User 870ab5b546
12-09-2007 17:35:15
Hi,
I have formulated this partial reactivity rule for SN2 substitutions:
| Code: |
match(ratom(1), "[H][C:1][H]", 1)
|| (match(ratom(1), "[H][C:1]", 1) && pKa(ratom(2)) <= 14) |
It works pretty well in many cases. However, when ratom(1) is Cl-, the substrate fails the reactivity rule. I think the reason is that Cl- returns "none" as the value for pKa(ratom(2)). Is there a way to test for this value?
On a similar topic, I assume that the Chemical Terms calculation uses the "static" model for pKa calculation? Can a parameter or a new method be introduced that would allow us to use the "dynamic" model?
-- Bob
User 870ab5b546
27-09-2007 19:38:00
Your tip worked for a while. Then we upgraded JChem, and now it's not working anymore. I checked that the evaluator.xml file in the Tomcat owner's .chemaxon directory still has the dynamicpKb method in it; it does. So why is JChem no longer getting information from this file?
Here is the code in evaluator.xml:
| Code: |
<Plugin ID="dynamicpKa" Class="chemaxon.marvin.calculations.pKaPlugin" JAR="pKaPlugin.jar">
<Param Name="prefix" Value="dynamic"/>
<Param Name="type" Value="acidic"/>
<Param Name="min" Value="-1000"/>
<Param Name="max" Value="1000"/>
</Plugin>
<Plugin ID="dynamicpKb" Class="chemaxon.marvin.calculations.pKaPlugin" JAR="pKaPlugin.jar">
<Param Name="prefix" Value="dynamic"/>
<Param Name="type" Value="basic"/>
<Param Name="min" Value="-1000"/>
<Param Name="max" Value="1000"/>
</Plugin> |
ChemAxon e08c317633
28-09-2007 11:02:30
It should work.
Please run these two commands and post their output:
| Code: |
| evaluate -e "pKa()" "CC(O)=O" |
| Code: |
| evaluate -e "dynamicpKa()" "CC(O)=O" |
Regards,
Zsolt
ChemAxon e08c317633
01-10-2007 08:29:25
Please modify the following line of the ${HOME}/.chemaxon/evaluator.xml file (HOME refers to the home directory of the user, who is running Tomcat):
| Code: |
| <Plugin ID="pKa" Class="chemaxon.marvin.calculations.pKaPlugin" JAR="pKaPlugin.jar"> |
to this:
| Code: |
| <Plugin ID="pKa111" Class="chemaxon.marvin.calculations.pKaPlugin" JAR="pKaPlugin.jar"> |
After the modification
| Code: |
| evaluate -e "pKa()" "CC(O)=O" |
should throw an exception, and
| Code: |
| evaluate -e "pKa111()" "CC(O)=O" |
should work.
| Code: |
evaluate -e "pKa111()" "CC(O)=O"
;;4.54; |
If it works like this, then please send me your evaluator.xml file.
Zsolt
User 870ab5b546
01-10-2007 12:13:20
The behavior was as you described.
I am attaching evaluator.xml.
One note: I have .chemaxon/evaluator.xml also in my own home directory. After I changed the one in root, the Tomcat owner, when I exited root and became myself again, pKa111 was not recognized. But when I changed my own evaluator.xml file from pKa to pKa111, then pKa111 was recognized properly.
Anyway, it appears that Tomcat is no longer recognizing the evaluator.xml file in root.
User 870ab5b546
09-10-2007 12:45:13
Köszönöm, and glad to hear I wasn't just doing something wrong.
User 870ab5b546
18-02-2008 13:58:35
Ahhh... Very clever workaround. May I suggest that you add this problem and its solution to the documentation? Neither the existence of the problem nor the solution is at all obvious.
Köszönöm.
ChemAxon d76e6e95eb
18-02-2008 14:48:36
If reactive sites are identified by the scheme and the reactivity rule, all isomeric products are be generated.
If a selectivity rule is given, it just prioritizes the reactive sites, some products are generated (the main products).
At least Reactor should work accordingly.
ChemAxon d76e6e95eb
01-03-2008 08:35:51
Bob, the pKa plugin calculates some acidic hydrocarbons, like the ones connected to carbonyls, but not all. I agree, that acetylenes should be included, maybe more, but we need to clarify the reasons of this limitation in the scope of a discussion with the developers first and consider enhancements. We will get back to you soon after.
User 870ab5b546
01-03-2008 22:35:23
Thank you for looking into this problem.
ChemAxon d76e6e95eb
04-03-2008 12:29:07
The pKa tool will consider all CH features. The tests are running currently, and if the modified algorithm performs well we try to make it available for you asap, hopefully in 5.0.2.
User 870ab5b546
04-03-2008 12:46:07
Thank you for making this enhancement. It will solve many problems for us.
User 870ab5b546
05-04-2008 18:45:08
Hello, I used MarvinSketch 5.0.2.1 to calculate the pKa values of propyne. Happily, pKa values are given for both H-bearing C atoms. Less happily, the values are significantly larger than they ought to be. The pKa of C(1) should be about 25, not 35.2, and the pKa of C(3) should be about 37, not 44.6. I am less concerned about the latter value than I am about the former one. So we have progress, but there are still tasks ahead.
Also, I tried to calculate the pKa values of propynyl anion in dynamic mode, and I was told that no ionizable atoms were found. The plugin should return a pKb value of about 25.
User 870ab5b546
22-04-2008 00:48:56
Thank you. And what about the too-large values for the pKa of C(sp)-H and propargylic H?
User 870ab5b546
05-05-2008 16:37:56
I'm sorry to hear that. Do you know how long the delay will endure? (Weeks, months...?)
User 851ac690a0
14-05-2008 06:55:58
Hi,
I think I will fix your pKa problem in this month.
Jozsi
User 870ab5b546
14-05-2008 13:51:23
That'll be great, köszönöm.