A user wrote:
I would like to do a conformational search with cxcalc, on a transition metal complex. But the problem is that the geometry around the metal is really poorly described with this force field. A possible solution would be to freeze the geometry around the metal from the input file, since the input file contains a metal geometry far better than could ever be obtained by this force field. But is this practically possible somehow, through the program?
Currently it is not possible to assign geometric constraints like this. However in the future we might consider implementing such functionality. (Btw, may we get the structure in question?)
I found something surprising when using cxcalc conformers. I found that this program could not generate low conformers that contain a square planar environment around the Pd(II). Instead, it finds the tetrahedral to be lower in energy, in clear disagreement with experiment for this 16 electron compound.
This was somewhat to my surprise, because I was in the assumption that cxcalc conformers used the Universal Force Field, which is known to handle these types of compounds quite well.
Also, in this respect, it would be interesting to simply freeze the environment around the metal, if it turns out the force field is not up to this.
I will attach two Pd(II) files (mol) I used for conformational search.
Dear Wouter Heyndrickx,
thank you for your email and we are apologizing for the delay.
Clean3D uses Dreiding forcefield that is modified to a great extent in order to extend its usability on the periodic system. However with transitional metal complexes still lot to do. We are working on a general solution to treat such complexes properly and does not tackle complexes one by one. (eg. Palladium with four ligands can also be tetrahedral as in Pd[(PF3)]4 .)
Also the MMFF94 forcefield was implemented and will be released in the near future. MMFF94 may solve this issue.
We are considering Your idea to freeze such regions, if valid 3D coordinates were found in the input file. However the common inputs of the Clean3D module are 2D molecules.
In case of 2D inputs of transition metal complexes we recommend to use Clean3D to obtain the 3D starting structure. Than perform geometry optimization that uses quantum chemical methods or specialized forcefield.
Dear Wouter Heyndrickx,
It seems that a workaround exists for this particular situation: although currently it is not possible to assign the correct geometry for this compound, attaching temporarily two extra (heavy) ligands (W or U for example) to the Pd center for the time of 3D coordinate generation will force the remaining ligands into planar situation. (see attached files)
I would like to note that after removing these extra ligands no further geometry optimization or energy calculation should be made on the structure using the current Dreiding implementation.
I was wondering if this freezing of certain atomic
coordinates around the metal during the conformational search is already available? Or
if there are concrete plans of implementing such option?
We are planning the implementation of this feature in the future, however we do not have any specific schedule about it.