We are pleased to introduce version 6.4 of our ChemDoodle 3D software. This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $15, and we have a free trial available at: https://www.chemdoodle.com/3d

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Executive Summary

ChemDoodle 3D v6.4 is a feature update to ChemDoodle 3D. The major new feature is the ability to add charges, radicals and electron pairs to atoms. This allows us to create a unique VSEPR force field which is perfect for students and instructors to use and demonstrate why certain atom centers, along with electron pairs, lead to certain shapes in molecular structures. Other notable features include more file output options and the export of atom typing data from our modeling engine.

Additions

  1. Electron pairs and single electrons (radicals) can now be added to atoms as physical objects. ChemDoodle 3D will automatically place them in appropriate positions around an atom, or you may manually place them. Use the Molecule>Reset Electron Positions menu item to restore the default automatic placement behavior. Radicals will be input and output from all relevant file types.
  2. Charges may be assigned to atoms. Charges will be input and output from all relevant file types.
  3. A new VSEPR force field has been implemented in the molecular modeling engine. The Valence Shell Electron Pair Repulsion (VSEPR) force field is a very specific Points-On-a-Sphere (POS) force field. The entire purpose of this force field is to produce ideal shapes for VSEPR theory. The VSEPR force field is perfect for students and instructors to use and demonstrate why certain atom centers, along with electron pairs, lead to certain shapes in molecular structures. Because the purpose of the VSEPR force field is to generate shapes, energy calculations are irrelevant to the user, as they have no physical significance. When using the VSEPR force field, the Minimizer widget will instead display the current molecular geometry and VSEPR shape of the atomic center you are editing. There is also an Enhanced Repulsion option included that when enabled, electrons will exhibit enhanced repulsion vs bonds. The repulsion constants are defined to produce close to accurate results for water and ammonia in the gas phase. There is no guarantee any other molecules will produce accurate experimentally measured results. This option is great for demonstrating why centers with electron pairs do not have ideal VSEPR shape angles. Please see chapter 5 of the ChemDoodle 3D User Guide for more information.
  4. A new Molecule>Save Atom Types... menu item function will output all atom typing information for applicable molecular modeling force fields in ChemDoodle JSON format to be used in other applications.
  5. There is now an option to center or not center coordinates on output. The default behavior is to center. This option is found in the Preferences in the Files tab.
  6. Added in relevant chemical file options from ChemDoodle 2D.

Fixes

  1. Corrected issue where atoms with large vdW radii would be cutoff when generating surfaces.
  2. Fixed problem where looped aromatic systems caused issues with MMFF atom typing.
  3. Handled the input of improperly formatted CONECT records in PDF files.
  4. Corrected Selector widget checkbox behavior when shapes were present in the scene.