Hi
I am studying interaction of Li ion with the carbonyl based compound as mentioned in the attached figure. In the attached figure I mentioned the results of Gaussian 09 code. In Figure A it interacted with the carbonyl group and the near O atom of neighbor ring without applying Freeze bond and Freeze dihedral option. In the Figure B I mentioned the interaction with the carbonyl group only because in this file I used Freeze bond and Freeze dihedral option using the redundant coordinates tool.
Now I am computing the same interaction using the DMol3 code. In DMol3 code which option I used for the freeze bond and freeze dihedral for interaction of Li ion with the carbonyl group? because I want that the Li ion interact only with the carbonyl group not with the O atom of neighbor ring.
Best Regards
Sure. Search the manual for word "constraint", http://www.esi.umontreal.ca/accelrys/pdf/dmol2K.pdf its mentioned multiple times, in particular paragraph E-5
"For example, referring to the N-phenylbenzamide geometry above (see Basis keyword, page E–2), the following CONSTRAINT input would define four constraints: the central N2-C1 amide bond distance constrained to 1.336 Å, the C5-N2-C1 angle constrained to 120.0˚, the H16-N2-C1-C5 dihedral angle constrained to 168.8˚, and the C5-C3 distance constrained to 4.12 Å:
CONSTRAINT 1 2 1.336
5 2 1 120.0
16 2 1 5 168.8
5 3 4.12
ENDCON
"
However request " because I want that the Li ion interact only "does not sounds very healthy. Normally one look for real minima or TS and not for structures constrained to very specific geometry. May be you should explian motivation better.
Without knowing the context of your calculations, I have to agree with Dmitry: having a Li ion with only a single coordination partner is very artificial and will most likely lead to at least odd results.
If possible, you should do something to saturate the ion's coordination sphere, for instance by adding explicitely modeled solvent molecules (dimethyl ether will usually do). Of course, you then have to take the solvent molecules also in your other calculations and evaluations into account.
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