ChemDoodle 3.2 has been released! We provide this upgrade, free of charge, to our existing customers. Just open up ChemDoodle and follow the directions to automatically update ChemDoodle.

Executive Summary

ChemDoodle 3.2 is a significant update containing major new features and improvements. Notable features include orbital objects, the expansion of condensed formulas in atom labels (allowing for the automatic proper handling of condensed formulas by the Properties widget and other algorithms), a more robust abbreviations system (that can be used in atom labels for all atom models) and integration with the ChemSpider database. Notable improvements include an evolution of the ChemDoodle rendering engine for improved rendering and performance as well as full control over the low level graphics settings, a new table layout for the Properties widget that conveniently updates when drawing a single molecule, and full compatibility to directly paste scalable vector graphics into the entire Microsoft Office suite on Windows and Mac OS X.


  1. Orbitals can now be added to structures. These are 2D graphics that can be attached to atoms or bonds or can be standalone. A gradient is used to give them a 3D appeal. Supported are atomic orbitals (s, p, d, f), hybrid orbitals (sp lobe, sp3), and bonding orbitals (σ, π). Orbitals can also be read from and written to ChemDraw files. There are two visual specifications for orbitals in the Preferences window under the Visuals tab under the Shapes subtab: Length Multiplier – Sets the default size of orbitals relative to the current bond length; Stroke Shaded Lobes – Sets whether or not outlines are drawn around shaded orbital lobes.
  2. The graphics engine in ChemDoodle has seen a significant upgrade and graphics rendering has significantly improved. Performance has also been significantly improved. Graphics controls for low level rendering are now exposed in the Preferences window under the Advanced tab. Change these only if necessary to favor speed or to affect how graphics are rendered. These rendering options will only affect devices with resolutions, such as bitmap images and monitors; scalable vector graphics remain perfect and unchanged.
  3. Added a new option to simulate soft clipping for bitmap images in the Advanced tab of the Preferences window. This makes Recessed bonds look much nicer.
  4. A new system for expanding condensed formulas and abbreviations in atom labels to their all atom models. There are several features that benefit from this:
    1. All calculations based on structures (properties, NMR spectra, etc.) will first expand the molecule, so proper results will now be obtained when using condensed formulas.
    2. Atom label errors are improved. ChemDoodle will alert you of unknown tokens and will properly evaluate atom valencies. For instance, a terminal label of CH3 will be approved while a terminal label of CH4 will not.
    3. Abbreviations can now be expanded. So Ph, Et, COOH, etc. will be properly expanded to the corresponding all atom models and can be used in condensed formulas. You can add your own custom abbreviations.
    4. Atom label token stacking is more intelligent and will now stack based on token groups. For instance, the label CH2CH2COOCH2CN will stack as (CH2)(CH2)(COO)(CH2)(CN).
    5. Complex shorthand notations are also supported, so C(CH3)3 will be expanded as a t-butyl fragment and CPh3 will be expanded as a triphenylmethyl fragment.
  5. The ChemSpider database has been integrated into the MolGrabber widget.
  6. The Properties widget now has a second mode that will be automatically activated when a single molecule, and only a single molecule, is being edited in the current document. The display will change to a table that will list the most important properties and will automatically update if allowed. There is a new checkbox at the top of the widget to disable automatic updating of the data, which will be useful for less powerful computers.
  7. Scalable vector graphics can now be directly pasted into the entire Microsoft Office suite, including Powerpoint and Excel.
  8. Added a Save Selection as Image… menu item to the File menu to quickly save just the selected content to an image.
  9. Added a Copy As submenu to the Edit menu to quickly copy selected structures as various datatypes at maximum compatibility on the system clipboard.
  10. Added a new drag erase gesture when using the Eraser tool. Press and drag over any objects to be removed and they will be highlighted. Release the mouse to delete all highlighted objects. If you drag over a previously highlighted object, it will be unhighlighted.
  11. ChemDoodle Web Components v3.1 is now included. The ChemDoodle Web Component generator has been updated accordingly. New default sizes are provided for standard iOS device resolutions.
  12. Molar Refractivity can now be calculated for structures.
  13. Some widget settings are now saved in the workspace, including the last selected widget and the database choice in the MolGrabber widget.
  14. The MolGrabber widget now provides a direct link to the chosen database’s website for the selected molecule. Press the Show Associated Data button and the top item will show the database’s compound id. Click on the compound id to visit the webpage for that molecule.
  15. Menu items for unrepresented keyboard shortcuts have been added: Flip Bond, Align Bond and Add Attribute.
  16. A new keyboard shortcut for adding attributes to hovered objects, Shift-A.
  17. Added a new visual specification to set whether the second bond line in double lined bonds are shrunken when next to an atom label.
  18. Radial gradient rendering is greatly improved for shapes to better portray 3D appeal.


