On 08/07/14 15:40, Greg Landrum wrote:
Hi Paul,
On Tue, Jul 8, 2014 at 2:55 PM, Paul Emsley <[email protected]
<mailto:[email protected]>> wrote:
I'm struggling to understand aromatic bond assignment. Are the
rings of flavin aromatic? I think that the answer to that is
probably yes, but what does that mean? I thought that a 6-membered
ring was considered aromatic if all of the bonds of the ring were
aromatic. Is this correct? Should I instead check for aromatic
systems by looking at the atoms of rings (instead of the bonds of
rings)? The RDKit-generated SMILES string seems to suggest
aromatic rings. I am confused.
Ah, the joys of aromaticity in "odd" systems.
This is one of the unusual cases where the RDKit documentation is
actually fairly complete. Here's the explanation of how aromaticity
works: http://rdkit.org/docs/RDKit_Book.html#aromaticity
For flavin, neither the rightmost ring (in your drawing) nor the
central ring are considered aromatic: neither satisfies the 4N+2 rule.
(The central ring has 7 pi electrons, the right ring has 5 pi
electrons). However, the two rings together form a conjugated ring
with 10 pi electrons. This ring is aromatic so all of the bonds
involved in forming the ring are aromatic. The bond connecting atoms
C4X and C10 is not aromatic because it's not part of an aromatic ring
(it's the "bonds between aromatic atoms do not need to be aromatic"
case). This last bit about the order of that bond seems "somewhat"
pedantic, but it is important for molecules like
9,10-dihydrophenanthrene
(http://www.chemspider.com/Chemical-Structure.12515.html), where the
bond connecting the two aromatic rings is certainly not itself aromatic.
Make sense?
Yes. Thanks. I shall think deeper and read further next time.
Paul.
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