fun with DYNAMICpKaPREFIX, some remaining bugs

Hi,





We finally installed JChem 3.2.1, and I've tried out the new DYNAMICpKaPREFIX, and it works GREAT! My program is so much simpler now. THANKS!





Some remaining issues to deal with:





(1) When I submit HCC^-, the plugin still does not recognize the negative C as being basic, so it returns no basic pKa value. It should (must!). You mentioned in a different post that the plugin needs to recognize a C as acidic to do the calculation. Surely you can recognize a negatively charged C as being basic! You should also recognize any neutral, sp-hybridized C bearing an H atom as being acidic.





(2) When I submit S^2-, and using double[] getpKaValues() to obtain an array of basic pKa's for the S atom, the plugin returns {6.9}, the same array as it returns for HS^-. The first basic pKa should be much larger.





(3) When I submit CH₂CHO^-, the plugin correctly returns 11.96 for the basic pKa of the O, but it does not return any value for the basic pKa of the first C atom. It should return 14.5.





(4) The DYNAMICpKaPREFIX apparently doesn't apply when I use getSortedValues(), computing the pKa values of the molecule as a whole. As a result, I need to calculate the acidic and basic pKa values each individual atom and then look at the highest basic and lowest acidic values to get the values for the molecule as a whole. I would like to see getSortedValues() take DYNAMICpKaPREFIX or STATICpKaPREFIX as a parameter.





-- Bob

Hi,








We are dealing with the problems you outlined in the 1st, 2nd, 3rd, and 4th points.





They will be fixed soon.








Jozsi

Good, thanks.





Here's another bug, perhaps related to the S^2- bug reported above. In the following compound, the basic pKa of the N is reported to be 9.2. It should be around 35.

Code:

<?xml version="1.0" ?> <MDocument>   <MChemicalStruct>     <molecule molID="m1">       <atomArray           atomID="a1 a2 a3"           elementType="C N R"           formalCharge="0 -1 0"           sgroupRef="0 0 sg1"           x2="-3.332291841506958 -4.665970963334994 -1.9986127196789223"           y2="5.878542385101318 5.108542385101318 5.108542385101319"           />       <bondArray>         <bond atomRefs2="a1 a2" order="1" />         <bond atomRefs2="a1 a3" order="1" />       </bondArray>       <molecule id="sg1" role="SuperatomSgroup" title="CO2H"                 leftName="HO2C" molID="m2">         <atomArray             atomID="a4 a5 a6"             elementType="C O O"             attachmentPoint="1 0 0"             x2="-1.2993751764297485 0.03430394539828718 -2.6330542982577843"             y2="4.587916838328043 5.357916838328045 5.357916838328043"             />         <bondArray>           <bond atomRefs2="a5 a4" order="1" />           <bond atomRefs2="a4 a6" order="2" />         </bondArray>       </molecule>     </molecule>   </MChemicalStruct> </MDocument>

And if you add a carbonyl group to the C adjacent to N, the pKb is reported to be 1.7. It should actually have a pKb of around 17.

Jozsi wrote:

They will be fixed soon.

Hi Jozsi,





Any idea when ChemAxon is planning to release a version of JChem with these fixes? Days, weeks, months?





We are planning to release a new version of ACE soon, and we need the pKa plugin to work properly.





Happy holidays,





Bob

Hi Bob,








We plan bug fix release by the beginning of the January of 2007.








Happy New Year!





Jozsi

Hi Jozsi,





We've downloaded and installed JChem 3.2.3. Of the bugs that I reported above:

JChem is still reporting the same pKb[0] and pKb[1] for S^2- as for HS^-.


JChem is still not reporting a pKb for the enolate C of CH₂=CH₂O^-.


JChem is still not reporting a pKb for the anionic C of HCC^-.

On the positive side, JChem is now reporting more accurate pKbs for CH₃CH₂NH^- and CH₃CONH^-. However, according to David Evans' pKa tables, the pKb of the latter compound is around 15, not 7.4 as JChem is calculating.





Perhaps I misunderstood you, but I thought these bugs would be fixed in JChem 3.2.3. When can I expect them to be fixed?





-- Bob

Hi Bob,





You did not misunderstand me.





I am very sorry but I had not got time to deal with your entire problem.





I hope I can fix your entire request in the near future.





Jozsi

Here's another bug: No pKa is reported for the N atom in CH₃CNH⁺, the nitrilium ion, and the pKa of the methyl C atom is reported as 24.8, the same for the neutral compound. I am still using DYNAMICpKaPREFIX.

Hi,





I understand Marvin 4.1.6 is due soon. Will any of the bugs we have discussed in the preceding posts be fixed in Marvin 4.1.6?





-- Bob

Hi Bob,








Yes, I fixed bugs.





e.g. pKa of negative carbon atoms calculated now.








Jozsi

Hi,





And I want to make sure this bug is fixed, too: When I calculate the basic pKa of each atom in the following compound, it does not give me a pKa for the C atom of the enolate. It should give me a value of 22.4.





-- Bob

Code:

<?xml version="1.0" ?> <MDocument>   <MChemicalStruct>     <molecule molID="m1">       <atomArray           atomID="a1 a2 a3 a4 a5"           elementType="C C O O C"           formalCharge="0 0 -1 0 0"           x2="-1.6265257765197143 -0.2928466546916786 -0.2928466546916786 1.0408324671363571 2.374511588964393"           y2="8.036875228881836 8.806875228881836 10.346875228881835 8.036875228881836 8.806875228881836"           />       <bondArray>         <bond atomRefs2="a1 a2" order="2" />         <bond atomRefs2="a2 a3" order="1" />         <bond atomRefs2="a2 a4" order="1" />         <bond atomRefs2="a4 a5" order="1" />       </bondArray>     </molecule>   </MChemicalStruct> </MDocument>