We are pleased to introduce version 6.6 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


Executive Summary

ChemDoodle 3D v6.6 is a feature update to ChemDoodle 3D. Major new features include the ability to perform full scene modeling simulations, an implementation of the FIRE optimizer, 3D molecular structure alignment, improved bond deduction with new bond order perception algorithms, and more.


  1. ChemDoodle 3D now allows full scene modeling simulations. Most small molecule force fields are optimized for describing individual discrete molecular structures. ChemDoodle 3D therefore will optimize molecular structures separately and individually as you are editing them. However, you may wish to optimize several discrete molecular structures at the same time and in relation to each other. To do this, you can change the optimization scope to optimize the entire scene. Please note, while you are able to optimize the entire scene, most force fields are not parameterized for multiple discrete molecular structures, and you will be relying on the through-space forces defined in the force field (mainly van der Waals and electrostatic), if defined at all. While minimizations of several discrete structures using through-space forces may look correct, please understand the theory behind the force field you are using and that any force field not specifically developed or parameterized for intermolecular forces will not lead to experimentally accurate coordinates.
  2. A new function to align molecular structures in 3D. Accessed via the Molecule>Align... menu item, choose the mapping algorithm, whether to overlap the structures, or allow inversions.
  3. Bond deduction has been significantly improved, allowing options for enforcing maximum valencies and changing the bond distance tolerance when using the Molecule>Deduce Covalent Bonds... menu item or opening a file with no bond information. New bond order perception algorithms are now available, including "All Single", Antechamber and Auto-UFF.
  4. A new optimizer for the molecular modeling engine is implemented, FIRE (Fast Inertial Relaxation Engine). The FIRE optimizer differs from the other optimization methods described here in that it does not employ a line search. Instead, it moves in successive small time steps, tracking the momentum of each particle as it slides to a lower energy state. Unlike a naive steepest descent approach where the momentum would be changed only by adding in the current force vector, in this method, the momentum is first steered partially toward the new downward direction before adding in the force. This gives it a slight added push downwards and compensates for the inherent inaccuracies in any discrete process. The result is a smoother descent toward a minimum than you would get using conjugate gradients or BFGS.
  5. Multicolor mesh support is included for 3MF model output, but be aware many programs may not be able to read or support such data.


  1. Fixed bug where turning on the optimizer could not be undone to restore original coordinates.
  2. Corrected 3MF model file output.
  3. Fixed bug when writing SLN strings where a bond order before a ring closure wasn't properly cleared.
  4. Improvements with XYZ file edge cases and reading of error files.
  5. Stopped behavior where the bond deducer was executed for bonds beyond the ones defined in MMTF files.