We are pleased to introduce version 11.13 of our ChemDoodle 2D software. This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $18, and we have a free trial available at: https://www.chemdoodle.com/


Advanced CIP stereodescriptors resolved by ChemDoodle 2D v11.13.

Executive Summary

ChemDoodle 2D v11.13.0 is a feature update wrapping up our latest massive work on stereochemistry. A new advanced CIP descriptor engine is implemented for the most accurate and consistent CIP assignments and the MDL/BIOVIA stereochemical drawing interpretation algorithm is now implemented along side the IUPAC specification. We believe ChemDoodle is now the industry leader for handling stereochemistry, especially in 2D drawings. Several issues have also been corrected, described below.


  1. A new advanced CIP descriptor engine has been implemented. Based on the work from Hanson et. al., the CENTRES library by John May is included which supports advanced and consistent CIP assignment for all stereochemical features supported by ChemDoodle. Assign "R", "S", "E", "Z", "M", "P" and the pseudo-asymmetric "r", "s", "e", "z", "m" and "p" descriptors with a simple menu function. A new chapter 15 in the user guide focuses solely on stereochemistry discusses all of these features in detail.
  2. The MDL/BIOVIA stereochemical drawing interpretation algorithm is now implemented along side the IUPAC specification for input drawing interpretation only (the IUPAC specification will always be used for output when using ChemDoodle functions). This option is found in the Preferences window, under the Functions tab in the Stereochemistry section.
  3. Significant speed improvements for generating isotopic distributions.
  4. Improvements to congested spiro structure layout.
  5. Minor improvements to JDX spectra input and much faster output to JDX format for simulated NMR spectra.


  1. Corrected issue where in certain cases involving double bonds in multiple equivalent rings, the second bond line would be locked in place and could not be flipped to the other side.
  2. Fixed issue where charges were no longer rendered after using the graph reduction functions.
  3. Lewis dot structures were incorrectly output with 60 degree angles for certain atom centers with 4 substituents, this has been rectified.
  4. A rounding error occured when rendering 4 membered rings with double bonds in certain style sheets, leading to only one side being fit correctly, this has been resolved.
  5. Improperly drawn rectangular geometry warnings are no longer flagged in rings of size 3 or 4.