benzyne

Hi,





Benzyne cannot currently be aromatized. It would be nice if it could be.





-- Bob

Hi Bob,





It was a bug that it could have been aromatized, but the current version is analogous to the expected method.


http://www.chemaxon.com/marvin/doc/user/aromatization-doc.html





Andras

If it was a bug in Daylight's algorithm, I think you should fix it in yours.





Benzyne is aromatic, even if Daylight's algorithm doesn't convert the bonds appropriately.





I thought you were going to tell me that you don't have a good way to represent an aromatic bond that is between double and triple. But if you can do it, then you should. Most users wouldn't expect benzyne not to be aromatized, I think.

Hi Bob,





You are right, benzyne is aromatic.


We will correct this bug.


Do you know other cyclic compounds which have a triple bond in an aromatic ring?


I think arynes, heteroarynes are, but what else?





All the best


Andras

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 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24 a25 a26 a27 a28 a29 a30 a31 a32 a33 a34"           elementType="C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C"           x2="-0.7700000000000004 0.7699999999999997 2.3099999999999996 -2.3100000000000005 -3.08 -2.3099999999999996 3.08 2.31 -0.7699999999999995 0.7700000000000001 8.47 10.01 11.549999999999999 6.930000000000001 13.09 14.63 15.4 14.63 13.090000000000002 11.561666674613955 10.021666674613954 6.160000000000001 6.930000000000001 8.47 2.369816323624946 2.3536728122053318E-15 -2.3698163236249448 -1.5229603127968698 1.2896270231736062 -2.3698163236249465 -1.4646270350945352 1.4646270350945387 2.428149720536566 -0.17500001192093148"           y2="1.3336791218280357 1.3336791218280357 1.3336791218280357 1.3336791218280357 0.0 -1.3336791218280355 0.0 -1.3336791218280357 -1.3336791218280355 -1.333679121828036 1.5158713682446663 1.5158713682446663 1.5158713682446663 1.5158713682446663 1.5158713682446663 1.5158713682446663 0.18219224641663054 -1.1514868754114052 -1.1514868754114052 -2.42683260032782 -2.42683260032782 0.18219224641663054 -1.1514868754114052 -1.1514868754114052 -8.768604943002657 -10.490377285677496 -8.76860494300266 -5.92438537475362 -6.7993853747536175 -7.2286049430026615 -10.014491114340078 -10.014491114340078 -7.228604943002658 -6.323499203416199"           />       <bondArray>         <bond atomRefs2="a1 a2" order="3" />         <bond atomRefs2="a2 a3" order="1" />         <bond atomRefs2="a1 a4" order="1" />         <bond atomRefs2="a4 a5" order="2">           <bondStereo>C</bondStereo>         </bond>         <bond atomRefs2="a5 a6" order="1" />         <bond atomRefs2="a3 a7" order="2">           <bondStereo>C</bondStereo>         </bond>         <bond atomRefs2="a7 a8" order="1" />         <bond atomRefs2="a6 a9" order="2" />         <bond atomRefs2="a8 a10" order="2" />         <bond atomRefs2="a9 a10" order="2" />         <bond atomRefs2="a11 a12" order="3" />         <bond atomRefs2="a12 a13" order="1" />         <bond atomRefs2="a11 a14" order="1" />         <bond atomRefs2="a13 a15" order="3" />         <bond atomRefs2="a15 a16" order="1" />         <bond atomRefs2="a16 a17" order="2">           <bondStereo>C</bondStereo>         </bond>         <bond atomRefs2="a17 a18" order="1" />         <bond atomRefs2="a18 a19" order="2">           <bondStereo>T</bondStereo>         </bond>         <bond atomRefs2="a19 a20" order="1" />         <bond atomRefs2="a20 a21" order="2">           <bondStereo>C</bondStereo>         </bond>         <bond atomRefs2="a14 a22" order="2">           <bondStereo>C</bondStereo>         </bond>         <bond atomRefs2="a22 a23" order="1" />         <bond atomRefs2="a23 a24" order="2">           <bondStereo>T</bondStereo>         </bond>         <bond atomRefs2="a24 a21" order="1" />         <bond atomRefs2="a32 a25" order="1" />         <bond atomRefs2="a25 a33" order="2">           <bondStereo>C</bondStereo>         </bond>         <bond atomRefs2="a33 a29" order="1" />         <bond atomRefs2="a29 a34" order="3" />         <bond atomRefs2="a34 a28" order="1" />         <bond atomRefs2="a28 a30" order="2">           <bondStereo>C</bondStereo>         </bond>         <bond atomRefs2="a30 a27" order="1" />         <bond atomRefs2="a27 a31" order="2">           <bondStereo>C</bondStereo>         </bond>         <bond atomRefs2="a31 a26" order="1" />         <bond atomRefs2="a26 a32" order="2">           <bondStereo>C</bondStereo>         </bond>       </bondArray>     </molecule>   </MChemicalStruct> </MDocument>

In the allene structure, the middle double bond is not part of the aromatic system.

Hi Bob,





We don't have capacity to solve this problem in the near future.





But for searching purposes you can standardize


(See: http://www.chemaxon.com/product/standardizer.html ) both query and the target using the following rule:

Quote:

[#6:5]=,:1[#6:4]=,:[#6:3][#6:2]#[#6:1][#6:6]=,:1>>[c:5]1[c:4][c:3][c:2]#[c:1][c:6]1

Please be careful, the aromatization will destroy the converted benzyne ring, so the aromatize action must appear before the benzyne transformation in the standardization queue.


Also note that this is for searching purposes, displaying the molecule in this form would be misleading.





Andras