I was trying to optimize a molecule using DFT/b3lyp in Gaussian. But after the optimization, it was found that some bonds are missing from the molecule in the optimized structure. And also in certain case, the optimized mlolecule was entirely different from the input structure. Can anyone help me why it happens and how can I solve this problem?
Dear Renjith,
can you please tell what molecule(s) you optimize, and also what basis set do you use? It might be no problem at all that some bonds are missing upon optimization or optimized molecule looks different from the input structure: if the input structure contained some bonds with length very far from those in the lower-energy structure, it could be totally fine that upon optimization the structure changes noticeably. But, of course, it might be an effect of a basis set or method, too. Also, did you check optimized structures by frequency analysis?
Best regards,
Aleksey.
Dear Renjith
Some bonds disappear in gaussian view program because they are longer than their usual length. The proper description is that they are weakened and not disappeared. The change in structure is some times due to the improper input that does not assign the right bond lengths and angles.
Dear Renjith,
most probably, this kind situation is usually happened due to the improper initial structure. check carefully your initial structure, whether some bond lengths are far from each other, or not. and then you can check your basis set. of course this could be an effect of a basis set.
No problem at all that some bonds are missing upon optimization or optimized molecule looks different from the input structure.Some bonds disappear in Gaussian view program because they are longer than their usual length.
Dr. T. Madhu Mohan i have the same problem, can any tell me how i can solve this problem ?
Aleksey E. Kuznetsov Prasanta Bandyopadhyay
I want to check noncovalent interactions between two molecules, but after optimisation, they are making bonds and dissociation also happens. I want retention of the structures. What is the command for that?
It depends upon many parameters. (I think you have used charge and spin multiplicities correctly)
1. Input geometry. Probably the two structures are too close.
2. Don't consider lines between atoms (in any visualizer) as bonds. Check the distance manually.
3. Level of theory.
Without looking at the problem specifically, It is very hard to comment.
One small recipe,
Suppose you are taking two monomer A and B, keep the distance between them at-least 3.5A. I mean 3.5 A between the nearest neighbor atoms between these two fragments.
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