User 870ab5b546
06-10-2011 18:21:46
Is it true that in JChem 5.4.1.1, when setConsiderTautomerization() is set to true, that setMicropKaCalc(true) has no effect?
I am comparing acidic and basic pKa values of cyclohexanone and its enolate.
plugin.setMaxIons(8); // default 8
plugin.setBasicpKaLowerLimit(pKaFunctions.SMALLEST_PKA);
plugin.setAcidicpKaUpperLimit(pKaFunctions.LARGEST_PKA);
plugin.setpKaPrefixType(pKaPlugin.DYNAMICpKaPREFIX);
plugin.setModel(pKaPlugin.MODEL_LARGE);
plugin.setConsiderTautomerization(true);
plugin.setMicropKaCalc(true);
plugin.setMolecule(molecule);
plugin.run();
Cyclohexanone (the alpha carbon is C(1)):
Oct 6, 2011 2:16:50 PM org.apache.catalina.core.StandardWrapperValve invoke
INFO: pKa.jsp: for atom C1, pKaAcidic = [20.685983401901414], pKaBasic = null, atomPKs = [20.685983401901414, NaN]
pKa.jsp: for atom C1, atomPKs = [20.685983401901414, NaN]
acidic pKa for atom C1: 20.685983401901414
pKa.jsp: for atom C2, pKaAcidic = [55.67068092863413], pKaBasic = null, atomPKs = [55.67068092863413, NaN]
pKa.jsp: for atom C2, atomPKs = [55.67068092863413, NaN]
acidic pKa for atom C2: 55.67068092863413
pKa.jsp: for atom C3, pKaAcidic = [56.24113024909185], pKaBasic = null, atomPKs = [56.24113024909185, NaN]
pKa.jsp: for atom C3, atomPKs = [56.24113024909185, NaN]
acidic pKa for atom C3: 56.24113024909185
pKa.jsp: for atom C4, pKaAcidic = [55.67068092863413], pKaBasic = null, atomPKs = [55.67068092863413, NaN]
pKa.jsp: for atom C4, atomPKs = [55.67068092863413, NaN]
acidic pKa for atom C4: 55.67068092863413
pKa.jsp: for atom C5, pKaAcidic = [20.685983401901414], pKaBasic = null, atomPKs = [20.685983401901414, NaN]
pKa.jsp: for atom C5, atomPKs = [20.685983401901414, NaN]
acidic pKa for atom C5: 20.685983401901414
pKa.jsp: for atom C6, pKaAcidic = null, pKaBasic = null, atomPKs = [NaN, NaN]
pKa.jsp: for atom C6, atomPKs = [NaN, NaN]
pKa.jsp: for atom O7, pKaAcidic = null, pKaBasic = [-7.346983334491181], atomPKs = [NaN, -7.346983334491181]
pKa.jsp: for atom O7, atomPKs = [NaN, -7.346983334491181]
basic pKa for atom O7: -7.346983334491181
Cyclohexanone enolate (C(1) is anionic):
INFO: pKa.jsp: for atom C1, pKaAcidic = [20.685983401901414], pKaBasic = null, atomPKs = [20.685983401901414, NaN]
pKa.jsp: for atom C1, atomPKs = [20.685983401901414, NaN]
acidic pKa for atom C1: 20.685983401901414
pKa.jsp: for atom C2, pKaAcidic = [55.67068092863413], pKaBasic = null, atomPKs = [55.67068092863413, NaN]
pKa.jsp: for atom C2, atomPKs = [55.67068092863413, NaN]
acidic pKa for atom C2: 55.67068092863413
pKa.jsp: for atom C3, pKaAcidic = [56.24113024909185], pKaBasic = null, atomPKs = [56.24113024909185, NaN]
pKa.jsp: for atom C3, atomPKs = [56.24113024909185, NaN]
acidic pKa for atom C3: 56.24113024909185
pKa.jsp: for atom C4, pKaAcidic = [55.67068092863413], pKaBasic = null, atomPKs = [55.67068092863413, NaN]
pKa.jsp: for atom C4, atomPKs = [55.67068092863413, NaN]
acidic pKa for atom C4: 55.67068092863413
pKa.jsp: for atom C5, pKaAcidic = [20.685983401901414], pKaBasic = null, atomPKs = [20.685983401901414, NaN]
pKa.jsp: for atom C5, atomPKs = [20.685983401901414, NaN]
acidic pKa for atom C5: 20.685983401901414
pKa.jsp: for atom C6, pKaAcidic = null, pKaBasic = null, atomPKs = [NaN, NaN]
pKa.jsp: for atom C6, atomPKs = [NaN, NaN]
pKa.jsp: for atom O7, pKaAcidic = null, pKaBasic = [-7.346983334491181], atomPKs = [NaN, -7.346983334491181]
pKa.jsp: for atom O7, atomPKs = [NaN, -7.346983334491181]
basic pKa for atom O7: -7.346983334491181
Note that the values are identical. If I comment out setConsiderTautomerization(), the values are different. Can you confirm?
Happily, I do NOT see this behavior in JChem 5.6.