Given an atom in a molecule, how do I know whether it is aliphatic/aromatic? I know that stuff like benzene becomes more stable due to delocalized pi-bonds and is thus called ‘aromatic’.
But from a molecular graph perspective, given a bunch of atoms connected together how do I know whether a node is aliphatic/aromatic?
rajarshi guha
[ Editor ]
from Bethesda, United States of America
You’d need to perceive aromaticity, after which individual atoms/bonds can be identified as aromatic or non-aormatic. See http://www.dalkescientific.com/writings/diary/archive/2007/11/30/opensmilesandaromaticity.html for a discussion
wdiwdi
[ Editor ]
from Frankfurt am Main, Deutschland
Rajarshi already gave some good advice in his post.
Basics are ring detection, electron assignment (formal charges, bond electrons, pi electrons, free electron pairs, relative orientation of pi systems if you want to be fancy) and the Huckel rule.
Whether not(aromatic) is the same as aliphatic, depends on the definition of your system. There is also anti-aromaticity as a separate concept from non-aromaticity,and of course in the real world, it is all a question of energies.
And no, aromaticity determination algorithms vary quite a lot in what kind of corner-case systems they perceive as aromatic. The Daylight system is actually quite an evil one, but if you are doing SMILES/SMARTS, you cannot simply replace it by a more sane definition for reasons of compatibility.
This is not a question. Could you update the title to be a question?