User 870ab5b546
29-04-2009 00:01:56
Can you explain the following results?
[bob@epoch bob]$ evaluate -e "pKa('acidic')" "CCOC(=O)CC1CCCC1"
;38.33;;;;23.75;;-7.04;51.97;53.67;55.25
[bob@epoch bob]$ evaluate -e "dynamicpKa()" "CCOC(=O)CC1CCCC1"
;38.33;;;;23.75;;-7.04;51.97;53.67;55.25
[bob@epoch aceorg]$ evaluate -e "dynamicpKa()" "COC(=O)CCC1CCCCC1"
;;;;23.18;;;-7.02;53.7;51.78;55.89;54.62
However,
[bob@epoch config]$ evaluate -e "acidicpKaLargeModel()" "CCOC(=O)CC1CCCC1"
51.15;38.33;;;;23.75;60.7;55.62;53.51;51.97;55.05
I don't understand why the isolated cyclopentane or cyclohexane C atoms should be about as acidic as HCl. And I don't understand why switching from a "small" model to a "large model" should yield such inconsistent results. And what is the role of setMicropKaCalc() in all of this?
Bugs like these are very frustrating to me and to my students.
Using JChem 5.1.05.
ChemAxon e08c317633
29-04-2009 11:11:45
It is a bug: if you set "min" and "max" parameters for the pKa calculation (see pKa calculation help), then basic pKa-s could be listed among acidic pKa-s. In your example -7.04 is a basic pKa, but it is listed among acidic pKa-s. This only happens, when "small" model is used, so please, use the "large" model until we fix this, it will work correctly.
We will fix this bug ASAP. The fix will be available in the next patch release (5.2.2).
> And what is the role of setMicropKaCalc() in all of this?
The "mode" is another pKa calculation parameter (see pKa calculation help). It can be "macro" or "micro", de default is "macro". This can be also set in the evaluator.xml config file, example:
<Param Name="mode" Value="micro"></Param>
Zsolt
User 870ab5b546
29-04-2009 18:05:09
Can you explain, in chemistry terms, what you mean by "macro" and "micro"? I am not familiar with these terms.
ChemAxon e08c317633
30-04-2009 11:01:59
bobgr wrote: |
Can you explain, in chemistry terms, what you mean by "macro" and "micro"? I am not familiar with these terms.
|
See the explanation here: Multiprotic Molecules
User 851ac690a0
30-04-2009 15:43:38
Hi,
...what you mean by "macro" and "micro"? I am not familiar with these terms.
Probably the "apparent" and the "intrinstic" terms are more frequently used in relation of pKa.
"macro pKa" = "apparent pKa"
"micro pKa" = "intrinsic pKa"
Jozsi
User 870ab5b546
30-04-2009 16:40:57
I am now using the large model, as you suggested, and I get this result:
[bob@epoch bob]$ evaluate -e "dynamicpKa()" "O=CC1CCCCC1"
;29.67;16.53;60.29;56.65;54.35;57.78;-7.02
This kind of result is NOT acceptable.
User 851ac690a0
30-04-2009 17:20:01
Hi,
This kind of result is NOT acceptable.
I think one of the problem you may mean is that the "aldehyde H" should be the most acidic. We talk about the molecule given on the figure.
Yes,ok, I will change the "aldehyde" description in the pKa calculator.
Jozsi
User 870ab5b546
30-04-2009 19:16:04
The result you show in the figure is correct. The hydrogen on the alpha-carbon should be most acidic. (I think that is the one you meant, but the term "aldehyde hydrogen" usually refers to the H attached to the carbonyl C, which is not acidic at all.)
Currently the large model makes the beta-carbon most acidic. *Very* frustrating.
When will these fixes be available?
User 851ac690a0
30-04-2009 20:02:13
Hi,
When will these fixes be available?
The large part of these bugs have been fixed. So the fixed version will be available in the next patch release by the end of may.
Jozsi