search

ncats / lychi

Layered Chemical Identifier
Apache License 2.0
14 stars 10 forks source link

Benzocyclobutadiene resonance forms #14

Open olegursu opened 10 years ago

olegursu commented 10 years ago

2 resonant forms of benzocyclobutadiene are assigned different hash keys.

example

benzocyclobutadiene is unstable, there are stable substituted derivatives.

caodac commented 10 years ago

Hi Oleg, we currently do not have an general approach to handle resonance beyond the standard aromaticity model. Do you have any recommendation here?

olegursu commented 10 years ago

The example above can't/shouldn't be handled by aromaticity models because it is not aromatic 8 pi electrons and breaks Huckel's rule, the non-substituted compound is unstable the substituted derivatives are most likely in form A according to experimental data. Considering how likely is to find these structures in a chemical library we can either ignore or add custom rule to transform form B to A if encountered.

caodac commented 10 years ago

Sure, we can make an exception in this particular case but is that sufficient? What about the general case of conjugate system in larger rings (e.g., clyclooctane)?

olegursu commented 10 years ago

I think we should make a distinction between aromatic resonance structures which can be identified using simple rules like Hukel's (or standard aromaticity model rules) and valence isomerism/tautomerism which aren't aromatic resonance structures like cyclooctatetraene or benzocyclobutadiene, or even more interesting flux structures like bullvalene, see http://onlinelibrary.wiley.com/store/10.1002/ijch.199900017/asset/199900017_ftp.pdf?v=1&t=hsi5rqrv&s=654aa96e799d8d90723fce232ecdf695f05b624e. Valence isomerism/tautomerism is beyond simple rules level of theory, we most likely need quantum ab initio methods to even consider handling these, if course if we find a particular example of valence isomerism/tautomerism which is frequent enough we can probably write rules to handle it.