RE: [InChI-discuss] InChI standard valences?

[Wolf-D. I. <wd...@xe...>]

W. D. Ihlenfeldt
Xemistry GmbH
wd...@xe...
  

> -----Original Message-----
> From: inc...@li... 
> [mailto:inc...@li...] On Behalf 
> Of Reinhard Dunkel
> Sent: Tuesday, March 07, 2006 12:35 PM
> To: inc...@li...
> Subject: [InChI-discuss] InChI standard valences?
> 
> I am looking at Appendix 1 "InChI Standard Valences" of "The 
> IUPAC Chemical Identifier - Technical Manual". Very useful! 
> So N and O+ can have three valences. But how could they also 
> have five valences, as stated? Wasn't it called the "Octet 
> Rule": atoms in the periodic system row Li through Ne can 
> have a maximum of four bonds? PubChem strictly specifies an 
> -NO2 group with separated charges, instead of two double 
> bonds to both oxygens. 

That is how we store and output it, because this is the propert valence
without violating the octet rule. For queries etc. it does not make any
difference - the query processor automatically compensates.

I don't remember having seen an O+ 
> specified with five valences.
> 
> Surprising is also that Appendix 1 specifies an uncharged S 
> with four valences should not be bonded to a hydrogen (marked 
> with a star in the appendix). Bleomycin
> (http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=2411)
>  would violate this assumption. 

That structure is certainly miscoded in PubChem. That should be an S+.
Surprisingly, it seems that all of the 3 depositors (Chembank, DTP, ChemDB)
have actually submitted that cpd without proper charges, meaning all have
this error in their original database.

Nevertheless, thanks for bringing this to our attention - the structure
standardizer should be smart enough to fix this automatically for the
standardized structures (CID records). This type of S environment is pretty
unambigous and adjusting the charge should be straightforward. 



Do these "Standard Valences" 
> influence a created InChI?
> 
> ThanX
> Reinhard
> 
> 
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