User 5508363905
23-02-2006 00:53:53
Does it make sense that the pKa calculator does not assign a pKa to the secondary amine in Furosemide CAS# 54-31-9?
User 851ac690a0
23-02-2006 01:09:37
Dear Carl,
I attached a picture from the calculated pKa values.
Which version of Marvin do you use now?
Jozsi
User 5508363905
23-02-2006 03:42:48
I used the online version available thru demos on the web site. I also tried 4.1.0alpha9 which gave the same result (no pKa value).
Any ideas as to why no pKa value was shown?
Thanks for the follow-up.
User 5508363905
23-02-2006 04:02:27
It's possible I didn't have the min & max pKa values specified correctly. I tried the 4.1alpha9 and it gave the same pKa's you provided. However, the pKa for the sulfonamide was 9.91 vs 10 shown in your response.
User 851ac690a0
23-02-2006 23:26:13
Dear Carl,
I forgot to mention that temperature is adjustable parameter.
at 293K : pKa = 10.0
at 298K : pKa =9.91
Jozsi
User 5508363905
24-02-2006 23:22:40
I ran a few other molecules for pKa and noticed I was not getting pKa values for some of the very weakly basic N's. I reran furosemide as a test and again I did not get a pKa value for the very weak secondary amine group in it. I'm using the alpha v9 online version. The pKa dialog box states the max pKa is 14 and the min pKa is 0. Any other input results in an error stating value out of range.
User 851ac690a0
25-02-2006 11:05:48
Dear Carl,
Try this setting:
Min basic pKa -10
Max acidic pKa 20
or without limits
Min basic pKa -100
Max acidic pKa 200
Jozsi
User 5508363905
27-02-2006 16:56:23
I have attached the error message I receive when using values outside 0-14 for pKa
User 851ac690a0
27-02-2006 17:40:05
Dear Carl,
"pH lower limit: value out of range [0.0, 14.0] : -10"
"pH upper limit: value out of range [0.0, 14.0] : 20"
These two messages refer to "pH" value and not for "pKa" value.
With these "pH" values you can set the "pH" axis of microspecies distribution. I attached a figure about the microspecies distribution of furosemide.
I am a little surprised because you were able to use our pKa calculator at this date "Fri Feb 24, 2006 11:22 pm", see one of your previous message.
Jozsi
User 5508363905
27-02-2006 18:03:35
Thank you. I was not paying attention when I edited the pKa options dialog.