pyrrole hydrogen dissappearing in reaction

Hello All,

we use react to generate fused molecules from heterocycles. And we have a problem of Hydrogens of N disappearing in the pyrroles. For example:

 Using a reaction defined in file "ring_fusion.smarts"

[c:1][c:2][c:3]([H:12])[c:4][Mg:5].[c:6][c:7][c:8]([H:13])[c:9]([Mg:11])[C,c
,s,n&H1,n&D1,n,o,se,Se,SiH2:10]>>[c:1][c:2][c:3]([C,c,s,n&H1,n&D1,n,o,se,Se,
SiH2:10])[c:4][c:7][c:6]

and reactants "reactant1.smiles"

c1([Mg])ccc([Mg])[nH]1

we do a reaction (with canonical smiles output) as follows:

react -r ring_fusion.smiles reactant1.smiles reactant1.smiles -f smiles:u

and the product is:

[Mg]c1c-c2[nH]c([Mg])cc2-n1

The problem is that one of the Hydrogens on the N of pyrrole rings of the product dissappears. I was wondering if you have any suggestions to fix this problem?

Many thanks,

Shule.

Hi,

The forming bonds between atoms 3-10 and 4-7 (numbers are atom maps) on the product side are "single or aromatic" bonds. These bonds are not present on the reactant side, so they cannot be query bonds. If these bonds are replaced with aromatic bond, then the reaction will work as expected:

$ react -r "[c:1][c:2][c:3]([H:12])[c:4][Mg:5].[c:6][c:7][c:8]([H:13])[c:9](-,:[C,c,s,nH1,nD1,n,o,se,Se,SiH2:10])[Mg:11]>>[c:1][c:2][c:3](:[C,c,s,nH1,nD1,n,o,se,Se,SiH2:10])[c:4]:[c:7][c:6]" "c1([Mg])ccc([Mg])[nH]1" "c1([Mg])ccc([Mg])[nH]1"
[Mg]c1cc2[nH]c([Mg])cc2[nH]1

If "single or aromatic" bond is used instead of aromatic, then single bond will appear in the product.  The hydrogen disappeared because an inconsistent aromatic ring was formed.

Zsolt

thank you Zsolt, this was very helpful!

Shule.