IMHO, all of the compounds you drew have some aromatic character. All are lower in energy than would be expected from the corresponding acyclic compounds, and all would probably show particularly high deshielding in their NMR spectra.
The problem with defining whether Lewis structures are aromatic is that aromaticity is fundamentally a molecular orbital phenomenon. Much of organic chemistry can be described quite well with Lewis structures, but aromaticity cannot. In fact, the explanation of the unusual stability of benzene was probably the first MO argument that was recognized by organic chemists as having some relevance to their field.[/img]
Ferenc
Joined: 21 May 2004
Posts: 598
ChemAxon personnel
Do you think we should handle these structures aromatic or non-aromatic in structure searching? The cd_smiles column of JChem Base tables stores aromatic structures in aromatic form. We are not sure if these molecules should be stored with aromatic bonds or as they are displayed in the image of Volfi. Should a substructure containing aromatic bonds provide hits for these structures? Or it is better if the user has to draw the substructure with single/double bonds to get hits?
For example searching with O=cncc or O=CNC=C should result the first structure as a hit?
Do you think we should handle these structures aromatic or non-aromatic in structure searching? The cd_smiles column of JChem Base tables stores aromatic structures in aromatic form. We are not sure if these molecules should be stored with aromatic bonds or as they are displayed in the image of Volfi. Should a substructure containing aromatic bonds provide hits for these structures? Or it is better if the user has to draw the substructure with single/double bonds to get hits?
For example searching with O=cncc or O=CNC=C should result the first structure as a hit?
I think we discussed this subject before. All aromatic resonance forms should be considered in any search. It is counterintuitive that it should be necessary to aromatize a structure before searching, and it is counterintuitive that only compounds that are in the database in aromatized form should match it. In other words, the default should always be aromatization. Perhaps, in the rare cases that aromatization is not desired, an option for nonaromatization could be provided.
-- Bob
Ferenc
Joined: 21 May 2004
Posts: 598
ChemAxon personnel
All aromatic resonance forms should be considered in any search.
If we would like to avoid serious speed problems, this requires a modified database structure. Presently, a structure table contains one row for each molecule. One solution is that another table is created just for resonant molecules. This table would store the alternative fingerprints and structures (cd_fp<n> and cd_smiles colums) of molecules having different resonance forms. We need to maintain compatibility with previous versions, but I think we can implement something like this, though it is a major change and requires time.
Ferenc
PS:
The rest of your comments are not strictly related to this issue. Hi level functions, like JChemSearch do consider aromaticity, but low levels, like MolSearch require aromatic conversion before usage. Your suggestion has advantages and disadvantages, but I suggest to discuss them in another topic.
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