dan2097 / opsin

Open Parser for Systematic IUPAC Nomenclature. Chemical name to structure conversion
https://opsin.ch.cam.ac.uk
MIT License
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O-methyl phenylphosphonothioic chloride - expected methyl ester, got trivalent chlorine #250

Open IngvarLa opened 8 months ago

IngvarLa commented 8 months ago

O-methyl phenylphosphonothioic chloride results in C[ClH]P(=S)(C1=CC=CC=C1)Cl

I had expected: COP(=S)(C1=CC=CC=C1)Cl

but I may be wrong, ChemDraw gave me: OP(C1=CC=CC=C1C)(Cl)=S

which also looks strange.

originally from a patent with 0 in place of O US04115557A EXAMPLE I

IngvarLa commented 8 months ago

O-(1-Methyl-2-methoxycarbonylvinyl) 4-Bromophenylthionophosphonic monochloride is another example where I get confused, I thought the O- should indicate that there is a P-ester, but I get a trivalent Cl CC(=CC(=O)OC)[ClH]P(O)(=O)C1=CC=C(C=C1)Br I was hoping for: CC(=CC(=O)OC)OP(Cl)(=O)C1=CC=C(C=C1)Br

IngvarLa commented 8 months ago

Another example - this one ChemDraw gets what I expect: phenyl (benzyloxy-glycinyl)-phosphorochloridate Opsin gives: C(C1=CC=CC=C1)ONCC(=O)[ClH]P(OC1=CC=CC=C1)([O-])=O ChemDraw: O=P(OC1=CC=CC=C1)(Cl)OC(CNOCC2=CC=CC=C2)=O

dan2097 commented 8 months ago

O-(1-Methyl-2-methoxycarbonylvinyl) 4-Bromophenylthionophosphonic monochloride is another example where I get confused, I thought the O- should indicate that there is a P-ester, but I get a trivalent Cl CC(=CC(=O)OC)[ClH]P(O)(=O)C1=CC=C(C=C1)Br I was hoping for: CC(=CC(=O)OC)OP(Cl)(=O)C1=CC=C(C=C1)Br

I presume you meant CC(=CC(=O)OC)OP(Cl)(=S)C1=CC=C(C=C1)Br ?

Another example - this one ChemDraw gets what I expect: phenyl (benzyloxy-glycinyl)-phosphorochloridate Opsin gives: C(C1=CC=CC=C1)ONCC(=O)[ClH]P(OC1=CC=CC=C1)([O-])=O ChemDraw: O=P(OC1=CC=CC=C1)(Cl)OC(CNOCC2=CC=CC=C2)=O

This example is more difficult to fix. In the first two cases conceptually the OH groups have already been substituted so definitely cannot be turned into chlorine, but in this example strictly speaking we're substituting phosphorochloridate which is P([O-])([O-])(=O)Cl. phenyl (benzyloxy-glycinyl) phosphorochloridate gives the expected interpretation

IngvarLa commented 8 months ago

Thanks Daniel. Yes, obviously meant the sulfur analog.
So, in phenyl (benzyloxy-glycinyl)-phosphorochloridate there is a bonus '-', as that should be rather rare I can add it to one of our dictionaries.