There are new updates to both of our desktop software applications today, ChemDoodle 2D v10 and ChemDoodle 3D v5. Please see below for changes. These new updates require our new subscription (or lifeltime) licenses, which can be purchased in our store. Site licenses get free access to the latest updates. To download the latest versions, please visit our download page. As always, if you have any questions, suggestions or bug reports concerning iChemLabs software, please contact us.

ChemDoodle 2D v10

Executive Summary

ChemDoodle 10 is a significant update to ChemDoodle. Major improvements include new IUPAC naming work, improvements to the structure cleaning system, inter-application communication with ChemDoodle 3D and SciFinder-n integration (see full description below). Additionally, we continue to improve the infrastructure of our applications and provide support on the latest operating systems while correcting any known issues. Enjoy and please tell your friends, colleagues and students about us! Your support helps us continue to provide the highest quality chemistry software in the market that is affordably priced.

New Features

  1. A significant amount of work has been invested in our IUPAC naming algorithms. The functional group system has been completely overhauled to expertly handle advanced, multivalent functional groups. Support is now provided for functional groups containing phosphorus, silicon, boron and many other elements. Complex support has been added for handling unique base chains (heteroatoms and siloxanes for instance) and better automatic choosing of base chains. Support for functional groups as base chains if there is no better carbon based option. Support for isotopes, including both modern and Boughton principle rules. Fixed all known IUPAC naming issues reported to us.
  2. SciFinder-n integration. We have been working with our partners from the CAS to initiate SciFinder-n queries from ChemDoodle. These features require a SciFinder-n account. While the features are implemented, it will be a few more weeks before the service is functional and accessible. A new update will be available to enable the features when the service becomes available.
  3. The structure cleaning algorithm has been significantly updated. New systems are in place for generating much better large or complex ring systems. A 3D embedding of very congested structures is now applied. The stochastic method is much more flexible allowing for better output in the most un-ideal structures.
  4. Inter-application communication between ChemDoodle and ChemDoodle 3D. Load 3D molecules of your 2D structures in ChemDoodle 3D with a single menu item click in ChemDoodle. Hot link your structure in ChemDoodle to ChemDoodle 3D, to draw in 2D and watch the molecule build in real-time in ChemDoodle 3D.
  5. ChemDraw reaction schemes can now be input and output from ChemDoodle.
  6. Accurate IUPAC locants can now be easily shown on structures as you draw them for increased clarity when analyzing IUPAC names or for other purposes.
  7. Twitter output now allows up to 280 characters and outputs a much higher quality image.
  8. New BioArt graphics with a space theme, including planets, moons and other interstellar objects.


  1. Fixed issue where reading in some stereo bonds from SMILES strings would lead to 180 degree angles.
  2. Fixed problem where cleaning structures did not adjust bond attribute placements.
  3. Resolved issue where changing isotopic mass numbers did not trigger an update to the molecule.
  4. Corrected custom mass number form where the number field was too small.
  5. Adding a highlight and cancelling styles customization can now be correctly undone.
  6. Fixed issue where the recent files cache could get corrupted, leading to a crash on startup on Windows.
  7. Resolved issues generating IUPAC InChI on Windows.
  8. Fixed issue where ChemDoodle could not be hidden on later versions of macOS.
  9. Improvements to z-ordering on macOS.

ChemDoodle 3D v5

Executive Summary

ChemDoodle 3D v5 includes all the infrastructure improvements provided in ChemDoodle v10. New inter-application features are now available to quickly visualize structures drawn from ChemDoodle 2D. ChemDoodle 3D v5 is required for these inter-application features to work.