Michigan Technological University: 3D Printed Molecular Models for Chemistry


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In the recently published ‘Printing 3D Models for Chemistry,’ authors Elisabeth Grace Billman-Benveniste, Jacob Franz, and Loredana Valenzano-Slough–all from Michigan Technological University–have produced a guide for 3D printing users on every level, from the do-it-yourself hobbyists working on projects in the home workshop to users on the professional and educational level.

While pointing out the many benefits of 3D printing for users around the world, the authors of this new guide, targeted toward chemists, also make it clear that the potential is not yet close to being tapped. As the options in software, hardware, and materials continue to expand, so will innovation in prototypes, parts, and customized molecular models for chemists. They also touch on current manufacturers like Ultimaker who may be offering a way to 3D print molecular models—but in their estimation, it falls short for their needs.

For this study, the authors considered the option of five different filaments (polylactic acid (PLA), acrylonitrile butadiene styrene (ABS), polyethylene terephthalate with glycol modification (PETG), thermoplastic elastomer (TPE), and polycarbonate (PC), but chose PLA ultimately, as it is easy to work with, generally reliable for performance and production, safe, and affordable.

For hardware, the research team settled on a LulzBot Taz 5 3D printer:

“While FDM-style machines are clearly the most appropriate for use in a classroom or lab setting for both affordability and safety, the Taz 5 was chosen in particular for its ease of use and balance between cost and quality of prints produced.”

The Lulzbot Taz 5 3D printer is shown above (image sourced from Lulzbot’s
official website)

The researchers embrace an open-source concept for all as they work to help those working in labs, schools, offices, and other industries to explore the potential for 3D printing in chemical model creation. They also place strong emphasis on the value 3D printed models have in nearly any arena because visual aids are so important in learning and retaining information.

While materials and 3D printers are discussed, the researchers also take the time to discuss the real nuts and bolts for users; for example, they recommend what types of tools to use for removing objects, as well as post processing—from paint scrapers to X-Acto knives. Even more importantly, they discuss the safety aspects, and recommended actions to take in terms of ventilation, avoiding burns, and other injuries like cuts.

The researchers go into detail regarding how to build 3D files and consequently, create molecular models.

“Virtually any molecular graphical interface may be used as long as the created molecule can be saved as a Protein Data Bank (PDB) file. In addition, molecular models may be sourced from online databases (including the CCDC) and saved as a PDB file format,” stated the researchers. “In most cases UCSF Chimera7 was used in order to convert the PDB file into either a stereolithography (STL) or virtual reality modeling language (WRL or VRML) file format. After converting the files to the correct file format, Blender8 was used to split the models and set up pins and holes.

“Two different slicers, Slic3r Prusa Edition10 and Cura Lulzbot Edition11 were implemented in this procedure. It is important to keep in mind that certain slicer packages offer useful features which may not be available in others.”

The flowchart above can be used to determine what software package should be used at each step of the g-code file preparation process

For this study, the researchers 3D printed a molecular model of a polycarbonate fragment. It was used later during presentations at conferences to escribe atom/molecule relationships. Models of water molecules were also 3D printed. They also went on to describe fabrication of more complex models, such as those being used for quantum mechanics.

A) The standard 2-dimensional angular momentum atomic vector model. B) The vector model of the atom as displayed in Fusion 360. C) The 3D printed vector model of the atom.

Excess material stuck in one of the cones as a result of the broken screw mechanism

Users should also find the section devoted to troubleshooting failed prints quite useful. The authors explain that it is normal for novices to have a difficult time at first in getting past printing failures and finding out how to make the necessary corrections. They point out that the 3D printing user community is enormous—as well as extremely supportive in most cases—and there are so many other outlets for learning too, from online articles to YouTube, FaceBook, and more.

The researchers explain that later they hope to explore and analyze both the pros and cons of materials and applications in which they may be useful. They may also investigate the uses of 3D printed models and how they should vary depending on age level or disciplines such as math or earth science.

“For educators or researchers who may not have the time or resources necessary to dedicate to a 3D-printer and other required materials, there are several ways to obtain 3D-prints with similar customizability options without owning a machine,” conclude the researchers. “The least expensive option is looking within a university or school for a 3D-printer. Makerspaces and some libraries may also provide access to 3D-printers.

“Using software and firmware in which all programs and their source codes are freely available and the blueprints for hardware components fully accessible provides users with the option for complete customizability of both the model design and manufacturing process. The emphasis in the open-source philosophy on sharing collective knowledge may be well attributed to the rapid advancement of 3D-printing technology and is predicted to be a powerful force in initiating a fourth industrial revolution of innovation and technology.”

3D printing is used by researchers in many different capacities today, but we are seeing increasing usage by chemists as they are able to use varied software to gain a better understanding of chemistry, examine the use of materials, create parts for flow chemistry, and much more. What do you think of this news? Let us know your thoughts! Join the discussion of this and other 3D printing topics at 3DPrintBoard.com.

A) The interstitial space can be visualized in Fusion 360 when the top red sphere is removed. B) The interstitial space is clearly visible in the physical 3D printed model as well.

[Source / Images: ‘Printing 3D Models for Chemistry’]

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