Visualization of Hyperconjugation and Subsequent Structural Distortions through 3D Printing of Crystal Structures

Abstract

Background Structural distortions due to hyperconjugation in organic molecules, like norbornenes, are well captured through X-ray crystallographic data, but are sometimes difficult to visualize especially for those applying chemical knowledge and are not chemists. Methods Crystal structure from the Cambridge database were downloaded and converted to .stl format. The structures were then printed at the desired scale using a 3D printer. Results Replicas of the crystal structures were accurately reproduced in scale and any resulting distortions were clearly visible from the macroscale models. Through space interactions or effect of through space hyperconjugation was illustrated through loss of symmetry or distortions thereof. Conclusion The norbornene structures exhibits distortion that cannot be observed through conventional ball and stick modelling kits. We show that 3D printed models derived from crystallographic data capture even subtle distortions in molecules. We translate such crystallographic data into scaled-up models through 3D printing.

A 3D Printer in the Lab: Not Only a Toy

“…Scanning for literature at this point will return plenty of 3D printable objects: molecular structural models, [ 4–;6 ] corals, [ 7 ] crystal structures, and 3D printed chips for obtaining crystals, [ 8 ] which are valuable models for teaching, and give the student a physical model of chemical structures, and so on (Figure 2b). There are, for example, instructions on how to convert crystallographic data to 3D printable models (Figure 2c) [ 9–12 ] or even how to convert NMR spectra to 3D prints (Figure 2d). [ 13,14 ] 3D printing and NMR do not end here: you can print sample tubes for solid‐state NMR, [ 15 ] whole NMR magnets, [ 16 ] and even scaffolds for making NMR coils.…”

A 3D Printer in the lab: not only a toy

“…Scanning for literature at this point will return plenty of 3D printable objects: molecular structural models, [4,5,6] , corals, [7] crystal structures and 3D printed chips for obtaining crystals, [8] which are valuable models for teaching, and give the student a physical model of chemical structures, etc (Figure 2b). There are, for example, instructions on how to convert crystallographic data to 3D printable models (Figure 2c) [9][10][11][12] or even how to convert NMR spectra to 3D prints (Figure 2d). [13,14] 3D printing and NMR do not end here: you can print sample tubes for solid-state NMR, [15] whole NMR magnets, [16] and even scaffolds for making NMR coils.…”

“…c) X-ray structures [10] and d) NMR 2D spectra can also be converted to 3D printable models. [11] downloadable from repositories.…”

A 3D Printer in the lab: not only a toy

“…Scanning for literature at this point will return plenty of 3D printable objects: molecular models, [4,5,6] crystal structures, which are valuable models for teaching, and give the student a physical model of chemical structures, etc (Figure 2b). There are, for example, instructions on how to convert crystallographic data to 3D printable models (Figure 2c) [7][8][9][10] or even how to convert NMR spectra to 3D prints (Figure 2d). [11,12] 3D printing and NMR do not end here: you can print sample tubes for solid-state NMR [13], or even whole NMR magnets.…”