How tautomers are defined by JChem

Hi all,

We have two structures (see files attached)

they are not tautomers from our chemists point of view.

but JChem cartridge considers that they are.

      select jc_compare((select structure from chem_structs where unit_id = -1016662343), 


      (select structure from chem_structs where unit_id = 345198431), 't:d tautomerSearch:y') from dual; 

returns 1

while

select jc_compare((select structure from chem_structs where unit_id = -1016662343), 


      (select structure from chem_structs where unit_id = 345198431), 't:d') from dual; 

returns 0

 

The environment is the following:

Oracle environment: 


Oracle Database 11g Enterprise Edition Release 11.2.0.4.0 - 64bit Production


PL/SQL Release 11.2.0.4.0 - Production


CORE	11.2.0.4.0	Production


TNS for Linux: Version 11.2.0.4.0 - Production


NLSRTL Version 11.2.0.4.0 - Production






JChem owner: JCHEM_GG_EDITORIAL






JChem Server environment: 


Java VM vendor: Oracle Corporation


Java version: 1.7.0_67


Java VM version: 24.65-b04


JChem version: 15.1.12.0


JChem Index version: 14102000


JDBC driver version: 11.2.0.3.0

Could you please comment on this. Is it a bug that they're considered tautomers or we're doing something wrong?

Thanks

Hi,

Jchem search using a generalized form of all tautomers during search. 

I have checked the all tautomer set of -1016662343.mol and found that 345198431.mol is not part of that tautomer set. So, as far as I see it is a bug in the generalization algorithm. However, to improve the generalization algorithm, or better to say, change it completely is a huge amount of work and we don't have currently the capacity to work on that. We actually have an idea how to improve it, so it may happen in the future, but this task has low priority currently.

Hi,

I have to correct myself as one of my colleague have checked in more detail the all tautomer set of -1016662343.mol and found that 345198431.mol is part of that tautomer set. In this case the generalization improvement I was talking about does not help at all...

Dear Alena, 

The two molecules you sent us are tautomer forms of each other in our model, which means that our tautomerization algorithm can transform the first into the second by re-placing the double bonds and protons. Our algorithm examines the possibility of protomer transformations and decided based on this if the two molecules are tautomer forms. So this should not be considered as a bug based on the tautomerization model.

However, in the chemical practice, these two forms should not be considered tautomers, so there is no chemical equilibrium between them.

I would also like to mention that our tautomerization model will be improved in the future. We will notify you about the improvements.  

Best regards, 

Daniel

Hi Daniel, volfi,

 

Thanks a lot for the detailed explanation. We'll be waiting for the news)

 

Regards,

Alena