GreenGroup/RMG-Java — Issue #238: Resonance forms for benzyne and benzyne like molecules not identified
Author: gmagoon
Created: 2011-12-17 18:03:20+00:00
State: open

It seems that RMG won't recognize the following forms of following resonance forms as equivalent to one another, probably because 1. this case doesn't involve radical sites and 2. RMG only moves one pair of electrons at a time when generating the resonance isomers, when it would need to move three pairs in this case:

1 C 0 {2,S} {6,D} {7,S}
2 C 0 {1,S} {3,D} {9,S}
3 C 0 {2,D} {4,D}
4 C 0 {3,D} {5,D}
5 C 0 {4,D} {6,S} {11,S}
6 C 0 {5,S} {1,D} {8,S}
7 C 0 {1,S} {10,S} {12,S} {13,S}
8 H 0 {6,S}
9 H 0 {2,S}
10 H 0 {7,S}
11 H 0 {5,S}
12 H 0 {7,S}
13 H 0 {7,S}

1 C 0 {2,D} {6,S} {7,S}
2 C 0 {1,D} {3,S} {9,S}
3 C 0 {2,S} {4,T}
4 C 0 {3,T} {5,S}
5 C 0 {4,S} {6,D} {12,S}
6 C 0 {5,D} {1,S} {8,S}
7 C 0 {1,S} {10,S} {11,S} {13,S}
8 H 0 {6,S}
9 H 0 {2,S}
10 H 0 {7,S}
11 H 0 {7,S}
12 H 0 {5,S}
13 H 0 {7,S}

Probably the best approach is to fix this in some sort of future update to aromaticity perception/treatment.