valence check problem? - "Inconsistent molecular structure"

User d664bc87ea

29-08-2012 10:37:01

MarvinView throws "Inconsistent molecular structure." messages for the structure in 
the attached mol file.

As we know, in case of mol v2000 format implicit hydrogens should be
added to atoms having a bond valence less than the lowest possible
valence state. (Bond valence is the sum of bonds weighted with bond
orders.) Therefore, the I atom has an implicit H atom and has a
correct valence state.

Product Version: MarvinView 5.10.3
Build Date: 2012-08-13
Internal build id: 5.10.3_b102
Operating System: amd64 Linux 3.0.0-19-generic
Java: Sun Microsystems Inc. Java 1.6.0_23

ChemAxon 25dcd765a3

31-08-2012 12:15:00

Hi,



As we know, in case of mol v2000 format implicit hydrogens should be
added to atoms having a bond valence less than the lowest possible
valence state.


Actually, what I know is that v2000 format does not handle the implicit Hydrogens so it should be calculated somehow, but it is not mentioned how to calculate it in the ctfile.pdf. Please let me know if you find some info about this. So we are using our algorithm to decide if we can add some implicit Hydrogen to the atom or the atom has valence error.


In this specific case the Iodine atom can have 3 valence if it has connection to some electronegative atom like Cl or O, but otherwise we think that the Iodine should get valence error. Please let me know if you find a structure which exists and does not fit into this rule. Is your attached structure exists chemically?


So in this case the valence error is the the correct solution.