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pKa value
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Nagabhushan.G

Joined: 17 May 2007
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Link to postPosted: Thu May 17, 2007 6:23 amPost subject: pKa value Reply with quote

Plz suggest me how to find out the pKa value from its molecular structure
Jozsef
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Joined: 25 May 2004
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Link to postPosted: Fri May 18, 2007 10:22 amPost subject: Reply with quote

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
JP

Joined: 30 May 2007
Posts: 3

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Link to postPosted: Wed May 30, 2007 2:11 pmPost subject: Reply with quote

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.
Tamas
ChemAxon personnel
Joined: 21 May 2004
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Link to postPosted: Fri Jun 01, 2007 5:16 pmPost subject: Reply with quote

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?
JP

Joined: 30 May 2007
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Link to postPosted: Fri Jun 01, 2007 11:05 pmPost subject: Reply with quote

Deleting my IE cache files did the trick. Thanks.
Dusko

Joined: 26 Mar 2015
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Link to postPosted: Mon Apr 20, 2015 5:34 pmPost subject: how does this actually work? Reply with quote

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

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
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Link to postPosted: Tue Apr 21, 2015 3:18 pmPost subject: Reply with quote

Hi !

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

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

Daniel

Dusko

Joined: 26 Mar 2015
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Link to postPosted: Thu Apr 23, 2015 11:16 pmPost subject: pKa model Reply with quote

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

Daniel
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Joined: 22 Jan 2012
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Link to postPosted: Fri Apr 24, 2015 11:48 amPost subject: Reply with quote

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

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