BINAP

Good morning,





I am trying to represent the structure of BINAP with Marvin Sketch and then convert it as a Smiles or Extended Smiles to save into the database.


The chirality seems to get lost.





Thanks


Catherine





PS I am using Marvin 4.1.5

This molecule is chiral, yet it has no stereogenic center.


We can describe configuration around tetrahedral centers in SMILES.





Moreover it is not possible to describe BINAP in SMILES because of its axial chirality.





Andras

You need to use 3D coordinates to describe BINAP in chiral form, because it is chiral only by virtue of its conformation. You can use MOL or MRV formats to include the 3D coordinates.





For example:

Code:

<?xml version="1.0" ?> <MDocument>   <propertyList>     <property dictRef="viewEulerAngles" title="viewEulerAngles">       <array size="3" dataType="xsd:double">-2.948274206092586 0.7138525045200579 0.1238312576276376</array>     </property>   </propertyList>   <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 a35 a36 a37 a38 a39 a40 a41 a42 a43 a44 a45 a46 a47 a48 a49 a50 a51 a52 a53 a54 a55 a56 a57 a58"           elementType="C C C C C C C C C C C C C C C C C C C C P P H H H H H H H H H H H H C C C C C C C C C C C C C C C C C C C C C C C C"           x3="4.105213751050888 3.676409866107244 3.7320027118744954 4.243181012810373 4.609557376783327 4.485771916261958 4.7318633206283724 5.056090234130277 4.708058753821775 4.176309061192116 4.521243197577686 5.493093492666828 6.881247945323145 7.779265889307941 7.31483479051512 5.9690990553364305 5.080747785998162 3.777684638817537 2.9179033451697696 3.272464253099408 5.86956089749235 2.1725880586341604 3.336880191685306 3.4147485702096514 4.326767094291609 4.959399007016734 4.840363332868233 3.897633059088046 7.253735210421554 8.771373169306827 7.9544920100392815 5.647760708428752 3.4543106380182245 2.0169740648853227 5.026262349055522 3.992929164004831 3.344157636115493 3.7112633631922 4.727074659273827 5.377713174591996 7.404779353077783 8.434833622897825 9.760214229281546 10.083493803588317 9.077084360268138 7.755578474839813 0.7425667997150422 0.03317667988903479 -1.1925417539205743 -1.7289546457717946 -1.0385863603620513 0.18946284621938414 1.9943213631624257 2.0156892414002603 1.923257972683437 1.7676318581399446 1.691455927316187 1.796316262037041"           y3="-0.3898159990323614 -0.8200116392629463 0.05819267654586602 1.3522701375184012 1.8023675950902203 0.9672673999047615 1.4236133424350106 0.3918317502396403 -0.9506025907749661 -1.3290779213156776 2.832522362730905 3.550468230284988 3.260585425070256 3.8843461033172724 4.821057979841591 5.204880266315745 4.61939505177936 5.119671316354832 4.619424979335177 3.5260913010436927 0.5983576014611395 3.1939719358450644 -1.775626433395378 -0.25191453094227334 1.975170595076745 2.7580571157933584 -1.703985803655435 -2.305227730406733 2.573552679624801 3.6420930583400484 5.236193185900821 5.920165658661307 5.881167669102901 5.091140059924754 0.3909522020486454 -0.5624490392289518 -0.7158831346346168 0.0873068808163957 1.046705413053203 1.1996394069391998 -0.050049135615961915 0.6999881889966195 0.2259414562342894 -1.0291447776345877 -1.8075456328308388 -1.3236456590812669 2.5147748644935897 2.885857369938837 2.2762486097388863 1.2881214861548078 0.9113766544569065 1.5191444826549563 4.357131494350388 3.953127687279392 4.887364445587896 6.253015393467039 6.675988716338947 5.738269178124965"           z3="0.533326093430326 1.80880096584442 2.8971343760946593 2.7176872297807124 1.4330119821336444 0.29356249088920067 -1.0474518833204165 -2.0125597375907196 -1.7298450276653763 -0.5011798544841451 -1.4318193863101236 -2.212291884332178 -2.187742537032619 -3.0776763210892923 -4.013155913985393 -3.9964629905321534 -3.067044589482772 -2.9807797927312847 -2.008650220368578 -1.1826731452536763 -3.4472486473379043 0.020360134992991063 1.9579909789532963 3.8188024280888726 3.522991923670209 1.3381581499213837 -2.407354862738129 -0.35966732947209357 -1.5290358889660478 -3.059989889559074 -4.694915005284695 -4.656755580862472 -3.5860225720667063 -1.936042015645063 -4.848205124492666 -5.012149606036243 -6.250334983469091 -7.34259757106873 -7.194386633605751 -5.956207576531425 -3.5125995964752623 -4.134309203298968 -4.193533697271964 -3.6540019202824983 -3.0610616894876994 -2.993059945662793 -0.43374735548889404 -1.600713927893153 -1.921216675587625 -1.079191668146332 0.0856618449105483 0.4064672252535406 1.2006458678406242 2.558923921528321 3.6093796207442517 3.3239107228131055 1.9875226064040221 0.9409087318365729"           />       <bondArray>         <bond atomRefs2="a1 a2" order="A" />         <bond atomRefs2="a1 a6" order="A" />         <bond atomRefs2="a1 a10" order="A" />         <bond atomRefs2="a2 a3" order="A" />         <bond atomRefs2="a3 a4" order="A" />         <bond atomRefs2="a4 a5" order="A" />         <bond atomRefs2="a5 a6" order="A" />         <bond atomRefs2="a6 a7" order="A" />         <bond atomRefs2="a7 a8" order="A" />         <bond atomRefs2="a8 a9" order="A" />         <bond atomRefs2="a9 a10" order="A" />         <bond atomRefs2="a7 a11" order="1" />         <bond atomRefs2="a20 a11" order="A" />         <bond atomRefs2="a12 a11" order="A" />         <bond atomRefs2="a12 a13" order="A" />         <bond atomRefs2="a12 a17" order="A" />         <bond atomRefs2="a13 a14" order="A" />         <bond atomRefs2="a14 a15" order="A" />         <bond atomRefs2="a15 a16" order="A" />         <bond atomRefs2="a16 a17" order="A" />         <bond atomRefs2="a17 a18" order="A" />         <bond atomRefs2="a18 a19" order="A" />         <bond atomRefs2="a19 a20" order="A" />         <bond atomRefs2="a2 a23" order="1" />         <bond atomRefs2="a3 a24" order="1" />         <bond atomRefs2="a4 a25" order="1" />         <bond atomRefs2="a5 a26" order="1" />         <bond atomRefs2="a9 a27" order="1" />         <bond atomRefs2="a10 a28" order="1" />         <bond atomRefs2="a13 a29" order="1" />         <bond atomRefs2="a14 a30" order="1" />         <bond atomRefs2="a15 a31" order="1" />         <bond atomRefs2="a16 a32" order="1" />         <bond atomRefs2="a18 a33" order="1" />         <bond atomRefs2="a19 a34" order="1" />         <bond atomRefs2="a20 a22" order="1" />         <bond atomRefs2="a8 a21" order="1" />         <bond atomRefs2="a21 a35" order="1" />         <bond atomRefs2="a21 a41" order="1" />         <bond atomRefs2="a35 a36" order="A" />         <bond atomRefs2="a35 a40" order="A" />         <bond atomRefs2="a36 a37" order="A" />         <bond atomRefs2="a37 a38" order="A" />         <bond atomRefs2="a38 a39" order="A" />         <bond atomRefs2="a39 a40" order="A" />         <bond atomRefs2="a41 a42" order="A" />         <bond atomRefs2="a41 a46" order="A" />         <bond atomRefs2="a42 a43" order="A" />         <bond atomRefs2="a43 a44" order="A" />         <bond atomRefs2="a44 a45" order="A" />         <bond atomRefs2="a45 a46" order="A" />         <bond atomRefs2="a22 a47" order="1" />         <bond atomRefs2="a22 a53" order="1" />         <bond atomRefs2="a47 a48" order="A" />         <bond atomRefs2="a47 a52" order="A" />         <bond atomRefs2="a48 a49" order="A" />         <bond atomRefs2="a49 a50" order="A" />         <bond atomRefs2="a50 a51" order="A" />         <bond atomRefs2="a51 a52" order="A" />         <bond atomRefs2="a53 a54" order="A" />         <bond atomRefs2="a53 a58" order="A" />         <bond atomRefs2="a54 a55" order="A" />         <bond atomRefs2="a55 a56" order="A" />         <bond atomRefs2="a56 a57" order="A" />         <bond atomRefs2="a57 a58" order="A" />       </bondArray>     </molecule>   </MChemicalStruct> </MDocument>

You can invert it to get the other enantiomer at http://epoch.chem.uky.edu/epoch-plugin/public/invertStereo.jsp this page.

Cool, thank you, I only edited your URL to get rid of some extra chars. Apparently it works fine for helicene also.