How Color and Dimension in ChemDraw Provide New Clarity


Organic chemistry has traditionally been visually represented in 2D flat, black and white structures. But humans are visual creatures and we tend to understand things more clearly when color and perspective are involved.

What happens when color and dimension are added to organic chemistry visualizations?

Until recently, ChemDraw users could only color atom types by element, or change the color of atom labels and bonds. In practice, this worked reasonably well with red and dark blue bonds. However, this became less useful when a 3rd color was needed (especially when using a low-quality projector in a room with no blinds!).

Color in ChemDraw

To tackle that problem, we introduced ring fill coloring for carbocycles and the complementary capability of highlighting bonds and atoms with color to facilitate communication.

A visual demonstration of the differences between the previously existing coloring capabilities of ChemDraw versus the new color highlights

Now, whether you are presenting to your peers at a conference or to your colleagues during your weekly lab meeting, you can finally say “the double bond in green” or “the amide bond in yellow” and be confident that your audience will know what you are talking about.

3D Chemistry Capabilities

Parallel to expanding coloring options, we also recently introduced a 3D Clean-up function. The algorithm was enhanced to better handle metal complexes while supporting aromatic circles in 3D – and more effectively render in-perspective double bonds (e.g., double bonds viewed “from the side” in 3D).

It is now easier than ever to create complex 3D structures including metallocenes. 2D molecules from the ChemDraw Templates folder can be readily transformed into accurate 3D renderings.

While we were improving this important capability, we discovered a limitation in the context of the communication of chemistry. A rotatable 3D model may be useful to the chemist viewing it in ChemDraw but displaying and sharing it outside of ChemDraw in an audience-facing presentation required a lot of extra steps.

Until now.

3D On Our Minds.

Native, interactive, and animatable 3D objects – including molecules – are already available in Microsoft PowerPoint, using the .3MF format. 3MF is an open-source 3D-printing format co-developed by major companies involved in 3D printing (including Microsoft).

With that use case in mind, we first implemented a “Save as 3MF” option to save molecules for 3D printing. We quickly realized that the full potential of this capability did not reside on the 3D printing side but rather on the PowerPoint 3D object side.

To this end, we created a “Copy as 3MF” action to copy a 3D Molecule to the clipboard as a 3MF object, allowing for easy pasting into PowerPoint slides. Early beta-tester feedback suggested we should offer several 3D rendering styles and implement the classical “Ball & Stick” representation and the “Stick only” representation:

ChemDraw 3D

The various ways to represent the same molecule of (+)-Plumisclerin A with advanced coloring options and 3D representations. Top row: ChemDraw representations; Bottom row: ChemDraw molecule copied as a 3MF object and pasted in PowerPoint.

As we were developing the 3MF feature and testing it with complex molecules like natural products, we felt that we needed to address the difficulty establishing a visual representation of skeletal 2D molecules in 3D.

This is a fundamental problem when presenting 2D and 3D chemistry. After all, when working with a 3D shape, correlated wedges, hashed wedges and overly elongated crossing bonds are a tough mental exercise!

While testing and developing the new 3MF export feature, we discovered this would be the perfect use case to show the power of the color highlighting capability introduced in ChemDraw version 20. We studied how to easily transfer color highlights from the 2D representation of the molecule to the 3D model so that – when presenting to an audience – a chemist could easily convey the right message or focus attention on the relevant parts of the molecule.

We generated 3D color “transparent tubes” from the 2D highlights and added them around the bonds on the 3MF models.

3D model with a molecule of Phlegmadine C

An illustration of the benefits brought by the ability to transfer color highlights to a 3D model with a molecule of Phlegmadine C. It is now much easier to correlate parts of the 2D structure with its 3D representation (bottom row vs top row).

It’s exciting to release new features to our users – and all the more so when they are well-received. The full 3MF/Color highlights capability has been getting rave reviews on Social Media.

Learn more about ChemDraw, the gold standard for communicating chemistry research.



Pierre Morieux, Ph.D.
Chemistry Product Marketing Manager, ChemDraw Wizard, PerkinElmer Informatics

Pierre Morieux is the Chemistry Product Marketing Manager at PerkinElmer Informatics, where he helps translate the various needs of chemists into time-saving and discovery-enabling integrated software applications. Before this role, Pierre has been the Global Product and Marketing manager for ChemDraw since 2017, where he has overseen the development and launch of versions 17 through 21 of ChemDraw and the ChemOffice Suite. Pierre was hired by PerkinElmer in 2012 as a Chemistry Field Application Scientist, a position he landed after publishing a viral YouTube video on “How to draw Viagra under 20 sec in ChemDraw”. Pierre holds a Chemical Engineering Degree from the ENSCP Chimie ParisTech (2006), a Ph.D. in Pharmaceutical Sciences from the University of North Carolina at Chapel Hill (2010) and did a Postdoc in Bioorganic Chemistry at the ISIS Institute of the University of Strasbourg, France.