pKa variation with structure representation

User 870ab5b546

06-05-2010 03:31:40

I am finding that depending on how I draw ethyl cyanoacetate, it is giving me wildly different pKa values, none of which are correct (C(2) should be 9).  JChem gives this structure a pKa of 18.8:


<?xml version="1.0" ?>
<cml>
<MDocument>
<MChemicalStruct>
<molecule molID="m1">
<atomArray
atomID="a1 a2 a3 a4 a5"
elementType="R C C R O"
sgroupRef="sg1 0 0 sg2 0"
x2="-12.368124961853027 -11.034445840024992 -9.546920067539826 -9.148338738081945 -8.21324094571179"
y2="3.4649999141693115 4.234999914169311 3.836418584711429 2.3488928122262642 4.606418584711429"
/>
<bondArray>
<bond atomRefs2="a1 a2" order="1" />
<bond atomRefs2="a2 a3" order="1" />
<bond atomRefs2="a3 a4" order="1" />
<bond atomRefs2="a3 a5" order="2" />
</bondArray>
<molecule id="sg1" role="SuperatomSgroup" title="CN" leftName="NC" molID="m2">
<atomArray
atomID="a6 a7"
elementType="C N"
attachmentPoint="1 0"
x2="-23.099999847412107 -24.63999984741211"
y2="6.545000076293945 6.545000076293945"
/>
<bondArray>
<bond atomRefs2="a6 a7" order="3" />
</bondArray>
</molecule>
<molecule id="sg2" role="SuperatomSgroup" title="OEt" leftName="EtO" molID="m3">
<atomArray
atomID="a8 a9 a10"
elementType="O C C"
attachmentPoint="1 0 0"
x2="-9.185212253046169 -10.518891374874205 -11.852570496702239"
y2="1.6959749752363447 0.9259749752363442 1.6959749752363438"
/>
<bondArray>
<bond atomRefs2="a9 a8" order="1" />
<bond atomRefs2="a10 a9" order="1" />
</bondArray>
</molecule>
</molecule>
</MChemicalStruct>
</MDocument>
</cml>

Likewise this structure with all groups ungrouped:


<?xml version="1.0" ?>
<cml>
<MDocument>
<MChemicalStruct>
<molecule molID="m1">
<atomArray
atomID="a1 a2 a3 a4 a5 a6 a7 a8"
elementType="C C C O O N C C"
x2="-11.68346822604581 -10.349789104217773 -8.862263331732608 -8.463682002274727 -7.528584209904572 -13.017147347873847 -9.55262644530201 -11.040152217787172"
y2="3.9576949021652466 4.727694902165247 4.3291135727073655 2.8415878002222 5.099113572707365 4.72769490216525 1.7526433571949167 2.151224686652799"
/>
<bondArray>
<bond atomRefs2="a1 a2" order="1" />
<bond atomRefs2="a2 a3" order="1" />
<bond atomRefs2="a3 a4" order="1" />
<bond atomRefs2="a3 a5" order="2" />
<bond atomRefs2="a1 a6" order="3" />
<bond atomRefs2="a7 a4" order="1" />
<bond atomRefs2="a8 a7" order="1" />
</bondArray>
</molecule>
</MChemicalStruct>
</MDocument>
</cml>

But for this structure it gives a pKa of 13.8 -- still not correct, but better:


<?xml version="1.0" ?>
<cml>
<MDocument>
<MChemicalStruct>
<molecule molID="m1">
<atomArray
atomID="a1 a2 a3"
elementType="R C R"
sgroupRef="sg1 0 sg2"
x2="-4.090624809265137 -2.756945687437101 -1.4232665656090655"
y2="1.5881249904632568 0.8181249904632569 1.5881249904632568"
/>
<bondArray>
<bond atomRefs2="a1 a2" order="1" />
<bond atomRefs2="a2 a3" order="1" />
</bondArray>
<molecule id="sg1" role="SuperatomSgroup" title="CN" leftName="NC" molID="m2">
<atomArray
atomID="a4 a5"
elementType="C N"
attachmentPoint="1 0"
x2="-5.678749980926513 -7.218749980926514"
y2="3.0799999237060547 3.0799999237060547"
/>
<bondArray>
<bond atomRefs2="a4 a5" order="3" />
</bondArray>
</molecule>
<molecule id="sg2" role="SuperatomSgroup" title="CO2Et"
leftName="EtO2C" molID="m3">
<atomArray
atomID="a6 a7 a8 a9 a10"
elementType="C C O C O"
attachmentPoint="1 0 0 0 0"
x2="0.9240000762939449 3.2340000762939445 1.6940000762939444 4.004000076293944 -0.6159999237060552"
y2="1.8205567502212876 0.486877628393251 0.4868776283932519 -0.8468014934347838 1.8205567502212876"
/>
<bondArray>
<bond atomRefs2="a8 a6" order="1" />
<bond atomRefs2="a6 a10" order="2" />
<bond atomRefs2="a9 a7" order="1" />
<bond atomRefs2="a7 a8" order="1" />
</bondArray>
</molecule>
</molecule>
</MChemicalStruct>
</MDocument>
</cml>

And now expand this structure, and it still gives me a pKa of 13.8, even though it seems identical to the second one:


<?xml version="1.0" ?>
<cml>
<MDocument>
<MChemicalStruct>
<molecule molID="m1">
<atomArray
atomID="a1 a2 a3 a4 a5 a6 a7 a8"
elementType="C C C N C O C O"
x2="-5.257594040864667 -3.923914919036632 -2.5902357972085968 -5.257594040864669 -1.2565566753805604 -1.256556675380561 0.07712244644747424 -2.5902357972085968"
y2="1.8127083237965897 1.0427083237965897 1.8127083237965897 3.3527083237965907 -0.4972916762034103 1.0427083237965902 -1.267291676203409 3.3527083237965902"
/>
<bondArray>
<bond atomRefs2="a1 a2" order="1" />
<bond atomRefs2="a2 a3" order="1" />
<bond atomRefs2="a1 a4" order="3" />
<bond atomRefs2="a6 a3" order="1" />
<bond atomRefs2="a3 a8" order="2" />
<bond atomRefs2="a7 a5" order="1" />
<bond atomRefs2="a5 a6" order="1" />
</bondArray>
</molecule>
</MChemicalStruct>
</MDocument>
</cml>

This is happening in both JChem 5.3 and 5.2.  Can you explain and fix?

User 851ac690a0

07-05-2010 16:05:17

Hi,


I have fixed these bugs.


Thanks for sending report.


Jozsi

User 870ab5b546

07-05-2010 16:06:53

Thanks.  When will the fix be available?

User 851ac690a0

07-05-2010 16:14:21

Hi,


The fix will be available at the begening of the next week.


Jozsi