We are pleased to introduce version 7.4 of our ChemDoodle 3D 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/3d

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ChemDoodle 3D now includes advanced stereochemistry features for working with chemical structures in 3D.

Executive Summary

ChemDoodle 3D v7.4 focuses on stereochemistry features, allowing you to easily and automatically force stereochemical configurations for stereogenic features in 3D molecules. Stereochemical information is now input from and output to SMILES, SLN and InChI. Pasting and loading 2D chemical drawings will now produce 3D structures with stereogenic features enforced via IUPAC rules. Allene and cumulene support has been added to the Universal Force Field. New precise transform functions have been added to the Content menu.

Additions

  1. ChemDoodle 3D now has parity with the stereochemistry features of ChemDoodle 2D, by allowing you to now force stereochemical configurations for stereogenic units present in chemical structures in 3D. ChemDoodle 3D will automatically conform the current structure to produce the preferred minimized stereoisomer. Please see section 16.4.3 of the ChemDoodle 3D user guide for instructions. As a disclaimer, it may not be possible to automatically enforce all of the stereogenic features of a chemical structure, if the structure has multiple features present and is heavily embedded. ChemDoodle 3D will warn you of such cases, and you may always use the real-time modeling engine to easily create your desired stereoisomer.
  2. When using the ChemDoodle 3D interface functions in ChemDoodle 2D, stereochemical configurations will now be respected.
  3. Pasting or loading 2D chemical drawings with stereochemistry defined will now produce 3D structures with the correct stereochemical configurations in 3D. Interpretation of the 2D structures follows IUPAC rules.
  4. Pasting or loading 0D/1D data, such as SMILES, SLN and InChI, will now produce 3D structures with the correct stereochemical configurations in 3D. Explicit hydrogens are also now automatically applied.
  5. Outputting SMILES, SLN and InChI will now include stereochemical configuration information based on the 3D structure, if supported by the format.
  6. We have added a new option for the Universal Force Field to support allenes and odd and even length cumulenes. You may disable this option by deselecting the Add Cumulene Torsions option in the UFF section of the Force Fields panel of the Settings window.
  7. The MMTF format has been discontinued by the RCSB. All MMTF support in ChemDoodle software is being removed. The RCSB BCIF format is now the primary format used by ChemDoodle 3D when importing RCSB data.
  8. There is now a right-click menu item to hide stereochemical configurations for a hovered atom or bond (Stereochemistry>Hide Configuration).
  9. New precise transform functions, including Translate, Rotate, Reflect, Invert, and Scale have been added to the Content menu. The functions will be applied to the entire scene or to selections of objects.

Fixes

  1. Corrected rare issue leading to jumbled results when no input coordinates were present.
  2. Corrected an issue where the application resolution was not updated when moving the application window to a different screen with a different resolution in multi-monitor environments.
  3. Fixed problem where the menu bar becomes disabled after saving a file using the file chooser.
  4. Updated to JOGL 2.5 to address a Mesa compatibility issue on some Linux computers.