This script calculates energies for bonds in a molecule by systematically deleting the bonds and calculating the energies of the individual fragments using DMol3.

bondEnergy = totalEnergyMolecule - (energyFragment1 + energyFragment2)

You can optionally choose whether to calculate the bond energies based on single point energies or geometry optimization of the individual fragments.

Once the energies are calculated, the names of the bonds are set to the energy of the bonds. A collection document is also created with the bonds colored by their energy.

There are options to control which bonds in the system are broken. The rules are:

• Always ignore the bonds in rings
• Optionally include bonds between hydrogen and heavy atoms
• Optionally include "unique" hydrogen atoms
• Optionally include symmetry to try and minimize the number of calculations

Warning: This script is set up to iterate over all structures in a folder so beware where you choose to run it!

Outputs:

• Atomistic structure document is updated with the bond names set to the energies
• Study table is created with the fragments and the energy
• Collection document has the structure with the bonds colored by their energies
• Summary.txt can be viewed on the server to see the calculation progress

Modules: Materials Visualizer, DMol3

Version: 5.0 or 5.5 to allow for symmetry

Cheers

Stephen