  1. Improved how the default style sheet is saved. The default style sheet will no longer be affected when ChemDoodle is closed. Both changing preferences and conforming a document will now ask if the new settings should be default. A new menu item, Save Document Settings…, is present in the Window menu for explicit saving the current document style sheet as the default settings.
  2. Fixed a bug where structures could not be dragged into the Line Notation Pad widget.
  3. Fixed bug where changing tabs when content was selected would change the colors of the selected content.
  4. Selected content is now properly remembered when switching between tabs.
  5. Fixed issue where a molecule still appeared selected if it was deselected using the alt+shift keyboard shortcut.
  6. Fixed bug where reading a lone atom from a file will have its label misplaced.
  7. Fixed issue where the SSSR finder was not enforcing linear independence.
  8. Fixed issue where the Euler facet ring finder was skipping rings.
  9. Colored in ring guides no longer appear in output.
  10. Fixed bug where an infinite loop started when cleaning complex multi-ring-substituted ring systems.
  11. Fixed bug where some structures were not being cleaned.
  12. Improved the cleaning of complex ring systems.
  13. When cleaning structures, triple bonds are now aligned parallel to their substituents.
  14. Improved boundary conditions for token alignment to favor the horizontal alignments.
  15. Fixed bug where some counters were not being calculated in the Properties widget.
  16. The Calligraphy stroke skew angle has been offset by 15 degrees to avoid ghosting effects with vertical bonds.
  17. The arrow size for the ACS Document 1996 chemical document settings has been set to 8 pixels by default.
  18. Changing the arrow specifications now will apply to arrows without having to reselect an arrow tool.
  19. ISIS Sketch files that are missing the closing tag are now read properly.
  20. Fixed conversion issues with ChemSketch files.
  21. Fixed PDB file issue where files that incorrectly contain 0’s in inappropriate places were not being read.
  22. Fixed issue with aromaticity detection where some 5 membered aromatic rings were not being properly detected. Changing any atom labels in rings will now recheck their aromaticity.
  23. Fixed issue when adding hydrogens as text to some structures, where nonexistent hydrogens were being found and “removed” so nothing would be added.
  24. Fixed slowdown when custom fonts were used.
  25. Changing the atom label vertical alignment now updates bond buffers.
  26. Aligning bonds now takes into account if the bond has been flipped.
  27. Attributes now move correctly in grouped content.
  28. Fixed bug where holding alt+shift to select a molecule would incorrectly move the hovered atom.
  29. Negative coordinates in CDX files are now properly read.
  30. Inserting a PDF or dropping it on the Doodle Board will search first for ChemDoodle metadata.
  31. There is no longer a clash on the system clipboard between the PICT and PDF formats on Mac OS X. Both should now always remain selected. You can now work with both Microsoft Office and iWork without having to change the clipboard settings.
  32. Macintosh Vector PICT output has been improved.
  33. Macintosh Vector PICT clips have been improved to remove the residual effect on clip borders.
  34. Windows Enhanced Metafile output has been improved.
  35. Removed small rectangle that appeared in EMF output to the top left of the origin that was only visible if content was offscreen.
  36. EPS output is now smaller.
  37. Improved ruler tracking when moving the Doodle Board scrollbars.
  38. Fixed issue with text input components where text would appear to “jiggle”.
  39. Fixed rare lasso repaint issue that would stop certain sides from displaying the crawling ants effect.
  40. Fixed issue that caused a crash when reading a corrupted workspace file.
  41. Fixed bug where some right-click menu items were displayed but were disabled.
  42. Fixed problem where stacking of off-document content was performed when clicking on the blue background, when stacking should only be performed by clicking on the red strips.
  43. Document rendering and application rendering have been separated.
  44. Missing references have been added.
  45. Fixed minor issues.
  46. Minor text fixes.