A molecular model
sometimes needs to be made into its physical representation.
Molecular building sets, containing plastic tubes for bonds and little hedgehogs for
atoms, are common, nice, and overpriced. They are also good just for a ball-and-stick model,
while a space-filling model may often be more desirable.
A 3D printer can produce a fairly good model.
There are issues to encounter. Molecules as freeform shapes are more suitable for the laser sintering from powder bed, where the unsintered powder acts as a support for the structure, which is often rich on overhangs and other annoyances and tends to touch the bed at just a few small spots. Multicolored printing may also be desired.
The molecules require some tinkering with the slicer.
A raft may be desirable for the first layer, with a fairly wide brim added (good results can be with 5 mm). Without this, the molecule will likely detach from the bed.
Enabling support material is also important. The models are rich on overhangs and atoms pointing to sides. Without support, such areas will misprint. Do not rely much on the automated decisionmaking; limit the unsupported overhangs to 45 degrees or less.
A molecule is loaded to or created in a suitable molecule editor; here, BALLView was used,
chosen by the merits of its good capabilities and opensource nature. Its conformation is
calculated using a suitable energy minimization algorithm; here, Molecular Mechanics - Energy Minimization
menu was used, with MMFF94 force field (others seem to complain) and Shifted LVWM algorithm.
The structure is then saved as a suitable chemical file format. Here, the .mol, or MDL Molfile
format is chosen for its simplicity.
BALLView is however somewhat non-intuitive for beginners.
The .mol file is then converted to the OpenSCAD .scad file using a custom script.
This is fortunately very easy; the model is a set of overlapping spheres, a section of the .mol file
contains just the atom types and their coordinates. The sphere diameter is used by its
van der Waals radius, which is not present in the file but can be find in tables and can be
substituted by a variable named by the atom.
For printing, a STL file is desired. Open the .scad file in OpenSCAD,
render the file (this can take annoyingly long, a 18-atom molecule on a decent laptop took almost two
minutes, luckily preview is faster). Possibly rotate it to a more printing-friendly position
before rendering. Export as STL.
Now import the STL file to a slicer; a Slic3r was used here.
The settings here are fairly critical. The molecules are shapes quite hostile to filament deposition printing. Support material has to be enabled in almost all cases. The balls are touching the printer bed at very small areas; a wide brim is desired (5mm works for a small molecule), and a raft may be also used. Thinner layers (0.2, maybe 0.3 mm) have to be used, as the spheres would be otherwise jagged.
At least two layers of shell may be desired. One layer can provoke too much of solid infill and slow things down.
The amount of infill is not critical.
Supervise the printing process. If the slicer setting was suboptimal, the molecule will detach from the bed, or the filament will hang down from overhanging areas, or parts of the molecule or support will detach from bed and ruin the print, or other kind of disaster happens. The complex molecular shapes are more prone to such mishaps than more compact engineering designs.
Removing the raft and supports is somewhat annoying. A file may be needed to get rid of the raft layer. Beware to not use one contaminated with metal dust or the plastic will get discolored by embedded particles.
A small torch can be used to burn off extraneous thin filaments dragged by the head, and somewhat smoothen the surface.
As the printouts are typically single-color, the molecule should be painted afterwards. Modeling paints, or at least Sharpie felt-tip pens, can be used here. Beware, sometimes the printed layers can wick the paint to where it does not belong. This may be eliminated by spraypainting the molecule with a transparent paint, or with black one if painting hydrogens white is less hassle than painting carbons black.
A molecule of naphthalene was chosen for its simplicity, flat geometry, and being less boring
than benzene. The scale was chosen to be 4 millimeters per angstrom.
The material is PLA. The printing temperature is 205°C for first layer, 195°C afterwards. The layer thickness is 0.2 mm, with 0.4 mm for first layer. There is 1-layer raft enabled, and 5mm brim. There are two layers for top and bottom, and two for shells.
 Model in OpenSCAD |  Naphthalene, as printed |  Naphthalene, as printed |  Naphthalene, as printed |
 Naphthalene, as printed |  Naphthalene, as printed |  Naphthalene, as printed |  Naphthalene, filed and flame-treated |
 Naphthalene, filed and flame-treated |  Naphthalene, felt-tip-pen painted |  Naphthalene, felt-tip-pen painted |  Naphthalene, felt-tip-pen painted |
Same model, van der Waals radius shrunk to 50%, bond length kept identical.
 Naphthalene, as printed |  Naphthalene, as printed |  Naphthalene, as printed |  Naphthalene, as printed |
 Naphthalene, filed and flame-polished |  Naphthalene, filed and flame-polished |  Naphthalene, painted |  Naphthalene, painted |
 Naphthalene, both versions |  Naphthalene, both versions |
A molecule of methanol was chosen for even more simplicity allowing bigger balls, and for having color scheme richer than just black/white. Scale of 8 mm/nm is chosen, vdW radius at 100%.
 Methanol, full van der Waals radius, as printed |  Methanol, full van der Waals radius, as printed |  Methanol, full van der Waals radius, as printed |  Methanol, full van der Waals radius, as printed |
 Methanol, painted |  Methanol, painted |
The same, bigger, with 50% vdW radius.
 Methanol, 50% van der Waals radius, mid-print |  Methanol, 50% van der Waals radius, as printed |  Methanol, 50% van der Waals radius, as printed |  Methanol, 50% van der Waals radius, as printed |
 Methanol, 50% van der Waals radius, as printed |  Methanol, 50% van der Waals radius, as printed |  Methanol, cleaned and flame-treated |  Methanol, cleaned and flame-treated |
 Methanol, painted |  Methanol, painted |  Methanol, painted |
- conversion script