User 870ab5b546
25-11-2014 22:43:22
The figure shows the following MRV of (Ph3P)2PdCl2 displayed in both MarvinSketch and Marvin JS.
<cml><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="Pd" x2="0.09624999761581421" y2="0.7699999809265137"/><atom id="a2" elementType="Cl" x2="1.1851944406430974" y2="1.8589444239537969"/><atom id="a3" elementType="Cl" x2="1.1851944406430974" y2="-0.31894446210076954"/><atom id="a4" elementType="P" x2="-1.9070694525640264" y2="1.8589444239537969"/><atom id="a5" elementType="P" x2="-1.9070694525640264" y2="-0.31894446210076954"/><atom id="a6" elementType="R" x2="-3.240748574392062" y2="0.45105553789923114" sgroupRef="sg1"/><atom id="a7" elementType="R" x2="-1.9070694525640264" y2="-1.8589444621007696" sgroupRef="sg2"/><atom id="a8" elementType="R" x2="-3.240748574392062" y2="-1.0889444621007702" sgroupRef="sg3"/><atom id="a9" elementType="R" x2="-3.240748574392062" y2="1.0889444239537962" sgroupRef="sg4"/><atom id="a10" elementType="R" x2="-3.240748574392062" y2="2.6289444239537976" sgroupRef="sg5"/><atom id="a11" elementType="R" x2="-1.9070694525640264" y2="3.3989444239537967" sgroupRef="sg6"/></atomArray><bondArray><bond atomRefs2="a1 a2" order="1"/><bond atomRefs2="a1 a3" order="1"/><bond atomRefs2="a5 a6" order="1"/><bond atomRefs2="a5 a7" order="1"/><bond atomRefs2="a5 a8" order="1"/><bond atomRefs2="a4 a9" order="1"/><bond atomRefs2="a4 a10" order="1"/><bond atomRefs2="a4 a11" order="1"/><bond atomRefs2="a4 a1" convention="cxn:coord"/><bond atomRefs2="a5 a1" convention="cxn:coord"/></bondArray><molecule id="sg1" molID="m2" role="SuperatomSgroup" title="Ph"><atomArray><atom id="a12" elementType="C" x2="-3.240748574392062" y2="0.45105553789923114" sgroupAttachmentPoint="1"/><atom id="a13" elementType="C" x2="-3.2407485743920654" y2="-1.0889444621007736"/><atom id="a14" elementType="C" x2="-4.574427696220104" y2="-1.8589444621007714"/><atom id="a15" elementType="C" x2="-5.908106818048137" y2="-1.0889444621007673"/><atom id="a16" elementType="C" x2="-5.9081068180481315" y2="0.45105553789923203"/><atom id="a17" elementType="C" x2="-4.574427696220096" y2="1.2210555378992316"/></atomArray><bondArray><bond atomRefs2="a12 a13" order="2"/><bond atomRefs2="a13 a14" order="1"/><bond atomRefs2="a14 a15" order="2"/><bond atomRefs2="a15 a16" order="1"/><bond atomRefs2="a16 a17" order="2"/><bond atomRefs2="a12 a17" order="1"/></bondArray></molecule><molecule id="sg2" molID="m3" role="SuperatomSgroup" title="Ph"><atomArray><atom id="a18" elementType="C" x2="-1.9070694525640264" y2="-1.8589444621007696" sgroupAttachmentPoint="1"/><atom id="a19" elementType="C" x2="-3.2407485743920637" y2="-1.0889444621007656"/><atom id="a20" elementType="C" x2="-3.240748574392061" y2="0.4510555378992356"/><atom id="a21" elementType="C" x2="-1.9070694525640228" y2="1.2210555378992325"/><atom id="a22" elementType="C" x2="-0.5733903307359884" y2="0.4510555378992285"/><atom id="a23" elementType="C" x2="-0.5733903307359893" y2="-1.088944462100771"/></atomArray><bondArray><bond atomRefs2="a18 a19" order="2"/><bond atomRefs2="a19 a20" order="1"/><bond atomRefs2="a20 a21" order="2"/><bond atomRefs2="a21 a22" order="1"/><bond atomRefs2="a22 a23" order="2"/><bond atomRefs2="a18 a23" order="1"/></bondArray></molecule><molecule id="sg3" molID="m4" role="SuperatomSgroup" title="Ph"><atomArray><atom id="a24" elementType="C" x2="-3.240748574392062" y2="-1.0889444621007702" sgroupAttachmentPoint="1"/><atom id="a25" elementType="C" x2="-1.9070694525640226" y2="-0.3189444621007693"/><atom id="a26" elementType="C" x2="-0.5733903307359878" y2="-1.0889444621007716"/><atom