Mod:3D

3D-Printable chemistry models

Shapeways is one commercial company that can produce full-colour 3D-printed models. As we start to generate such content, it is desirable to try to keep track of what is available from local activity (the Shapeways catalogue already contains much chemistry). The list below illustrates some of this activity:

1. Chiral molecular-scale metal wire, More details.
2. Left handed DNA and right handed DNA duplex (CGCG)
3. Six π-MOs of Benzene: http://shpws.me/oYY1 http://shpws.me/oYY6 http://shpws.me/oYYa (occupied) http://shpws.me/oYYh http://shpws.me/oYYk http://shpws.me/oYYp (unoccupied)
4. Four π-MOs of cis-butadiene: http://shpws.me/oYZa http://shpws.me/oYZd (HOMO),http://shpws.me/oYZn (LUMO), http://shpws.me/oYZp
5. The MOs of Coper phthalocyanine, mauveine (HOMO and LUMO) and an octaphyrin (corresponding to the artwork on the student resource-centre windows)
6. The NBO orbitals showing the overlap leading to the gauche effect in 1,2-difluoroethane.
7. Molecular orbital for {144}-annulene indicating a topological linking number of 18.More details.
8. Transition state for cyclohexene oxide+CO₂ co-polymerisation using the Williams Zn-catalyst

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Transition states for asymmetric epoxidation

Shi Fructose-catalyst	Jacobsen Mn-catalyst
Sharpless Ti-catalyst	Sodeoka-Hii Pd-catalyst

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Instructions on how to generate 3D-printable models (orbitals)

1. Run a QM calculation, select the desired orbital and create a Gaussian cube file containing the wavefunction (medium or fine grid).
2. Acquire Jmol 13.3 or greater.
3. Run Jmol.jar and open File/console
4. >load bd_mol15.cub
5. >cpk 200
6. >set bondradiusmilliangstroms 500
7. >isosurface sign color yellow green cutoff 0.02 bd_mol15.cub
8. >set exportscale 12.0
9. >write bd_mol15.wrl
10. Upload the .wrl file to the manufacturer

You should replace the values above with ones relevant to your model. The isosurface cutoff can be adjusted to produce a good-looking model. Similarly the bond radii and the atom size (CPK). The exportscale controls the cost of the resulting model. If printed in full-colour sandstone, a model with largest dimension ~15 cm is going to be a reasonable cost.

An alternative output format which is accepted by some manufacturers is .obj. This produces not a single file but two or even three. These have to be zipped into a compressed archive before uploading.

Instructions on how to generate 3D-printable models (ball&stick)

1. Acquire suitable coordinates. If from a crystal structure, it is probably best to save as a .pdb file rather than .cif. Ensure you edit the connectivity to avoid any components which are disconnected from the main model. If necessary, connect them using an explicit bond.
2. Acquire Jmol 13.3 or greater.
3. Run Jmol.jar and open File/console
4. >load Z-CGCG.pdb
5. >cpk 150
6. >set bondradiusmilliangstroms 300
7. >set exportscale 8.0
8. >write Z-CGCG.wrl
9. Upload the .wrl file to the manufacturer

An alternative output format which is accepted by some manufacturers is .obj. This produces not a single file but two or even three. These have to be zipped into a compressed archive before uploading.

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Software

A variety of software for viewing, validating and editing the 3D models is available.

1. Chimera is very good for viewing a .wrl model on your computer after generation.