ChemDoodle 3.3 has been released! We provide this upgrade, free of charge, to our existing customers. Thank you for helping us to make ChemDoodle a very popular application.

Note: ChemDoodle will be fully supported on Mac OS X 10.7.

Executive Summary

ChemDoodle 3.3 is a significant update containing major new features. Notable features include explicit control over atom label formatting, rendered bond merging for aesthetic joins, a simple workspace resizing system so the application does not occupy the entire screen on large resolution devices, new “Kekulize” functionality, dozens of new molecular descriptors, and retrosynthetic arrows.


  1. Atom label text formatting. ChemDoodle’s default atom label formatting, based on chemical interpretation, can now be overriden. You now have full control to completely format all aspects of the atom label text, from styling, to color and alignment. While very complex labels can now be drawn, this is mainly to allow access to italics and superscripts so common labels can now be easily drawn, such as “iPr”, “iPr” and “R10” for example.
  2. Rendered bond merging for aesthetic bond joins. Wedge-Single, Wedge-Wedge, Wedge-Bold, and Bold-Bold bonds now neatly fit together.
  3. New molecular descriptors are calculated:
    1. Degree of Unsaturation
    2. Rotatable Bond Count
    3. Branching Index
    4. Chi Molecular Connectivity Indices – Up to third order for both simple and valence models.
    5. Kappa Shape Indices – Up to third order for both simple and alpha models.
    6. Critical Pressure
    7. Critical Temperature
    8. Critical Volume
    9. Enthalpy of Formation (ideal gas at 298K)
    10. Enthalpy of Fusion
    11. Enthalpy of Vaporization (at Tb)
    12. Gibbs Enery of Formation (ideal gas, unit fugacity, at 298K)
    13. Heat Capacity (ideal gas, at 298K)
    14. Liquid Viscocity (at 298K)
    15. Normal Boiling Point
    16. Normal Freezing Point
  4. New arrow types:
    1. Retrosynthetic
    2. Bold
    3. Rearrangement
  5. A new function to select by SMARTS. ChemDoodle now has a full implementation of the SMARTS matching protocol; further features that access this functionality will be provided as ChemDoodle evolves.
  6. A new SMILES option to preseve bond orders on output. In essense, aromaticity will not be output to SMILES.
  7. The ChemDoodle workspace now sizes appropriately. On smaller screens, ChemDoodle will still expand to the full view, but on larger devices, ChemDoodle will only take as much room as necessary. When resizing the workspace, the widgets will be appropriately placed to the right of the window. The workspace size and location are now preserved between sessions.
  8. A new Kekulize function that assigns double bonds to sets of bonds to maximize pi electron delocalization. If a structure consists of only single bonds, this function will affect the entire structure. If a structure has any resonance bonds assigned, only those bonds will be affected. SMILES input now automatically Kekulizes input.
  9. Text area font colors can now be changed.
  10. Designating all resonance bonds in a ring now forces that ring to be defined as aromatic.
  11. New keyboard shortcuts to add rings to bonds using the shift key. Alternate bond types are now assigned using the alt key.
  12. Adding rings to bonds now automatically selects the most appropriate orientation if the mouse pointer is close to the bond.
  13. A new option to skip the current update. Once chosen, you will no longer be notified of the current update, but will be of subsequent updates. Choosing the Check for Updates menu item in the Help menu will override this choice.
  14. Renovated the keyboard shortcuts PDF.


  1. Fixed bug on Linux, where EMF output was missing atom labels.
  2. Fixed bug where EPS clipping was not preserved correctly.
  3. Provided a workaround for a Mac bug caused by the latest Mac Java updates, where the Preferences… menu item did not appear in the ChemDoodle menu.
  4. Fixed SMILES bug where double digit ring indexes were not written.
  5. SMILES reading no longer places explicit hydrogens on chiral centers.
  6. Explicit Hydrogens are now output to SMILES.
  7. Emptying the lasso now updates the Properties widget.
  8. Fixed issue where reaction text areas were not properly accounted for when distributing objects.
  9. Fixed bug where using parenthesis incorrectly in condensed notations caused problems during label expansion.
  10. A Linux natural serif font is now used to correctly show font icons on Linux.
  11. Hydrogen counts are now modified by radicals.
  12. Attributes now rotate with structures instead of preserving their distance vector from the atom they describe.
  13. Menu items to calculate descriptors now warn when the structure cannot be sensibly expanded.
  14. Changing fonts to bold/italic now resizes the lasso.
  15. Fixed issue where completely undoing all actions in a text area did not allow you to redo anything.
  16. Underline and strikethrough rendering in text areas now always draws a 1 pixel solid line.
  17. Using the font edit buttons in the text area toolbar no longer steals focus from the text area.
  18. Fixed issue where arc angles could not be set to 0 in the Format Arc… window.
  19. Arrows now correctly conform to document settings.
  20. Charges are now appropriately assigned to the nitro group abbreviation.
  21. Aromaticity detection is significantly improved, especially for fused ring systems.
  22. Changing bond orders in rings now reassesses aromaticity.
  23. Fixed rare bug where sometimes dragging a structure from the MolGrabber widget caused undo/redo issues.
  24. An informative error is now displayed by the MolGrabber widget if a database is inaccessible.
  25. Fixed bug where certain visual aids were saved to the workspace, but upon a new session, the View menu was not properly updated to show they were enabled.