electron-flow arrow starting at coordinate bond

User 870ab5b546

26-08-2014 17:40:13

See the attached figure. The electron-flow arrow that originates at the coordinate bond points much closer to the C atom than to the Pd atom. If anything, the arrow should point much closer to the Pd atom (the electrophile) than to the C atom, but I would be happy if it pointed halfway between them as well. The rule would be, when a two-electron electron-flow arrow originates at a coordinate bond and points to an incipient bond, it points to the position halfway between the two atoms of the incipient bond, as if it were a one-electron electron-flow arrow.

ChemAxon 2c555f5717

28-08-2014 10:30:59

Dear Bob,


   Could you please attach an mrv source? I could not even draw a molecule like this, it seems to me that drawing electron flow arrow from coordinate bond is a not supported feature.


Regards:
Balázs 

User 870ab5b546

28-08-2014 13:02:02

Sure it's allowed. I used Marvin 2014.8.25.0 to draw it, but it's been permissible for quite a few versions now.


<?xml version="1.0" encoding="UTF-8"?>
<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/help/formats/schema/mrvSchema_14_8_4.xsd" version="ChemAxon file format v14.8.4, generated by v14.8.25.0">
<MDocument>
<MElectronContainer id="o1" occupation="0 0" radical="0">
<MElectron atomRefs="m1.a4" difLoc="-0.30941578531160907 0.30941578531160907 0.0"/>
<MElectron atomRefs="m1.a4" difLoc="-0.4226698230675705 0.11325403775596055 0.0"/>
</MElectronContainer>
<MElectronContainer id="o2" occupation="0 0" radical="0">
<MElectron atomRefs="m1.a4" difLoc="0.30941578531160907 0.3094157853116082 0.0"/>
<MElectron atomRefs="m1.a4" difLoc="0.11325403775596143 0.4226698230675696 0.0"/>
</MElectronContainer>
<MElectronContainer id="o3" occupation="0 0" radical="0">
<MElectron atomRefs="m1.a4" difLoc="-0.30941578531160996 -0.30941578531160996 0.0"/>
<MElectron atomRefs="m1.a4" difLoc="-0.11325403775596143 -0.4226698230675714 0.0"/>
</MElectronContainer>
<MElectronContainer id="o4" occupation="0 0" radical="0">
<MElectron atomRefs="m1.a5" difLoc="-0.4226698230675705 -0.11325403775596132 0.0"/>
<MElectron atomRefs="m1.a5" difLoc="-0.30941578531160907 -0.30941578531160985 0.0"/>
</MElectronContainer>
<MElectronContainer id="o5" occupation="0 0" radical="0">
<MElectron atomRefs="m1.a5" difLoc="0.11325403775596143 -0.4226698230675713 0.0"/>
<MElectron atomRefs="m1.a5" difLoc="0.30941578531160907 -0.30941578531160985 0.0"/>
</MElectronContainer>
<MElectronContainer id="o6" occupation="0 0" radical="0">
<MElectron atomRefs="m1.a5" difLoc="-0.11325403775596143 0.4226698230675706 0.0"/>
<MElectron atomRefs="m1.a5" difLoc="-0.30941578531160996 0.3094157853116092 0.0"/>
</MElectronContainer>
<MChemicalStruct>
<molecule molID="m1">
<atomArray atomID="a1 a2 a3 a4 a5 a6 a7" elementType="C C Pd Cl Cl X O" sgroupRef="sg1 sg1 0 0 0 0 0" x2="-1.8480000495910645 -1.8480000495910645 -3.828000068664551 -5.1616791904925865 -5.1616791904925865 -1.8480000495910645 0.5720000267028809" y2="2.2880001068115234 0.7480001068115234 1.628000020980835 2.3980000209808354 0.8580000209808344 1.5180001068115234 3.124000072479248"/>
<bondArray>
<bond id="b1" atomRefs2="a1 a2" order="2"/>
<bond id="b2" atomRefs2="a3 a4" order="1"/>
<bond id="b3" atomRefs2="a3 a5" order="1"/>
<bond id="b4" atomRefs2="a6 a3" convention="cxn:coord"/>
</bondArray>
<molecule id="sg1" role="MulticenterSgroup" molID="m2" atomRefs="a1 a2" center="a6"/>
</molecule>
</MChemicalStruct>
<MElectronContainer id="o8" occupation="0 0" radical="0">
<MElectron atomRefs="m1.a7" difLoc="0.11325403775596143 -0.4226698230675714 0.0"/>
<MElectron atomRefs="m1.a7" difLoc="0.30941578531160907 -0.30941578531161085 0.0"/>
</MElectronContainer>
<MElectronContainer id="o9" occupation="1 1" radical="0">
<MElectron atomRefs="m1.a7" difLoc="0.30941578531160907 0.3094157853116082 0.0"/>
<MElectron atomRefs="m1.a7" difLoc="0.11325403775596143 0.4226698230675696 0.0"/>
</MElectronContainer>
<MEFlow id="o10" arcAngle="-140.0" headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.25" baseElectronContainerIndex="1" baseElectronIndexInContainer="-1">
<MEFlowBasePoint atomRef="m1.a7"/>
<MAtomSetPoint atomRefs="m1.a7 m1.a1" weights="0.25 0.75"/>
</MEFlow>
<MEFlow id="o11" arcAngle="-257.0544339526754" headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.25" baseElectronContainerIndex="1" baseElectronIndexInContainer="1">
<MAtomSetPoint atomRefs="m1.a6 m1.a3"/>
<MAtomSetPoint atomRefs="m1.a3 m1.a2" weights="0.25 0.75"/>
</MEFlow>
</MDocument>
</cml>

ChemAxon 2c555f5717

29-08-2014 09:48:48

Dear Bob!


   I have written a ticket to our todo list. I have found the source cause of this behavior: we have a hard-coded request for this behavior. We will inform you if this request will be fulfilled.


Regards:
Balázs 

User 870ab5b546

29-08-2014 13:27:51

Thanks. This is a fairly minor esthetic issue, so I wouldn't make it very high priority. But I don't think it would be hard for you to fix.