I would like to use the conformation plugin for generating inputs for quantum chemical calcs of carbocations. But trigonal carbocationic center (sp2) is pyramidal after the conformation plugin or after "Clean in 3D". May I correct any parameters to do trigonal C+ to be flat?
Currently it is not possible to define the arrangement of the ligands around a center. (The only exception is chirality.) However as a workaround adding temporal extra ligands or double/aromatic bonds might help. (I would like to note that we are working on the implementation of MMFF force field which is expected to handle these situations correctly)
For example: the center atom is recognized as SP3: c1ccc(cc1)[C+](c1ccccc1)c1ccccc1
Marking two bonds of the center as aromatic c1ccc(cc1)-[c+](:c1ccccc1):c1ccccc1 will do the trick and the center is recognized as SP2.
Alternatively adding two temporal heavy ligands will force the center closer to planar: [W][C]([W])(c1ccccc1)(c1ccccc1)c1ccccc1
If You have any further questions, please feel free to ask them
Thank for quick response and for value advices. I will try.
It will be great!
|I would like to note that we are working on the implementation of MMFF force field which is expected to handle these situations correctly |