We are pleased to introduce version 12.2 of our ChemDoodle 2D software. This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $19, and we have a free trial available at: https://www.chemdoodle.com/


An atom-to-atom mapping for a drawn reaction of the acylation of benzene.

Executive Summary

ChemDoodle 2D v12.2 is a feature and maintenance update, correcting a number of issues brought to our attention. The main new feature is atom mapping functionality and input/output of reaction atom-to-atom mapping to a number of chemistry file formats. This update is recommended for all users.


  1. A new tool is provided in the Arrows toolbar for manually applying atom-to-atom mappings. Most will use this feature for reaction applications. Input and output of reaction atom-to-atom mapping is fully supported in ChemDoodle Documents, ChemDoodle JSON, ChemDraw CDX, ChemDraw CDXML, SMILES, and MDL RXN files. ChemDoodle will display warnings for atom mappings in certain situations. Please see sections 7.8 and 9.12 of the ChemDoodle user guide for more information.
  2. Margin highlights on rulers may now be disabled in the Settings>Appearance panel.


  1. The "presets" folder in the user's Documents folder has been renamed to "styleSheets". Simply move the contents of the "presets" folder into the "styleSheets" folder if you wish to continue using any saved style sheets.
  2. The Predefine Measured Mass option for stoichiometry tables has been removed as it did not offer any additional benefit.
  3. Due to performance issues in large documents, all stereochemistry checkers are now disabled by default. You may turn them back on in the Settings>Warnings panel.
  4. Corrected issue with stereochemical wedge application in cyclic bridged systems.
  5. Fixed infinite loop when cleaning certain pinwheel structures.
  6. IUPAC naming using von Baeyer rules is now much faster.
  7. Corrected minor issues with the expansion of abbreviations that match element names.
  8. TLC plate background colors and styles are now properly applied.
  9. v3000 MOL file output now includes the chiral flag in the counts line when appropriate.
  10. Some improvements for MarvinSketch MRV styles.
  11. Fixed round-trip editing issue where EMF data containg both ChemDraw and ISIS/Sketch file information included was not processed.
  12. Corrected rare round-trip editing error when pasting EMF data into ChemDoodle from PowerPoint.
  13. Directly editing OLE objects will no longer center content in pages. Now, the page is centered in the scroll panel view on edit.
  14. Corrected an issue with grouped shapes that could cause fractional metrics to be disabled in vector graphic output, leading to packed text.
  15. Fixed issue where Java file chooser UIs would not update for Light/Dark mode changes.
  16. Fixed issue where the master right-click menu's UI would not update properly for Light/Dark mode changes.
  17. Improved right click menu handling.
  18. Fixed button icons for shapes with shadows.
  19. Fixed bug where before the initial settings file was created, starting a new document would not revert the style sheet.
  20. Fixed issue where changing the application font did not apply to everything.
  21. Fixed bug where the periodic table would fail to print.
  22. Subgrouping is now applied in the Settings>Warnings panel, making it much easier to understand.
  23. Corrected quick start guide typos.