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Chemical terms pKa structure result
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Michael

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Link to postPosted: Tue Jul 05, 2016 2:02 amPost subject: Chemical terms pKa structure result Reply with quote

I'm trying to get a chemical term (IJC, 16.4.11.0) to return the equivalent of JChem for Excels JCpKaImage. Any help would be appreciated. I've got  majorMicrospecies("7.4") to return a structure, but would like to see the pKa values and sites as I can do in JChem for Excel. Any help would be appreciated.

Mike

Ondrej
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Link to postPosted: Thu Jul 07, 2016 2:28 pmPost subject: Reply with quote

Hi Mike,

can you attach a screenshot from JChem 4 excel so that I can quickly get an idea about what you are trying to accomplish?

 

thx,

Ondrej

Ondrej
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Link to postPosted: Thu Jul 07, 2016 3:05 pmPost subject: Reply with quote

Hi Mike,

I opened some example file with JCpKalmage and saw there basically calculation of strongest acidic and basic dissociation constants. I am not sure whether this is what you are interested in, but anyway:

acidicpKa("1") returns the strongest pKa

basicpKa("1") returns the strongest pKb

 

see also the description of various chemical terms at https://docs.chemaxon.com/display/docs/Functions+by+Categories

Michael

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Link to postPosted: Thu Jul 07, 2016 11:13 pmPost subject: JCpKaImage example Reply with quote

See the attached example of the JCpKaImage function. Basically just trying to give visual representation of predicted pKa values and the functional groups associated with the values.

Ondrej
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Link to postPosted: Fri Jul 08, 2016 9:42 amPost subject: Reply with quote

Dear Mike,

If you intend to have structure image containing values for particular functional groups, I am afraid this is not easy. Anyway, do you want to do this within Instant JChem or standalone?

Ondrej
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Link to postPosted: Fri Jul 08, 2016 1:11 pmPost subject: Reply with quote

Dear Mike,

at the moment we cannot display this in the IJC gridview. What you can do is the following:

1) double click on the molecule

2) go to calculations -> protonation -> pKa

3) set the options and see the results

You could for example save the result as some image file.

 

The alternative way is to use molmatrix widget. Currently it is limited to show only one field,

so you can display eg a molecule with strongest acidic pKa. This is probably not what you would prefer,

but it is the solution we have now.

 

Would an extension like in JChem for Office very important for you? If so, we may consider the implementation in the future.

 

Michael

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Link to postPosted: Mon Jul 11, 2016 2:51 amPost subject: Reply with quote

Thanks Ondrej,

This confirms my suspicion that it isn't possible. I do find the JChem 4 Excel pKaImage function very useful as it links the predicted pKa values to specific functional groups. In simple cases, the location of ionization is obvious, but that's not always the case. For now, the majorMicrospecies function (eg showing ionization at a given pH) is the most suited to this task.

Would be great if pKaImage or similar were available in future releases of IJC.

Mike

Ondrej
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Link to postPosted: Mon Jul 11, 2016 2:58 pmPost subject: Reply with quote

Dear Mike,

 

we have discussed internally pKaImag. We think this is a potentially useful feature not just for you but also for other clients. We will add it to the list of improvements. However, currently we are quite loaded by other issues, so I cannot promise you when you can expect this feature in IJC.

Ondrej

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