User 7c5047cd7b
15-10-2005 09:51:18
Hello
I would like to hear your suggestion about a standardizer's rule.
The attachment is including rule1.xml, Q1.mol
Please test the following command:
standardize -c rule1.xml Q1.mol -f mol -o 1.mol
I would appreciate you delete Reaction ID="1-E" and test again.
You would find the Q1.mol be changed by the rule.
Reaction ID="1-E" is a EXACT type rule.
It should not change the Q1.mol.
I would like to know the reason.
Best regards
Alex
ChemAxon fb166edcbd
17-10-2005 13:25:49
This seems to be a bug in our molecule handling, although the input structure Q1.mol is strange because of the C- atom in the benzene ring. We will investigate the problem and let you know the result.
User 7c5047cd7b
17-10-2005 14:17:02
Hello Nora
The question and the mol came from one of our customers.
Thank you for your help.
ChemAxon d76e6e95eb
18-10-2005 13:01:38
The implicit hydrogen calculation for your structure is problematic, since your compound is probably not correct.
http://mbm.snu.ac.kr/journal/61-NpBz.pdf
http://www.sfu.ca/chemistry/students/courses/chem260/labs/Chem%20260%20Laboratory%204.pdf
We found some literature references to the benzene anion radical, but it is different from your structure. It contains hydrogen atom on each carbon. The plus electron is probably located on a LUMO orbital, which might be stabilized in some complexes.
Your structure is probably a typo, and even the corrected version is unlikely to appear in a registration database which is the main focus of standardization.
User 7c5047cd7b
19-10-2005 01:09:19
Hello Gyuri
Thank you for your information.
Regarding the structure, I will discuss with the customer.
I would like to know
why the rule(Reaction ID="1-E") changed the structure.
It is an EXACT type rule.
It should not change the structure.
Best Regards
ChemAxon fb166edcbd
19-10-2005 11:39:31
The reason is technical: for EXACT type transformations, Reactor should process the reaction for each molecule fragment separately, and finally fuse the parts. This process - although in our case no transformation is performed and the original molecule should be obtained at the end - changes this molecule because a valence check is made some time during the process.