Aromatic Conversions

Aromatic Conversions & Limitations

Aromatic Conversions

The SMILES interpreter in the EPI Suite programs will convert certain aliphatic rings to aromatic rings if aromaticity is detected.  For example, the following conversions are made:

C1=CC=CC=C1 --->  c1ccccc1 (benzene)

N1C=CC=C1   --->  n1cccc1  (pyrrole)

O1C=CC=C1   --->  o1cccc1  (furan)

S1C=CC=C1   --->  s1cccc1  (thiofuran)

N1=CC=CC=C1 --->  n1ccccc1 (pyridine)

NOTE:   The carbonyl function, -C(=O)-, SHOULD be entered in upper case at ALL times...all ring members of a ring containing  -C(=O)-  SHOULD be entered in upper case  with the exception of members of a fused aromatic ring.  Carbonyl containing rings are considered as aliphatics by the EPI Suite SMILES interpreter...keto rings are aliphatic while the enol-form may be aromatic.   See the tautomer help topic for additional information.

Concerning differences with other SMILES interpreters:  the EPI Suite interpreter will never convert a C=O entry to an aromatic c=O.  The current EPI Suite SMILES interpreter has the ability to “kekulize” most aromatically designated rings that contain a carbonyl group ... in fact, any ring that is entered with an aromatic carbonyl (c=O) must be kekulized by the SRC SMILES interpreter before the structure can be evaluated.  For example, the SMILES notation for Maleic Hydrazide (using aromatic carbonyls) can be:

O=c1ccc(=O)[nH][nH]1

The EPI Suite SMILES interpreter automatically “kekulizes” the SMILES to the following:

O=C1C=CC(=O)NN1

The current EPI Suite SMILES interpreter will kekulize ring contain an aromatic carbonyl.

Aromatic Limitations

Certain valid aromatic structures are flagged as "Illegal Structures" by some of the EPI Suite programs.  This is because the estimation techniques used by the program can not evaluate that type of structure.  An example is the compound azulene which is comprised of a fused 7-member ring and a 5-member ring.  It is flagged as illegal by some (but not all) EPI Suite programs because a 7-member aromatic was found.  Currently, some (but not all) EPI Suite programs will not accept an aromatic ring with 7 or more ring-members.  Some estimation methods have not been extended to include 7-member aromatic rings due to lack of data. Azulene (and similar structures), can be estimated by entering the “upper case” (aliphatic) SMILES (e.g.  C1=CC=C2C=CC=C2C=C1).