We are pleased to introduce version 12.12 of our ChemDoodle 2D software. This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $29, and we have a free trial available at: https://www.chemdoodle.com/

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ChemDoodle 2D v12.12 has excellect support for inorganic compounds and complexes.

Executive Summary

Version 12.12.0 is a massive update for ChemDoodle 2D. Our main focus is expanded support for inorganic compounds and complexes, including haptic bonds and multi-center attachments, their use in formula and mass calculations, and perspective ring templates. We are committed to continuing to build new capabilities for inorganic chemistry. Additional highlights include expanded SMARTS support, automatic lone pair placement, a new pKa estimator, and numerous improvements to drawing, tables, rendering and file exchange.

Additions

  1. Improved support for inorganic compounds and coordination complexes, including ionic and covalent representations of haptic bonding. A dedicated chapter explains bond representations, multi-center attachments, chemical models and worked examples. Please see chapter 5 of the user guide for more information.
  2. Added support for reading and writing multi-center attachments in MDL V3000 files, ChemDraw CDX/CDXML, Marvin MRV and iChemLabs ChemDoodle Documents.
  3. Added a pKa estimator using the SMARTS pKa method. Please see section 14.9.3 of the user guide for more information.
  4. Expanded SMARTS matching to support disjoint patterns, component-level grouping, reaction SMARTS and reaction atom mappings.
  5. Added the SMARTS atomic primitives ', |, #X, #N, #G, #M, i, d, k, Z and z, along with the $ bond primitive for quadruple bonds. These primitives were chosen based on extensions and usage in other toolkits. Please see section 12.2.7.1 of the user guide for the definitions of these extensions.
  6. SMILES output now writes $ for quadruple bonds, complementing the existing input support and preserving these bonds during round trips.
  7. Chemical labels now recognize # for triple bonds and $ for quadruple bonds between label components. Periods, spaces and bullet characters are also supported as fragment separators. Improved interpretation of charges. Please see section 14.4 of the user guide for syntax examples.
  8. A new Place Lone Pairs function automatically calculates and adjusts the number of lone pairs on selected atoms. Formal charge assignment has also been made more consistent, and both functions are now grouped in the Structure>Atom Properties submenu. Please see section 14.3 of the user guide for instructions.
  9. Holding down the space key while drawing bonds, chains, rings and templates now temporarily disables atom auto-connect.
  10. Selected content can now be placed into a table cell by dragging it with a selection tool and releasing the mouse over the desired cell. Please see section 10.10.3.1 of the user guide for instructions.
  11. Styles can now be applied to an entire row or column of table cells at once, making it easier to define different borders and other styles for header rows. Hover over the row or column anchor, right-click and select Format Table Row/Column... to edit its cell styles. Please see section 10.10.3.5 of the user guide for more information.
  12. The Prismane Builder tool now creates polyprismanes. Drag horizontally to adjust the width and vertically to adjust the number of levels. Please see section 6.4.2 of the user guide for instructions.
  13. Electron pusher control distances are now adjustable for finer control over arrow shapes.
  14. Added an Undetermined rendering option to the Nucleophile Hint style for electron pushers, available under Styles>Shapes>Pushers.
  15. Added perspective ring templates for Cp-, benzene, Ind-, Flu- and tropylium, along with new metallocene templates. Added a Diamondoids template set.
  16. The Settings and Styles windows are now resizable.

Fixes

  1. Corrected an issue where stoichiometry table calculations did not account for repeat units.
  2. Improved bond overlap clearing when a bond passes close to or through an atom between other bonds, and when a bold or wedge bond is drawn on top.
  3. Improved aromatic circle rendering in three-, four- and five-membered rings.
  4. Hover detection along with rendered hover and selection indicators now account for the document scale, including the optimize zone and bond-side detection. Shapes that are hovered are no longer rendered on top unless they are fully obscured.
  5. Templates used during structure cleaning now preserve bond z-orders, maintaining the correct perspective in generated 2D layouts.
  6. Corrected functional group mapping for imides.
  7. Element symbols outside the organic subset now require brackets in SMARTS, resolving ambiguous element declarations.
  8. Broadened stereochemistry perception for bridged structures based on IUPAC ST 1.2.3 to accommodate a wider range of drawings.
  9. Corrected an issue with ion prioritization.
  10. Corrected duplicated "a" characters in Hantzsch-Widman based IUPAC names for tetrazole and similar ring systems.
  11. Fixed an occasional overlap between bonds and automatically placed stereochemical attributes.
  12. Closing a dialog with the escape key now executes the same close behavior as clicking its close button.
  13. Corrected SLN output that omitted some ring return indexes.
  14. Fixed an EPS output issue where preserved chemnum tags were present in the file but did not render. When Preserve chemnum Tags is enabled, any label containing the chenum tag as a substring in the label will be output as text, regardless of whether Render Text as Shapes is enabled. Please see section 17.9.8 of the user guide for more information.
  15. On macOS, dialogs no longer pop over other applications when ChemDoodle starts in the background.
  16. Fixed a crash when placing a template containing a structure that requires kekulization, such as a benzene ring drawn entirely with resonance bonds.
  17. Aromatic circles in template previews now use the correct preview color when being drawn.
  18. Templates containing manually placed attributes are now laid out correctly in the Templates widget and when being drawn.
  19. Fixed an issue where updating a resized ChemDoodle figure through round-trip editing in PowerPoint on Windows reverted its scale.