Hi! I have a periodic crystalline material containing only Si and O atoms, with an organic molecule with a F atom occluded within the material. During optimization, the F atom, which is bonded to a benzylic C, has a tendency to move away from the C, whether to bond with Si, or to bond to some other part of the molecule. I currently use the fix_molecule and noauto keywords.
Is there a way to keep the F bonded to the benzylic C? I was thinking to fix the distance between the C and F atoms, but could not find keywords for it, except maybe connect? An alternative would be to fix the F atom’s coordinates. Could you advise on the best way forward and its implementation?
As you’ve specified “noauto” then the molecule keywords (mole, molmec, molq) won’t automatically find any bonds (assuming you’ve also given one of these) and so the molecule functionality won’t do anything unless you specify the bonds explicitly with “connect”. Assuming you have a sensible molecular force field for your organic then this should help keep F away from C. If not, then you need to add a repulsive non-bonded term for F-Si to the force field.
Thank you for your reply! I was sloppy in my question. In my original input file I have already used connect to connect the correct C to the correct F with a single bond. I have 2 follow up questions:
Even though connect is specified, the F still floats away from benzylic C. Why does that happen?
How can a repulsive non-bonded term be added for F-Si? I am using the Dreiding force field. I was unable to find documentation on this, and none of the keywords look like they help to add repulsion.
Just because there is a bond, doesn’t mean that the atoms will stay together - you need a harmonic potential to act between them. You should check that there is a “harmonic” potential that is specified with “bond” (i.e. “harm bond”) acting between these atoms.
This will automatically happen based on the Lennard-Jones potentials in Dreiding, provided the atoms are not bonded or next nearest neighbours.