ChemAxon Forum Archive » Structure based predictions: Calculator Plugins & Chemical Terms

"canonical resonance form"?

User 870ab5b546

09-12-2006 15:29:45

Hi,





What does "canonical resonance form" mean to you? I thought it meant "best resonance form", but apparently not. When I submit (CH3)2C+OH to the resonance plugin:





Code:
        resPlugin.setMolecule(molecule);


        resPlugin.setTakeCanonicalForm(true);


        resPlugin.run();


        Molecule molRes = resPlugin.getStructure(0);






it properly returns (CH3)2C=OH+. But when I submit (CH3)2C=OH+, which is itself the best canonical resonance form, it returns (CH3)2C+OH. From this behavior, it seems that you define "canonical resonance form" as "best resonance form other than the one submitted".





I would like the submitted resonance form to be included in the list of returned resonance forms. If the submitted resonance form is the best, then it should be first in the list of returned resonance forms.





-- Bob

User 851ac690a0

09-12-2006 21:40:03

Hi,
Quote:
What does "canonical resonance form" mean to you?
Canonical form means a 'common parent structure' for all alternative resonance forms of a molecule.








If I see well then problem occurs if the gross charge of the submitted molecule is not zero.





It is a bug, I will fix as soon as possible.








If you submit a molecule without gross charge then the canonical structure will be generated well.











Jozsi

User 870ab5b546

09-12-2006 22:11:13

Jozsi wrote:
Canonical form means a 'common parent structure' for all alternative resonance forms of a molecule.
But any resonance structure could be a "common parent structure". For example, (CH3)2C+O- could be a common parent structure of all resonance forms of acetone, but I doubt you would call it a canonical form. Do you mean the lowest energy resonance structure, that is, the best description of the actual electronic state of the compound? In that case, (CH3)2C+O- would not qualify for acetone, because (CH3)2C=O would be a much better description of the actual electronic state.

User 851ac690a0

09-12-2006 23:38:40

Hi,


Quote:
Do you mean the lowest energy resonance structure, that is, the best description of the actual electronic state of the compound?
Yes, this is property of the generated canonical form.





One of common parent structure of the A, B, and D structures below is acetone. Acetone is the canonical form of the three structures.





A, C[C+](C)[O-] ----> CC(C)=O


B, C [C-](C)[O+] ---> CC(C)=O


D, CC(C)=O ---> CC(C)=O





(this arrow '---> ' refers to the canonicalization.)











Jozsi

User 870ab5b546

24-02-2007 21:50:53

Hi, will this bug be fixed in Marvin 4.1.6, too?

User 851ac690a0

25-02-2007 12:47:33

Hi Bob,





Yes, I fixed this bug as well.





Jozsi