calculating logD at a specific electrolyte concentration

Quick (hopefully) question from a newbie:

 

I am trying to calculate the logD at electrolyte concentrations different from the default 0.1 mol/L for Cl- and Na/K+. But how would I add the corresponding query? If I am simply using logd('7.4') as a chemical term, I get the results for the default electrolyte concentrations at pH7.4.

 

Works perfectly fine in Marvin Sketch if I go to Calculations->Partitioning->logD->General Options and fill in the two fields for both elektrolyte groups. But I have quite a few chemicals to go through and I would like to avoid having to calculate each logD manually.

 

Thomas

Dear Thomas,

if I understand well, go in gridview >add new chemical terms field> choose logD >  change  logd('7.4') to

logd('pH you calculate')

Another possibilities you can find in following documentation Partitioning Functions

Hope it help.

Best Regards

Bastik

Sorry, but I don't think that is what I'm looking for. Changing logd('ph7.4') to e.g. logd('pH8.0') would allow my to calculate the logD for all chemicals in the grid at pH8.0 - but still at a Cl concentration of 0.1 mol/L and a Na/K concentration of 0.1 mol/L. However, I need to calculate the logD at different electrolyte concentrations.

 

How would I achieve that for the whole list of chemicals that I'm working on? Say, for example: how would I calculate the logD at pH8.0 for a Cl concentration of 1 mol/L and a Na/K concentration of 2 mol/L?

 

Thomas

ThomasBackhaus wrote:

How would I achieve that for the whole list of chemicals that I'm working on? Say, for example: how would I calculate the logD at pH8.0 for a Cl concentration of 1 mol/L and a Na/K concentration of 2 mol/L?

It is the Chemical Terms expression you need:

logd("8.0","anion:1 kation:2")

See also http://www.chemaxon.com/marvin/help/chemicalterms/EvaluatorFunctions.html#notes

Unfortunately, the 1 mol/l and 2 mol/l concentrations are out of the range we support:

  -a, --anion                    <Cl- concentration>

                                 (default: 0.1, range: [0.0, 0.25])

  -k, --kation                   <Na+ K+ concentration>

                                 (default: 0.1, range: [0.0, 0.25])

HI,

 

Sorry for the late reply, but thanks! That was exactly what I was looking for.

It's a bit of a pity that JChem doesn't support higher electrolyte concentrations, though. I'm trying to calculate the logD in seawater. Not sure how exotic that is, but perhaps it would be an idea to see whether the range of electrolyte concentrations could be extended in a future JChem version.

 

Best wishes

Thomas