Interactive Molecular Model Assembly with 3D Printing

3D printing is an increasingly available and accessible technology. This protocol can be used to print and assemble physical molecular models that retain the dynamical qualities of real molecular systems. Interactivity with molecular models is usually limited to showing connectivity.

3D printing can open up the exploration of conformation in this train, and molecular motion at a variety of scales. It is difficult to convey motion in a static manuscript. So it is valuable to be able to see how models can be printed, assembled, and manipulated.

To prepare the model files for 3D printing, download the provided supplementary stereolithography files and upload the files to a computer with a slicer program. Import one of the carbon_atom_SP3, hydrogen atom or carbon-carbon bond files into the slicer program and select the millimeter format for the units if the option is available. Click Import in the models panel of the main window and import both the hydrogen atom dual bottom and hydrogen atom dual top files from the resulting file browser.

To scale the imported model to the desired size, double-click the graphical model in the main display to open a model editing panel that enables the translation, rotation, and scaling of the target model. To duplicate the models to generate a model array, select the Duplicate Models option from the Edit menu and enter the number of model parts in the dialog box. Click Center and Arrange in the models panel of the main window to arrange the models near the center of the build platform and use Add from the process panel of the main window to set the appropriate model processing settings for target prints.

Then slice the model into print layers to generate a G-Code toolpath and click the Prepare to Print button in the main window. To prepare the printer for model printing, coat the surface of the unheated printer bed with blue painter's tape and use a glue stick to apply a thin layer of polymer to the tape. Then place a ventilated enclosure over the printer bed to minimize air currents that may disturb the print annealing.

After printing, remove the printed parts from the printer bed and remove the raft or brim structures from the base of the parts, if used. Rubbed the base of the model part with medium to fine grit sandpaper to remove any remaining attached raft filaments. And sand the base of the carbon_atom_SP3 model parts with 120 to 320 grit sandpaper to remove any surface defects.

Next, smooth the surface with the 320 grit sandpaper and use a polish cloth to polish the surface to the desired finish. When all of the pieces have been polished, insert the connector ends of the carbon-carbon bond and the hydrogen atom model parts into the sockets on the carbon_atom_SP3 model parts according to desired bonding topology. Squeezing the model parts together until an audible click is heard.

Once connected, the single bond should rotate freely about this connection without separating, then assemble the rest of the printed parts according to the desired molecular structure filling any open socket with a hydrogen atom model part to saturate all of the carbon_atom_SP3 model parts. For a ring-like cyclohexane, pose the ring with a carbon-carbon bond model part between carbon_atom_SP3 model parts. Here are the parts necessary for constructing an interactive molecular model are shown.

Six carbon atoms, six carbon-carbon bonds, and 12 hydrogen atoms. These mono-colored hydrogens print in about 50 to 60%less time due to the lack of a new ooze shield structure and a lack of polymer retractions in switching between active extruders. The assembled cyclohexane structures are functionally equivalent, even if the dual extruder prints tend to look moderately more refined.

The PLA models are relatively more refined than ABS models straight off the printer. Acetone treatment results in a smooth and high gloss finish. Note that acetone can also dissolve inner support structures and models with layer defects, however, resulting in model collapse.

The assembled cyclohexane structures are all able to flex, distort and adopt relevant conformers in the same manner. The smallest of these models is the most prone to print flaws, making this size potentially too small and not recommended without tweaking the relative size of the parts. While slow to print, large models are potentially more effective for communication in lecture settings.

Since the atoms can readily rotate relative to one another, the structures can be distorted to snap into different representative conformers of cyclohexane. As in molecular simulations, the chair conformation basin is restricted, limiting available motions while structures in the boat basin can fluidly access a variety of boat and twist boat conformations. Preparing the printer bed is essential to ensuring a well-adhered first layer.

Without this layer, the print will likely fail. This protocol provides a cyclohexane model as an example, but any interactive saturated hydrocarbon model can be printed and assembled with the provided stl files.