Lasercut Molecular Models

Understanding 3D molecular geometry is a challenge for students new to chemistry. The task of mentally lifting a 2D drawing off the page and rotating it in your head is tough to do. Chemical educators frequently address this issue by providing students with 3D models, and this instructable provides some tools for creating such models for the classroom and some ideas for exercises based on VSEPR theory.

Subject: Chemistry. Grade Level: 11/12/first year university (this will depend a lot on what country you're in!)

[Note: this instructable is based on two J. Chem. Ed. publications, "Applying handheld 3D printing technology to the teaching of VSEPR theory" and "Open source laser cut model kits for the teaching of molecular geometry". I am corresponding author of both of these papers, and this instructable is intended to extend their reach to a broader audience. Figures and text are all new]

3D printing pens such as the 3Doodler offer the potential to physically draw things in three dimensions - including molecules. We tried this with first year undergraduate students with limited success - they had fun but made a mess and produced objects that were only recognizable as molecules by someone with a sympathetic and attuned eye. We provided them with 2D templates (attached) that could be traced over and assembled, and the results were definitely better but the process was slow and remained subject to the vagaries of the patience, artistic talent and accuracy of the student. The ratio of making to understanding was too high to fulfill our pedagogical goals, regardless of how much fun the exercise was.

What the 3D printing pen DID teach us was that the templates were an efficient means of making high quality models. We prototyped some parts based on the templates we had designed for the printing pens, and these worked really nicely when cut out of plywood. However, for the classroom we wanted to use different colors and to make them out of transparent acrylic, and we encountered a problem: such acrylic (plexiglass) is NOT of uniform thickness and to get intersecting parts to fit securely, that is exactly what you need.

This problem was solved by making multiple cuts so the joints could fit securely for a range of different acrylic thickness (3 mm +/- 10%). This worked well, and ensured tight fits regardless of the variations in material.

The individual files are attached as .stl files in case someone would like to 3D print them. The .dxf file is also attached for lasercutting purposes - note that the files are designed expressly for 3 mm material, and will not work with different thicknesses. The 3D printing files are of course scalable to whatever size desired.

Note: if you'd like to make these in large volume, use the "nestedpartsX.dxf" files. They are optimized for a laser cutter with a 800 × 500 mm bed, but can be trimmed to suit smaller bed sizes. Do not resize or they will no longer work for 3 mm acrylic.

Each model set consists of 26 pieces for a total of 13 different models, which should be made in 5 different colors. Each color represents a different number of electron domains. It doesn't matter which color is assigned to which number of electron domains, but in the example shown:

Red (2 electron domains): one model (0 lone pairs), linear
Yellow (3 electron domains): two models (0 and 1 lone pair), trigonal planar and bent
Green (4 electron domains): three models (0, 1 and 2 lone pairs), tetrahedral, trigonal pyramidal and bent
Blue (5 electron domains): four models (0, 1, 2 and 3 lone pairs), trigonal bipyramidal, see-saw, T-shaped and linear
Clear (6 electron domains): three models (0, 1 and 2 lone pairs), octahedral, square pyramidal and square planar

When produced on scale, these sets are inexpensive - a few dollars each, not counting cutting time. 3D printed parts would be cheaper but of course much slower to make.

1. Build molecular models based on the VSEPR model

Ask the students to make models of the following molecules: CO₂ (two electron domains); BCl₃, SnCl₂ (three electron domains); CCl₄, NBr₃, SCl₂ (four electron domains); PCl₅, SeF₄, ClF₃, XeF₂ (five domains); SF₆, BrF₅, XeF₄ (six domains). Attached is a summary table of all shapes, molecular sketches plus some additional examples of molecules and ions of given electron domain numbers.

If given a bag of all 26 parts and no hints, this task is quite a puzzle. But students can be given lots of guidance, depending on their level, e.g. (easy) that each color corresponds to a certain number of electron domains; (easier) which color corresponds to which electron domain; (easiest) a picture of the completed set.

A quick refresher: the Valence Shell Electron Pair Repulsion (VSEPR) theory allows prediction of the shape of molecules in many cases involving main group atoms. It is conceptually simple, and has a broad field of application. To use VSEPR in determining the shape of a molecule, the following steps are used:

1. Draw the Lewis structure of the molecule.
2. Count the number of electron domains around the central atom.
3. Arrange the electron domains so that the repulsions are minimized (this gives the electron domain geometry).
4. Use the arrangement of the atoms to determine the molecular geometry.

2. Sketch accurate 2D representations of 3D molecules

Encourage students to rotate the models to get a best possible view (i.e. where none of the atoms or bonds are hidden behind others). This exercise is more fun for the non-artistic if the students are encouraged to use their phones. Get them to snap a photo of the model, then turn up the brightness on their displays and trace the photograph (see photos above). They'll get perfectly proportioned figures every time! They will get different results depending on how far away they take the photo.

Feedback or ideas of your own for lessons based on these models? Please post in the comments below.