2D, 3D, let’s explore molecular geometry

It should go without saying that I am a fan of incorporating digital fabrication tools into chemistry instruction. A while back, Scott McIndoe and his colleagues published a paper in the Journal of Chemical Education on using laser cut models to teach molecular geometry. At first, it seems counter-intuitive to use a 2D design process to teach 3D topics. On top of that, if you have access to a laser cutter, you probably have access to a 3D printer, so why not just use the 3D printer?

3D printing is great for rapid prototyping; however, when you want to scale up production – say, for example, you want models for a classroom of 100 students – then 3D printing is not a great solution. Laser cutting is one of the fastest, easy-access digital fabrication tools available, and build times can be drastically reduced if a laser-cutter solution is available.

Then again, one needs access to a laser cutter. And that is something I (sadly) do not have at present.

So I took Scott’s design and adapted it to 3D printing. Yes, his paper provides some STLs to print, but if you want to create different sizes, then you have to do some scaling. I wanted a parametric approach, so I resorted to OpenSCAD to recreate his design. The code is below, in case you are interested.

Why would you want to use this? I don’t know, perhaps you want to make super thin molecules or super small molecules. All I know is, now you can.

Now Lego Yoda can teach molecular geometry. I honestly have no idea what to do with a 0.2 mm thick tetrahedral molecule, but now I’ve got one.
Origin: @mcindoe
Reference: https://pubs.acs.org/doi/10.1021/acs.jchemed.8b00553

ca_d = 12; // diameter of central atom
ca_g = 5;  // length of the gap in the central atom 
oa_d = 10; // diameter of the outer atom
bond_w = 5; // width of the bond
bond_l = 25; // length of the bond
th = 0.2+3*0.35; // piece thickness (my printer is set to 0.2 mm first layer and 0.35 subsequent layers)
allowance = 0.05; // adjust gap size for tighter/looser fit, YMMV
$fn = 25; // Keeps round parts round

n is the number of bonds (1, 2 or 3).  Setting tet to true will force a 109.5 degree bond angle.  NOTE: you shouldn't call this function, use makepiece
module makebonds(n,tet=false) {
    for(i =[1:n]) {
        rot = tet?125.25+(i-1)*109.5:i*360/(n+1);

n is the number of bonds (1-3).  Setting tet to true will force a 109.5 degree bond angle
module makepiece(n,tet=false) {
    rot = (tet && (n==1))?70.5:0;

// Example usage 
for(i=[ [-10,-20,0], [10,20,0] ]){

Making COVID stay away

Do a web search on 3D printing and COVID, and you’ll find endless examples of the 3D printing industry (both commercial and hobbyist) mobilizing to create personal protective equipment (PPE) in response to the severe shortages that many countries face. If you have any experience with 3D printing, helping out is as simple as downloading the design files (such as this one for face masks or this one for face shields), sending them to the printer, and waiting 3+ hours for the printer to do its job.(*)

Finished print of the US version of Prusa’s face shield.

So when Tim of Adirondack oral and maxillofacial surgery contacted Zak Robinson, my colleague over in the Physics department, and lamented his inability to secure PPE for his staff, Zak and I got to work. Both of us use 3D printing in our teaching and research activities at SUNY Brockport, and when the pandemic shut down the campus for the remainder of the semester, we each brought home our printers so we could carry on with our making.

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3DP Point group set

I’ve been working on a set of 3D printed molecules for studying point groups. The set below contains 12 molecules that represent some of the point groups commonly taught in undergraduate inorganic chemistry classes. The structures are made using Mathematica’s curated data sets and a few molecules pulled from other sources. I split the set into two series for printing, each taking about 3 h to print.

#Make ready for COVID

There’s a lot of buzz on the interweb about 3D-printing personal protective equipment (PPE) in light of the severe shortages across the country and especially close by to me. (I’m sure it has nothing to do with sending much of our supply to china last month.) I wanted to see how easy it was to actually do.

I’ve got my 3D printer, a Prusa MK2, up-and-running in my home office. I followed these instructions for making a mask and this design for the face shield. Both designs are reported to be printable without the use of supports or other fancy settings, so I loaded them on the build plate and off I went. After 5 hours of printing (3 for the mask, 2 for the shield) I ended up with this.

Green screen added for future special effects 🙂

I’m surprised at how well these designs printed with no modifications needed. I’ve got some temperature calibration to tweak because both designs have overhangs that printed poorly but only affected the aesthetics of the final object. Double sided tape worked just fine to keep the document transparency in place. I’m now ready to fight the coronavirus … or clean the litter box.