We are pleased to introduce version 11.9 of our ChemDoodle 2D software. This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $15, and we have a free trial available at: https://www.chemdoodle.com/


Some new feature highlights in ChemDoodle 2D v11.9.

Executive Summary

ChemDoodle 2D v11.9 focuses on improvements to our cheminformatics functions, specifically a new blazing fast ring search algorithm for very fast performance when editing very large and complex structures, further advancements in our 2D layout algorithm for really nice structure cleaning of very complex systems, and the handling of isotopes that have no abundance on Earth in our molecular mass/elemental analysis/molecular formula tools.


  1. Isotope data is now included for isotopes with no natural abundance on Earth. This allows for the calculation of masses and elemental analysis on structures drawn with a wide range of isotope mass values, including tritium (3H). If no mass data is available for the specified isotope, the elemental analysis and isotopic distribution functions will display an appropriate error to notify you of the missing information. Mass calculations on isotopes with no mass values will display a "NaN" value. Molecular formulas will now properly handle any isotope definitions, even if no mass data is available.
  2. A much faster smallest set of smallest rings algorithm (SSSR, RP-Path) is now used by ChemDoodle, allowing for very fast handling of even large and complex embedded structures in a short amount of time. Because the new SSSR algorithm is so fast, the Ring Search Cutoff performance option is no longer necessary and has been removed.
  3. Vastly improved structure cleaning. Better handling of macrocycles, embedded systems containing macrocycles and better overlap resolution. Partial cleaning has been improved and will be more flexible when selecting parts of ring blocks. The templates used for cleaning have been curated for better graphics.
  4. Improvements to SMARTS matching performance.


  1. Sorted rings by size when coloring in rings, so each ring could be clearly seen.
  2. Fixed problem where bezier curves read in from older ChemDoodle Documents would not load properly.