ChemAxon Forum Archive » Structure manipulation: Canonicalization / standardization

Help to standardize

User dfeb81947d

14-12-2005 15:50:25

Dear Support,





I want to transforme C-PO4²- into C-PO4H2


transforme C-NH2+-C into C-NH2-C


and C=NH+-C into C=NH-C





I add in a xml file (for standardization):


Code:
   <Reaction ID="phosphate" Structure="[O-:2][P:1][O-:3]>>[H:5][O:2][P:1][O:3][H:6]"/>


   <Reaction ID="ammonium" Structure="[H:3][N+:1][H:2]>>[H:3][N:1][H:2]"/>






is it correct?





Thank you for your help


Warmest Regards


Jacques

ChemAxon d76e6e95eb

14-12-2005 17:27:07

Quote:
I want to transforme C-PO4²- into C-PO4H2
I propose to have the single PO- ion neutralization twice to neutralize all ions in the following compound:





CCCCCCCCCCCC(=O)SCC\N=C(/O)CC\N=C(/O)[C@@H](O)C(C)(C)COP([O-])(=O)OP([O-])(=O)OC[C@@H]1O[C@H]([C@H](O)[C@@H]1OP([O-])([O-])=O)n2cnc3c(N)ncnc23





Code:
<Reaction ID="phosphate" Structure="[O-:2][P:1]>>[O:2][P:1]"/>


<Reaction ID="phosphate" Structure="[O-:2][P:1]>>[O:2][P:1]"/>



Quote:
transforme C-NH2+-C into C-NH2-C
This seems valence problematic case, I assume, that you need C-NH-C in the end.
Quote:
and C=NH+-C into C=NH-C
Same as above, you probably need C=N-C, don't you?

User dfeb81947d

15-12-2005 10:01:51

Dear Gyuri,





I'm sorry I meant of course C-NH-C and C=N-C.


in that case I would have:


Code:



<Reaction ID="ammonium" Structure="[C:3][N+:1][C:2]>>[C:3][N:1][C:2]"/>


<Reaction ID="ammonium" Structure="[C:3]=[N+:1][C:2]>>[C:3]=[N:1][C:2]"/>






is that exact?





Thank you so far for your help





Kind Regards


Jacques

ChemAxon d76e6e95eb

15-12-2005 16:02:01

I suppose that this will neutralize all kind of ammonium ions:





Code:
<Reaction ID="ammonium" Structure="[N+:1][H:2]>>[N:1]"/>






Please do not forget, that counterions often appear in ammonium compounds. See general and specific counterion removal examples here:


http://www.chemaxon.com/jchem/doc/user/Standardizer_files/examples/Examples.html#08


http://www.chemaxon.com/jchem/doc/user/Standardizer_files/examples/Examples.html#20

User dfeb81947d

16-12-2005 09:52:55

thank you for your help.





Warmest regards