pKa value

Plz suggest me how to find out the pKa value from its molecular structure

Hi,








Please visit these sites:


Here you can find information about the pKa calculation.


http://www.chemaxon.com/product/pka.html


http://www.chemaxon.com/marvin/chemaxon/marvin/help/pKa.html








At this site you can try the pKa calculator( Java required).


http://www.chemaxon.com/demosite/marvin/index.html





At this site you can download the Java to run Java applications, if it is not installed on your computer.


http://java.sun.com/javase/downloads/index.jsp








Jozsi

I have used this plugin on the demosite before easily, but now I am unable to get it to calculate the microspecies of choline or betaine (which I have done before). When I click the OK button it doesn't seem to do anything. If I uncheck the microspecies box, it pops up a window with the apparent pKa values, but it will not do it with microspecies checked. Edit: When I checked the console I see this message:





Java Plug-in 1.6.0_01


Using JRE version 1.6.0_01 Java HotSpot(TM) Client VM


User home directory = C:\Documents and Settings\Administrator





Exception in thread "Thread-98" java.lang.NoSuchFieldError: m


at chemaxon.marvin.calculations.pKaPluginDisplay.getResultComponent(Unknown Source)


at chemaxon.marvin.plugin.CalculatorPluginManager.a(Unknown Source)


at chemaxon.marvin.plugin.CalculatorPluginManager.a(Unknown Source)


at chemaxon.marvin.plugin.CalculatorPluginManager.a(Unknown Source)


at chemaxon.marvin.plugin.CalculatorPluginManager.callback(Unknown Source)


at chemaxon.marvin.plugin.PluginManager.callback(Unknown Source)


at chemaxon.marvin.common.swing.MolPanel.run(Unknown Source)


at java.lang.Thread.run(Unknown Source)








Yesterday the demo was behaving strangely with most of the menus garbled so I updated my Java to version 1.6.0 update 1 and that seemed to take care of the display problems, but I'm wondering if I am doing something wrong or whether the pKa plugin is broken? I am using WinXP Pro SP2 and IE7.

I could not reproduce this error.


Probably, it is a caching problem in your browser. There may be some deprecated classes in you browser/JRE cache that can cause the error (by mixing different versions of classes).


I suggest to delete the browser and the JRE cache, it may help.


See How I can clear JRE cache?

Deleting my IE cache files did the trick. Thanks.

Hello, please could you give some reference about how is the pK actually calculated in Marvin? Is it based on the QM, some equations like Hammett-Taft, or it uses a database of micro-pKs and some interaction parameters, or other? I assume that there must be some algorithm to calculate the free energy of the protonation (micro)species in order to calculate their distribution (abundance)? Thanks in advance!

Dusko

Hi !

You can find the details of our pKa prediction model below:

https://docs.chemaxon.com/display/CALCPLUGS/pKa+calculation

Daniel

danielszisz wrote:

Hi ! You can find the details of our pKa prediction model below: https://docs.chemaxon.com/display/CALCPLUGS/pKa+calculation Daniel

Hi Daniel,

this describes the acid-base equilibria in multi-protic molecules once either macro- or micro- pKs are known. My question is - where do these come from in Marvin? For example, they can be calculated based on the free energies of the protonation species, but how does Marvin actually do it?

Dusko

Hi !

The link I sent you contains the articles for the references on how we calculate the pKa. I put the references here, too.

http://www.chemaxon.com/conf/Prediction_of_dissociation_constant_using_microconstants.pdf

https://www.chemaxon.com/conf/Calculating_pKa_values_of_small_and_large_molecules.pdf

We don't use thermodynamical data in the pKa prediction. It is based on partial charge distribution of the molecule. 

Please see the details in the attached references.

Daniel