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pkb calculation
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Tatiana

Joined: 07 Feb 2011
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Link to postPosted: Fri Jun 06, 2014 8:32 pmPost subject: pkb calculation Reply with quote

 

Hello,

 I calculated pkb for atoms using cxcalc and obtained some strange results for carbonyl oxygen, 

bpKa1 bpKa2 bpKa3
Number of atoms 4 6 5
value 7,29 -4,82 -20,29

In all cases where I observed such situation the carbonyl oxygen was found next to guanidine,

Can rely to these results?

Thanks

Jozsef
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Joined: 25 May 2004
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Link to postPosted: Wed Jun 11, 2014 10:18 amPost subject: Reply with quote

Hi,

 

1-AcetylGuanidine is a moderately strong basic compound. So the calculated pKa value is  7.29 must be  a good approximation.

The second and the third protonation constants are low values. I think this is in agreement with our expectation. 

Two figures are attached. The pKa of 1-acetylguanidine is calculated with default setting and non default setting.

 

Jozsi   

noshin

Joined: 07 Jan 2015
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Link to postPosted: Thu Jan 08, 2015 9:32 amPost subject: pka calculation of irinotecan hydrochloride Reply with quote

In calculating pKa some groups in a pharmaceutical composition called irinotecan hydrochlorid'm in trouble . How do I calculate the pKa of your site. Thank you a lot

noshin

Joined: 07 Jan 2015
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Link to postPosted: Thu Jan 08, 2015 10:44 amPost subject: pka calculation of irinotecan hydrochloride Reply with quote

 

In calculating pKa some groups in a pharmaceutical composition called irinotecan hydrochlorid'm in trouble . How do I calculate the pKa of this group (red ) in pH, 3, 4.5 and 7. 

 

Jozsef
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Link to postPosted: Sat Jan 10, 2015 12:35 amPost subject: Reply with quote

Hi,

 

I attached one more figure from the most relevant protonation sites.

The protonated cation is stabilized by resonance as shown on the figure.

 

The very law pKa value  as  "-20.29" of  the keto group is not realistic.

The pKa value of  (-1.5)  -  (-2.5)  would be more realistic for a  keto type amide group. I applied this value on the figure. This problem will be fixed asap.

 

Jozsi

Jozsef
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Link to postPosted: Sat Jan 10, 2015 7:15 pmPost subject: Reply with quote

Hi,

 

How do I calculate
the pKa of your site. 

Here is a from step to step recipe how to use the "site".

Steps. See the "zipped" file too.

1. Open the "www.chemaxon.com" site in your web browser, Fig. 1

2. Click on the "Product" tag.  Fig. 2

3. Click on the "MarvinSketch" tag. Fig. 3.

4. The product page of  the MArvinSketch will appear. Fig. 4

5. Click on the "Try Online" tag. Fig.5

6. Sometimes , you need to install a certain "java plugin". Fig. 6.

6.a. Just click on the "Activate Java Platform ..."

6.b. In 1-2 minutes the activation process will be successfull and the "MarvinSketch"  graphical user interface will be loaded. Fig. 6b

7. On the MarvinSketch canvas you need to draw the structure of the molecule you want to  calculate pKa value. Fig. 7

8. Click on the "Calculations" tag. Fig. 8

9. Click on the "Protonation" and the "pKa" tags. Fig. 9

10. The "pKa calculation" option panel will be appearing. Fig. 10

11. To run the pKa calculation just click on the "OK" button.  The result will appear in a new window Fig. 11

11.a. When the "warning-information"  window appear  just click on the "OK"  Fig.11a

12. In case of  very weak basic or acid groups you may need to change the default calculation limits. Fig.12

13. In this example the "Min basic pKa"  and the "Min acidc pKa" limit changed according to Fig. 13

14.   And the calculated pKa values according to the new limits are shown on the Fig.14.

 

Please try to do these steps. If you are OK, we can continue the discussion further.

 

Jozsi

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