We are pleased to introduce version 11.12 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/

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Stoichiometric and additive IUPAC naming via ChemDoodle 2D v11.12.

Executive Summary

ChemDoodle 2D v11.12.0 is a feature update with a focus on IUPAC naming. Major new abilities include an Attempted PIN (Preferred IUPAC Name) in addition to Traditional IUPAC naming, more nomenclature systems including thorough stoichiometric and additive naming, UTF8 text format output, a lot of new trivial name inclusions and significant new rule and scope support. Additionally, several issues have been corrected, described below.

Additions

  1. IUPAC naming has been upgraded, please see the updated chapter 14 of the ChemDoodle User Guide for detailed instructions:
    1. We now include a second type of IUPAC name output, an Attempted Preferred IUPAC Name (PIN) in addition to the Traditional IUPAC name. Traditional IUPAC names will be modified by the options in ChemDoodle, while the PIN will not be. ChemDoodle will try its best to generate the PIN, but is not guaranteed to, which is why it is called an Attempted PIN. The Structure>Structure to IUPAC Name menu item will now display both name types. Auto-updating labels will display the Attempted PIN, but can be changed to show the Traditional IUPAC name instead in the Functions panel of the Preferences window. Please see chapter 14 of the ChemDoodle User Guide for further explanation.
    2. More nomenclature systems, including stoichometric and additive naming for polyatomic or metal complexes. Hydrate naming is supported. ChemDoodle will attempt to intelligently name your structures as clearly as possible using the best nomenclature system, and will respect zero-order bonds when separating structures. ChemDoodle will automatically split a structure to better name complexes if it feels this will lead to a clearer name (such as NaCl drawn with a single bond, ChemDoodle will split it and name it as sodium chloride). Dative bonds may be used to specify coordination centers, and ChemDoodle will default to naming those centers additively.
    3. Added an option to prefer chain length over unsaturations, which is compliant with P-44.0 of the 2013 Blue book.
    4. IUPAC names may now be output into pure UTF8 characters to preserve most formatting without markup languages.
    5. Ring assemblies now use parenthesis if the base name starts with a number. Fixed issue affecting complex ring assemblies.
    6. Improved efficiency for generating von Baeyer names regarding structures with multiple complex ring systems connected by chains.
    7. Made error clearer when there is no defined maximum coordination for an element, but one is required.
    8. Stopped infinite loop involving a rare substructure.
    9. Fixed bug involving pentavalent Pnictogen functional groups.
    10. Many new options have been added. These options are described in the ChemDoodle User Guide, chapter 14.
    11. Most of the common names from the Principles of Chemical Nomenclature and Red book tables are now included.
    12. Better support for replacement chain nomenclature in small structures containing no carbon atoms.
    13. Aluminium is now used instead of aluminum, caesium now used instead of cesium.
    14. Improvements to lambda notation when charges are present.
    15. Individual isotopic elements are now correctly designated.
  2. 2D cleaning improvements for bulky spiros.

Fixes

  1. Improved coordinate covalent bond rendering to better represent a plus on the non-arrow end.
  2. Fixed bug where stereochemical projections were not recognized if a condensed label existed in the structure.
  3. Some users experienced application hanging on macOS when accessibility features or 3rd party applications using macOS accessibility APIs are enabled. This update stops the hanging and allows the software to continue to function. There will still be an issue with the file chooser, as that is a compatibility issue on the Java side that we cannot control. But in ChemDoodle 2D and 3D, you may switch to the non-native file chooser which will not be affected if you wish to use such accessibility software and ChemDoodle 2D at the same time. Do this by going into Preferences for the ChemDoodle 2D application, selecting the Files tab, and then unchecking “Use Native Filechooser” in the Filechooser settings. Then restart the ChemDoodle 2D application.
  4. LabArchives posting has been fixed.
  5. Linux KDE URL launches are not functional with Java, so we included a workaround to launch URLs when running ChemDoodle 2D on Linux with KDE.