Inconsistent molecular structure error

Dear support,








I have this following error during LogP calculation for some structures :














Inconsistent molecular structure























Kiet

The "Inconsistent molecular structure" message indicates an error in the input molecule. In the attached test5.mol there is a valence error in the molecule (see the attached image, the nitrogen with valence error is underlined in red). If the input molecule is inconsistent, then logP can not be calculated.





Zsolt

I have the same error with the structure : test.mol





because Of The S which has 3 valence instead 2 or 4. However the H associated to S atom is implicit so the S has well 4 valence. Why do Chemaxon tools give me error?





The implicit H is bad interpreted by Chemaxon tools?

Hi,








1. The nitrogen ligand that has valence error have to have "+1"  formal charge because its lone-pair is donated into the 'd-hybrid' shell of the given Pt atom.





So, If you adjuste "+1" formal charge on that nitrogen atom then the valence error will disappear.








2.Setting of "+1" formal charge for sulfur atom may be  an adequate solution for your second compound as well.








Adding of an implicit "H" ,of course ,  will resolve the valence error.  Unfortunately this "H" addition is not possible now.





We are going to fix this problem asap.











Thanks for reporting problems.








Jozsi

Hi,

Quote:

However the H associated to S atom is implicit so the S has well 4 valence. Why do Chemaxon tools give me error?

Would you please send us a reference that proves the existance of compounds including a Sulfur atom with 4 single bonds? We don't think it exists, and unless this we do not intend to change the valence check algorithm.





Sulfur atoms with 3 single bonds usually have a positive charge, but AFAIK the three substituents in this case are alkyl groups or hydrogens, and in your test.mol compound there is a hydroxyl group, which I don't think is stable with a positive charge (would form a sulfoxy group immediately I suppose). So setting a positive charge is probably closer to reality, but still questionable.








Best regards,





Akos

Sulfur dioxide : sulfur with 4 valences

Quote:

Sulfur dioxide : sulfur with 4 valences

But I mean Sulfur with 4 single bonds.

Hi,














Sulfurane derivatives are typical representatives of the 4-single-bonded sulfur compounds.














Jozsi

Thanks Jozsi to take my attention to the sulfuranes. Unfortunately, I don't think they prove that we should add an implicit hydrogen to SR3 substructures. E.g. I found  the following info in an article at Encyclopedia Britannica:





"The s-sulfuranes, sulfurane S-oxides, and persulfuranes are termed hypervalent compounds because their valences are expanded beyond eight. Because of this fact, these types of compounds are relatively unstable, with the central atom seeking to return to the octet state by extruding one or more ligands."





Or do you think we should support hypervalent compounds in our valence check?








Best regards,





Akos

Ok for the S linked to 4 simple bonds.





But what about S linked to 1 double bond and 2 single bonds (with 1 bond implicit with H)? I have example of structures.

Some further info from an article:





"Many examples for tetracoordinated sulfur compounds are known from the literature, for instance, the classic fluorinating agent sulfur tetraÑuoride and the related organosulfur trifluorides which can be prepared by exchange reactions with free or silylated alcohols or amines. Also oxochloro- and azachlorosulfuranes can be obtained by the reaction of the respective alcohol or amide with t-butyl hypochlorite. All of these compounds are stabilized by highly electronegative substituents, i.e., they have significant ionic character.


Only very few reports describe the spectroscopic signatures characteristic for the formation of delta-sulfuranes with purely organic substituents. Some evidence for the existence of tetraphenyl sulfurane and the related 2,2'-biphenylylene diphenyl sulfurane comes from low temperature NMR experiments.


It appears that thermodynamic stability can be achieved if SR4 compounds contain polarized bonds. This effect is probably due to the ability of r-electron withdrawing groups (Hal, OR, Ph) to remove some of the electron density from sulfur, reducing the repulsion between the bonds and the lone pair."





It is also against the existense of S-H bonds in these compounds.

Quote:

Ok for the S linked to 4 simple bonds. But what about S linked to 1 double bond and 2 single bonds (with 1 bond implicit with H)? I have example of structures.

Yes, please send examples (or references). Thank you in advance.





Best regards,





Akos

example:

Hi,

Quote:

Or do you think we should support hypervalent compounds in our valence check?

This is supported by Marvin's valence check for a long time. (may be not completely)








I think the "SHR3"  type structure can exist.  So I would not exclude the "S-H"  bond in the "SR4" type strucutres.








Jozsi

In the last example, the H linked to the sulfur is implicit. Normally this atom was not drawn but as Marvin warned ther is an valence error, I have to draw the H bond.

Hi,








The valence error can be resolved by adding a "H" atom or a "+" charge or even to set a radical electron for the sulfur atom.








I think the best valence form can be created by adding a "+" charge to the sulfur atom. Because  this "+" charge can be stabilized by resonance.














Jozsi