2.9mm and are perfect to use M3 set-screws with hex inset (see image).

These are 8mm long and a bit too short, longer ones — 12mm — are on their way.

The only issue is that in complex models, you will not always be able to screw all atoms together, so a piece of balsa wood with 3mm diameter is a perfect fit. I am trying more options to create the best connections.


I already have a few orders, more about this in a next blog post. It is very interesting to print and build the molecule structures. One of my orders is to build an oxytocin molecule. This consists out of 129 atoms. C43H60O12N12S2. It will be quite a structure!


Contact me if you are interested in 3D printed atoms.

またね (Until next time),

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