User 870ab5b546
01-06-2007 03:21:21
Hello,
In JChem 3.2.3, when I take the canonical resonance form of:
I get:
I suggest that you do not aromatize at all when you generate a canonical resonance form, because aromaticity is not easily represented in Lewis structures, and a user may want to use either Daylight or ChemAxon aromatization or neither. In fact, it can be argued that drawing multiple resonance structures of aromatic compounds is a better way of representing them than drawing "aromatic bonds".
In JChem 3.2.3, when I take the canonical resonance form of:
| Code: |
| <?xml version="1.0" ?> <MDocument> <MChemicalStruct> <molecule molID="m1"> <atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13" elementType="N C C N N C C N C N O O O" formalCharge="0 0 0 0 -1 0 0 0 0 0 0 0 0" mrvMap="0 0 0 0 3 0 0 0 0 0 0 0 0" x3="5.764261874480287 4.430592533432028 4.430592533432028 5.764261874480287 7.097931215528545 7.097931215528545 3.0969231923837697 1.7632538513355112 1.7632538513355112 3.0969231923837697 3.0969231923837697 0.5248375239237646 8.336347542940292" y3="13.691366866896372 12.921349926337333 11.38131604521925 10.61129910466021 11.38131604521925 12.921349926337333 13.691366866896372 12.921349926337333 11.38131604521925 10.61129910466021 15.121366866896372 10.666316045219249 13.636349926337333" z3="0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0" /> <bondArray> <bond atomRefs2="a1 a2" order="2" /> <bond atomRefs2="a1 a6" order="1" /> <bond atomRefs2="a3 a2" order="1" /> <bond atomRefs2="a7 a2" order="1" /> <bond atomRefs2="a3 a4" order="2" /> <bond atomRefs2="a10 a3" order="1" /> <bond atomRefs2="a4 a5" order="1" /> <bond atomRefs2="a5 a6" order="1" /> <bond atomRefs2="a6 a13" order="2" /> <bond atomRefs2="a7 a8" order="1" /> <bond atomRefs2="a7 a11" order="2" /> <bond atomRefs2="a8 a9" order="1" /> <bond atomRefs2="a9 a10" order="1" /> <bond atomRefs2="a9 a12" order="2" /> </bondArray> </molecule> </MChemicalStruct> </MDocument> |
I get:
| Code: |
| <?xml version="1.0" ?> <MDocument> <MChemicalStruct> <molecule molID="m1"> <atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13" elementType="N C C N N C C N C N O O O" formalCharge="0 0 0 0 0 0 0 0 0 0 0 0 -1" hydrogenCount="0 0 0 0 0 0 0 1 0 1 0 0 0" mrvMap="0 0 0 0 3 0 0 0 0 0 0 0 0" x3="5.764261874480287 4.430592533432028 4.430592533432028 5.764261874480287 7.097931215528545 7.097931215528545 3.0969231923837697 1.7632538513355112 1.7632538513355112 3.0969231923837697 3.0969231923837697 0.5248375239237646 8.336347542940292" y3="13.691366866896372 12.921349926337333 11.38131604521925 10.61129910466021 11.38131604521925 12.921349926337333 13.691366866896372 12.921349926337333 11.38131604521925 10.61129910466021 15.121366866896372 10.666316045219249 13.636349926337333" z3="0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0" /> <bondArray> <bond atomRefs2="a1 a2" order="A" /> <bond atomRefs2="a1 a6" order="A" /> <bond atomRefs2="a3 a2" order="A" /> <bond atomRefs2="a7 a2" order="A" /> <bond atomRefs2="a3 a4" order="A" /> <bond atomRefs2="a10 a3" order="A" /> <bond atomRefs2="a4 a5" order="A" /> <bond atomRefs2="a5 a6" order="A" /> <bond atomRefs2="a6 a13" order="1" /> <bond atomRefs2="a7 a8" order="A" /> <bond atomRefs2="a7 a11" order="2" /> <bond atomRefs2="a8 a9" order="A" /> <bond atomRefs2="a9 a10" order="A" /> <bond atomRefs2="a9 a12" order="2" /> </bondArray> </molecule> </MChemicalStruct> </MDocument> |
I suggest that you do not aromatize at all when you generate a canonical resonance form, because aromaticity is not easily represented in Lewis structures, and a user may want to use either Daylight or ChemAxon aromatization or neither. In fact, it can be argued that drawing multiple resonance structures of aromatic compounds is a better way of representing them than drawing "aromatic bonds".