I have performed some optimizations on my new Pd complex. It contains thiophosphorous ligands chelated to a Pd atom. I could optimize the structure by B3LYP/6-31G* for all atoms except Br and Pd ( lanl2dz). When I wanted to perform TS computations, I inserted an phenylbromide to the complex and I formed a hexa-coordinated complex. It could optimize by B3LYP/3-21G* for all atoms except Br and Pd. However, I faced a serious problem when I continue the computations on B3LYP/6-31G*. The phenyl molecule collapse on the Pd atom. I couldn't find scientific explanation to it. could you please help me to find a solution for that?
Thanks in advance
If you upload input and output file here, it is much easy to solve ur problem
What i can say without any file to solve ur problem
1. check fixed distance is available
2. check the variation of geometries in optimization output file
3. perform same basis set
Best regards
Collapse of moleule's gemetry usually means a problem with the basis set, likely a wrong definition of it. Since you're using lanl2dz with pseudopotentials, remember that it has to be specified twice in the input, once in the basis set section and once in the pseudopotentials section. E.g.:
# b3lyp/gen pseudo=read
and then at the end of file, after geometry specification
C N H O 0 (and any other atoms you have in your system)
6-31G*
****
Pd Br 0
LANL2DZ
****
Pd Br 0
LANL2DZ
Also, 6-31G* is actually available for Br, you can get it from https://bse.pnl.gov/bse/portal and add to the input file. See http://joaquinbarroso.com/2011/11/02/gen-keyword-gaussian/ on how to do it.
Dear Prof. Trzaskowski
Thank you very much for your answer. I actually do the same in output as you said. at first I used 6-31G* for Br atom but it collapse on pd. so I thought changing basis set may help. However, I changed the B3LYP to PBE and mPW1PW91 and I faced the problem again. with 3-21G* it works but when I switched to 6-31G*, the geometry collapsed. Is it a scientific problem? Or just my failure in operating the computation?
I am looking forward hearing from you
Best
Somayeh
using same minimal basis set like 3-21G, and fixe the optimal geometry of tis optimisation, the you can restart an optimisation using 6-31g*
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