We are pleased to introduce version 12.4 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/


ChemDoodle 2D includes stereochemistry support for atropisomers along with IUPAC naming support.

Executive Summary

Version 12.4.0 is a feature update for ChemDoodle 2D. Included is significant work on IUPAC naming output, support for atropisomer stereochemistry, improved and adjustable crosshair background guides, a reaction sprout function, and more.


  1. Significant updates for IUPAC naming. Much of the focus has been on PIN support and syntax for PINs. Included is advanced support for stereochemistry output, compliant with the latest specification and coverage of more complex stereochemical entities including atropisomers. Also included are new impressive algorithms for resolving indicated hydrogens in mancude ring blocks. Xi symbols used when wavy bonds invalidate a stereochemical configuration. Non-integer support for locants in base templates. Many edge cases have been resolved.
  2. IUPAC naming options in the Settings window have been clarified.
  3. Full support for atropisomer stereochemistry. You may use the full functionality of the ChemDoodle stereochemistry engine for atropisomers, including recognition, configuration setting, flipping, forcing and warnings.
  4. A new Sprout function is included in the Reaction menu. This function will generate a reaction out of any number of selected molecules. The selected molecules will become reactants, and copies will be created as products for further edit.
  5. The crosshair drawing guides have been reworked. You may now move the crosshair location when using a selection tool. Double clicking on the cross hair will recenter it. Crosshair grid breakdown is now optimized for the current rendering scale of the document. Each page within a document will have its own crosshair, which may be moved independently of the others. And you may choose between US and Metric modes for the crosshair rulers.
  6. The Windows installer will now produce a log when run in silent mode. Please see section 1.5.5 of the ChemDoodle user guide for more information.


  1. Resolved stereochemistry issues when resonance bonds were present.
  2. Resolved wedge assignment issue for clustered stereocenters when an even numbered cumulene is involved.
  3. Fixed SMILES input issue where tetrehedral geometry was not recognized with a lone electron pair.
  4. Corrected out of SMILES where allenes with implicit hydrogens were mishandled.
  5. Fixed minor issues regarding the rendering of warning descriptions on the document.
  6. The Warnings panel in the Settings window now included subtitles, as intended.
  7. The drawing guides have been improved with thinner lines, which are nicer on high-DPI displays.
  8. Fixed problem where the non-native open file dialog appeared behind the application when using the Recover MS Office Files window.