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Space filling molecular models: Starter set

3D model description

Space-filling molecular models are valuable when you want to show that actual volume a molecule occupies, as opposed to its connectivity. Nowadays this is done mostly using computer graphics, but this doesn't give you something you can pass around the classroom like an actual physical model does. Real models are also good for amusing cats and small children. This contribution represents a starter set with tetrahedral carbon, oxygen, nitrogen, and two sizes of hydrogen. "Why two sizes of hydrogen?" I hear you exclaim. When hydrogen bonds to an electronegative atom like oxygen or nitrogen, it loses some of its electron density and its Van der Waals radius decreases. "Okay, I'll pretend I understood that, but I thought in covalent bonds atoms shared electrons." Yes, but atoms share electrons like kids share a ball at the playground; the big kid gets the ball most of the time. Not everyone likes to make this distinction, so use the size of hydrogen you like. These models are the same scale as CPK models, i.e, 1.25 centimeters per Angstrom. The oxygen has a dihedral angle of 107 degrees, which is a good value for alcohols and which is probably more information than you wanted to know. The bonds were inspired by the Parametric Snap Pins by Emmett. The bonds tend to be tight and require quite a bit of force to insert, so I have included a tool useful for doing this. A dowel with an appropriate sized hole in the end works just as well, but isn't as much fun to make. The bonds can be reused a few times, but they become less snug with use. The color of the atoms doesn't matter but the ones I show are traditional.

By the way if you do actually consider using these to amuse cats and small children, it may be wise to consider gluing the atoms firmly together. They should be pretty hard to get apart, but they could be a choking hazard if it happens.

3D printing settings


Da Vinci




Doesn't Matter


0.2 mm


10%, 30% for insertion tool

Three perimeters works well. I used ABS.

  • 3D model format: STL





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