Posted: Mon Jan 26, 2009 11:33 amPost subject: Different calc. results for resonance formulas

Hi, there are more problems with resonance formulas describing one molcule/ion, here a dianion.

The dianion shown in the attached screenshots is described in the paper L.L.Miller et.al. J Amer Chem Soc 1990, 112, 1206. The dianion has D2h symmetry and cannot be formulated with only one resonance formula (like f.e. polymethine cyanine salts). Of the four major resonance formulas one can draw two are shown in the upper part of the screenshot (The other two are symmetry related).

The lower parts of the screenshots show the effect of "aromatization". Neither the "General aromatization" nor the "Basic aromatization" correspond to the symmetry of the dianion.

Calculations for this dianion give different results for these two resonance formulas describing the same dianion. In the screenshot are the different "Conformers Dreiding energies". Also other calculation tools, f.e. "Charge", "Protonation", "logP" and "Steric Hindrance" give different results.

The Marvin Huckel calculation tool is able to handle the pi-system of this dianion in correct D2h symmetry, both resonance formulas give the same result, see second screenshot bf0495.

Calculations for this dianion give different results for these two resonance formulas describing the same dianion.

As we discussed before structure based calculations (for example conformer/energy) will consider different bond systems (the resonance formulae) as different molecules. If this is unecceptable in a specific application then one can use some standardization before the calulation or invoke calculations for the resonant structures and merge the results.

Quote:

The lower parts of the screenshots show the
effect of "aromatization". Neither the "General aromatization" nor the
"Basic aromatization" correspond to the symmetry of the dianion.

I suggest that since aromatization can consider only rings as aromatic it is not always possible to reflect the symmetries of the structure. (Andreas might correct this.)

Regards,

Gabor

Andras ChemAxon personnel
Joined: 07 Jun 2004
Posts: 930

Aromatization methods are designed to make simple and fast calculations to decide which bonds are aromatic. This is rather used as some kind of standardization. For more sophisticated aromaticity decision it is suggested to use quantum chemical calculations.

"As we discussed before structure based calculations (for example conformer/energy) will consider different bond systems (the resonance formulae) as different molecules."

I must give the answer by attaching once more the IUPAC definitions.

These are not different molecules. It is not "inacceptable", it's wrong. There may be a user formulating only one of these resonance formulas, getting a result and believing it's the correct result (f.e. the left resonance formula in the post before). This user will not recognize that something is wrong.

And so Marvin must do "some standardization" before the calculation and as default.

Concerning the overuse of "aromatization" I will start a new topic ASAP.

here may be a user formulating only one of these resonance formulas, getting a result and believing it's the correct result

I agree, but currently we have no resources to enhance conformer tool into this direction.

Quote:

And so Marvin must do "some standardization" before the calculation and as default.

A minimal standardization is done by the conformer tool, however this must satisfy a diverse set of use cases. (An example: adding explicit hydrogens would be an obvious step, however since it interfere with the molecular topology it can not included in the Molecule.clean(3,...) method!)

We recommend to use our Standardizer tool for further standardization.

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