id="a27" elementType="C" x2="-0.57339033073599" y2="-2.6289444621007707"/><atom id="a28" elementType="C" x2="-1.907069452564027" y2="-3.3989444621007676"/><atom id="a29" elementType="C" x2="-3.240748574392062" y2="-2.628944462100768"/></atomArray><bondArray><bond atomRefs2="a24 a25" order="2"/><bond atomRefs2="a25 a26" order="1"/><bond atomRefs2="a26 a27" order="2"/><bond atomRefs2="a27 a28" order="1"/><bond atomRefs2="a28 a29" order="2"/><bond atomRefs2="a24 a29" order="1"/></bondArray></molecule><molecule id="sg4" molID="m5" role="SuperatomSgroup" title="Ph"><atomArray><atom id="a30" elementType="C" x2="-3.240748574392062" y2="1.0889444239537962" sgroupAttachmentPoint="1"/><atom id="a31" elementType="C" x2="-1.9070694525640226" y2="1.858944423953798"/><atom id="a32" elementType="C" x2="-0.5733903307359869" y2="1.0889444239537953"/><atom id="a33" elementType="C" x2="-0.5733903307359896" y2="-0.45105557604620405"/><atom id="a34" elementType="C" x2="-1.907069452564027" y2="-1.221055576046201"/><atom id="a35" elementType="C" x2="-3.240748574392061" y2="-0.4510555760462016"/></atomArray><bondArray><bond atomRefs2="a30 a31" order="2"/><bond atomRefs2="a31 a32" order="1"/><bond atomRefs2="a32 a33" order="2"/><bond atomRefs2="a33 a34" order="1"/><bond atomRefs2="a34 a35" order="2"/><bond atomRefs2="a30 a35" order="1"/></bondArray></molecule><molecule id="sg5" molID="m6" role="SuperatomSgroup" title="Ph"><atomArray><atom id="a36" elementType="C" x2="-3.240748574392062" y2="2.6289444239537976" sgroupAttachmentPoint="1"/><atom id="a37" elementType="C" x2="-3.240748574392064" y2="1.088944423953793"/><atom id="a38" elementType="C" x2="-4.574427696220103" y2="0.31894442395379485"/><atom id="a39" elementType="C" x2="-5.908106818048136" y2="1.0889444239537984"/><atom id="a40" elementType="C" x2="-5.908106818048131" y2="2.6289444239537993"/><atom id="a41" elementType="C" x2="-4.574427696220095" y2="3.398944423953797"/></atomArray><bondArray><bond atomRefs2="a36 a37" order="2"/><bond atomRefs2="a37 a38" order="1"/><bond atomRefs2="a38 a39" order="2"/><bond atomRefs2="a39 a40" order="1"/><bond atomRefs2="a40 a41" order="2"/><bond atomRefs2="a36 a41" order="1"/></bondArray></molecule><molecule id="sg6" molID="m7" role="SuperatomSgroup" title="Ph"><atomArray><atom id="a42" elementType="C" x2="-1.9070694525640264" y2="3.3989444239537967" sgroupAttachmentPoint="1"/><atom id="a43" elementType="C" x2="-3.2407485743920637" y2="4.1689444239538"/><atom id="a44" elementType="C" x2="-3.240748574392061" y2="5.708944423953801"/><atom id="a45" elementType="C" x2="-1.9070694525640242" y2="6.4789444239537985"/><atom id="a46" elementType="C" x2="-0.5733903307359893" y2="5.7089444239537945"/><atom id="a47" elementType="C" x2="-0.5733903307359898" y2="4.168944423953796"/></atomArray><bondArray><bond atomRefs2="a42 a43" order="2"/><bond atomRefs2="a43 a44" order="1"/><bond atomRefs2="a44 a45" order="2"/><bond atomRefs2="a45 a46" order="1"/><bond atomRefs2="a46 a47" order="2"/><bond atomRefs2="a42 a47" order="1"/></bondArray></molecule></molecule></MChemicalStruct></MDocument></cml>
Note that in Marvin JS, the lone pairs of the P atoms are to the left of the P, whereas the starting points of the coordinate bonds are to the right of the P. This depiction makes it look like the P has a lone pair in addition to its complement of four bonds. Either the lone pair should not be displayed, or it should be displayed at the starting point of the coordinate bond. Note that in MarvinSketch, the lone pairs are correctly not displayed.