Aromaticity

[From a user email...]





What exactly are your rules for aromaticity perception? I am interested in the programmatic rules embedded in JChem so that I can predict whether JChem will treat a particular bond as aromatic or not.

We provide two different aromatization algorithms:





1. ChemAxon type(in-house method):


Locate all rings in the molecule under a limit (Eg: ring size < 18).

Code:

Do    If the ring is aromatic set the bonds to aromatic. until aromatic rings found. The ring is aromatic if: ●   ring size > 4 ●   the atoms in the ring     ●   are  B, C, N, O, Si, S, Se, Te, P, As,     ●   has max 4 ligand     ●   has 1 double bond in the ring     ●   or has no double bond in the ring but the atom can donate electron or free orbit ●   4n +2 Huckel law is fulfilled OR ●   has only aromatic bond ●   azulene type

2. Daylight type(aromatization similar to the one used in the Daylight toolkits and DayCart):


is implemented according to: http://www.daylight.com/smiles/smiles-convent.html#AROM

Why is the following structure with 22 pi electrons not aromatic in JChem/Marvin?

Chemaxon type:


Only ring size under 18 atom is considered during the calculation. This limit can be increased in the API.





Daylight type:


The daylight method works on SSSR so this molecule and even more the following one is not aromatic according to Daylight.


C1=CC2=CC=C3C=CC4=CC=C5C=CC6=CC=C1C7C2C3C4C5C67


(Tested on canonical SMILES generator:


http://www.daylight.com/daycgi_tutorials/cansmi.cgi)

Why is the bond shared by the size 7 and 5 rings aromatic? I would think that only the outer size 10 ring bonds are aromatic.

Special rule is introduced to treat this ring system as aromatic in ChemAxon type aromatization.


The reason for this:


(From http://www.uea.ac.uk/~c286/aromaticnotes.htm)


"An interesting non-benzenoid aromatic compound is Azulene, which has large resonance energy and a large dipole moment."

guest wrote:

Why is the bond shared by the size 7 and 5 rings aromatic? I would think that only the outer size 10 ring bonds are aromatic.

You can draw a series of strongly contributing resonance structures in which one of the C atoms in the 7-membered ring is cationic and one of the C atoms in the 5-membered ring is anionic. In many of these resonance structures, the ring-fusion bond is written as a double bond. So it is perfectly appropriate to treat that bond as an aromatic bond when aromatizing azulene.

Bob,





Thank you for the confirmation!





Szabolcs