Aromaticity detection problems in thermo?

[rwest]

Compare the thermo for the kekulized benzene
http://rmg.mit.edu/database/thermo/molecule/1%20C%200%20%7B2,S%7D%20%7B6,D%7D%0D%0A2%20C%200%20%7B1,S%7D%20%7B3,D%7D%0D%0A3%20C%200%20%7B2,D%7D%20%7B4,S%7D%0D%0A4%20C%200%20%7B3,S%7D%20%7B5,D%7D%0D%0A5%20C%200%20%7B4,D%7D%20%7B6,S%7D%0D%0A6%20C%200%20%7B1,D%7D%20%7B5,S%7D%0D%0A

with the aromatic version
http://rmg.mit.edu/database/thermo/molecule/1%20C%200%20%7B2,B%7D%20%7B6,B%7D%0D%0A2%20C%200%20%7B1,B%7D%20%7B3,B%7D%0D%0A3%20C%200%20%7B2,B%7D%20%7B4,B%7D%0D%0A4%20C%200%20%7B3,B%7D%20%7B5,B%7D%0D%0A5%20C%200%20%7B4,B%7D%20%7B6,B%7D%0D%0A6%20C%200%20%7B1,B%7D%20%7B5,B%7D%0D%0A

Not sure how widespread this is, or what the consequences are for building models.
(Does it depend on how we define our reactants?)

What if we make an aromatic thing via reactions from non-aromatic things - do we detect it?

[jwallen]

My understanding is that aromaticity perception in RMG-Py is somewhere between incomplete and nonexistent (or maybe sitting on an unmerged branch somewhere?), hence the problem. Probably porting over the RMG-Java algorithm as-is would be a reasonable start.

[connie]

Was an aromaticity perception function ever written on the QMthermo branch?

[nickvandewiele]

at least not by me.

On Fri, Jan 18, 2013 at 5:21 PM, Connie Gao notifications@github.comwrote:

Was an aromaticity perception function ever written on the QMthermo branch?

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Reply to this email directly or view it on GitHubhttps://github.com//issues/106#issuecomment-12429195.

e-mail: nickvandewiele@gmail.com
phone: +32 478 46 18 56

[rwest]

Nor by me.
Where did your aromaticity stuff get to @nickvandewiele? Was it all in Java?

[rwest]

Now that we are incorporating RDKit and relying on it quite heavily (on a topic branch, soon to be merged - #135) I wonder if it would make sense to use their aromaticity perception code? I think we should at least look into it.

[connie]

Any updates on what to do regarding aromaticity perception? At this point we have removed all aromaticity (no Cb bonds are kept), so we are no longer picking up benzene thermo nor aromatic-specific kinetics. Another question is- after kekulization of benzene, do we always allow RMG to pick up regular single/double bond kinetics even though it is benzene?

[rwest]

The ability to react aromatic bonds is no worse than it was - just specify the Cb bonds in adjacency list format not SMILES. However, that ability is not great. We don't perceive aromaticity, and cannot make benzene from scratch.

[connie]

Currently closed via #322