Using SMIRKS having atom mapclass in Reactor

User a52207e61b

07-05-2010 20:47:46

I tried to use this SMIRKS 


[a:1]([*:2])1[a:3]([*:4])[a:5]([*:6])[a:7]([*:8])[c]([OH])[c]([OH])1>>[a:1]([*:2])1[a:3]([*:4])[a:5]([*:6])[a:7]([*:8])[c](=O)[c]([OH])[c]1


on this SMILES 


OC1=C(O)C2=C(C=C1)C=CC1=C2C=CC=C1.


Daylight's interface generates the exact product I expect. I tried using SMIRKS without mapclasses (essentially SMILES) and they work. Can someone please explain what the matter is or if Reactor and JChem can perform reactions using SMIRKS?

ChemAxon d76e6e95eb

10-05-2010 07:14:57

Any atoms does not match hydrogens, so you might consoder to remove them or replace them. The mapping is not complete, but OK, since Reactors internal automapper corrects it. However, the reaction itself seems a bit strange for me, are you sure, that you expect that 7 member ring as aromatic?

ChemAxon e08c317633

10-05-2010 07:53:54

Gyuri is right about the 7-membered aromatic ring, but if you want to go with this, then the correct form of the reaction is:


[*,#1]a:1:a([*,#1]):a([*,#1])[c:4]([O:5][H:6])[c:3](O[H]):[*:2]:1[*,#1]>>[*,#1][*:2]:1:[c:1][c:3](O[H])[c:4](=[O:5]):a([*,#1]):a([*,#1]):a:1[*,#1]

Note: only changing atoms are mapped.


Reactor generates two results:


react -r "[*,#1]a:1:a([*,#1]):a([*,#1])[c:4]([O:5][H:6])[c:3](O[H]):[*:2]:1[*,#1]>>[*,#1][*:2]:1:[c:1][c:3](O[H])[c:4](=[O:5]):a([*,#1]):a([*,#1]):a:1[*,#1]" "OC1=C(O)C2=C(C=C1)C=CC1=C2C=CC=C1"
Oc1cc2c(ccc3ccccc23)ccc1=O
Oc1cccc2ccc3ccccc3c2c1=O

 Zsolt