View source for Rep:AM4463Appendix

This page contains JSmol structures for molecules optimised at the AM1 level as part of the ''Transition States and Reactivity'' computational experiment. The orbitals are hidden by default. To view them, click the appropriate button below each JSmol applet. Please be patient when loading the structures and their orbitals. For the relevant section of the wiki for this experiment, click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=AM4463#Diels-Alder_Cycloaddition '''here'''].

===Ethene===
<jmol>
<jmolApplet>
<color>white</color>
<uploadedFileContents>ETHENE_AM1_am5713.LOG</uploadedFileContents>
<name>ethene</name>
<script>frame 12; center 000; zoom 300; rotate x 90; rotate y 90;rotate x 10; abc=0; set antialiasdisplay on</script>
</jmolApplet>
<jmolbutton>
<script>if (abc==0) abc=1; frame 12; mo 6; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; elseif (abc==2) abc=1; frame 12; mo 6; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>ethene</target>
<text>Toggle HOMO</text>
</jmolbutton>
<jmolbutton>
<script>if (abc==0) abc=2; frame 12; mo 7; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; elseif (abc==1) abc=2; frame 12; mo 7; mo nodots nomesh fill translucent;mo titleformat "";else; abc=0; mo off; endif</script>
<target>ethene</target>
<text>Toggle LUMO</text>
</jmolbutton>
</jmol>

===Butadiene===

<jmol>
<jmolApplet>
<color>white</color>
<uploadedFileContents>BUTADIENE_AM1_am5713.LOG</uploadedFileContents>
<name>butadiene</name>
<script>frame 14; center 000;rotate x 90;rotate y -45;rotate x 25;zoom 250;abc=0; set antialiasdisplay on</script>
</jmolApplet>
<jmolbutton>
<script>if (abc==0) abc=1; frame 14; mo 11; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; elseif (abc==2) abc=1; frame 14; mo 11; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>butadiene</target>
<text>Toggle HOMO</text>
</jmolbutton>
<jmolbutton>
<script>if (abc==0) abc=2; frame 14; mo 12; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; elseif (abc==1) abc=2; frame 14; mo 12; mo nodots nomesh fill translucent;mo titleformat "";else; abc=0; mo off; endif</script>
<target>butadiene</target>
<text>Toggle LUMO</text>
</jmolbutton>
</jmol>

===Ethylene + Butadiene Transition State===

<jmol>
<jmolApplet>
<color>white</color>
<uploadedFileContents>ETHENE_BUTADIENE_TS_GUESS_2_BERNY(AM1).LOG</uploadedFileContents>
<name>ethenets</name>
<script>frame 34; center 000;rotate z -90;zoom 180;abc=0; set antialiasdisplay on</script>
</jmolApplet>
<jmolbutton>
<script>if (abc==0) abc=1; frame 34; mo 17; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; elseif (abc==2) abc=1; frame 34; mo 17; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>ethenets</target>
<text>Toggle HOMO</text>
</jmolbutton>
<jmolbutton>
<script>if (abc==0) abc=2; frame 34; mo 18; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; elseif (abc==1) abc=2; frame 34; mo 18; mo nodots nomesh fill translucent;mo titleformat "";else; abc=0; mo off; endif</script>
<target>ethenets</target>
<text>Toggle LUMO</text>
</jmolbutton>
</jmol>

===Maleic Anhydride===

<jmol>
<jmolApplet>
<color>white</color>
<uploadedFileContents>MALEIC_ANHYDRIDE_AM1(OPT).LOG</uploadedFileContents>
<name>maleic</name>
<script>frame 20; center 000;rotate x 180; rotate y 90;rotate x -50;zoom 180;abc=0; set antialiasdisplay on</script>
</jmolApplet>
<jmolbutton>
<script>if (abc==0) abc=1; frame 20; mo 18; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; elseif (abc==2) abc=1; frame 20; mo 18; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>maleic</target>
<text>Toggle HOMO</text>
</jmolbutton>
<jmolbutton>
<script>if (abc==0) abc=2; frame 20; mo 19; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; elseif (abc==1) abc=2; frame 20; mo 19; mo nodots nomesh fill translucent;mo titleformat "";else; abc=0; mo off; endif</script>
<target>maleic</target>
<text>Toggle LUMO</text>
</jmolbutton>
</jmol>

===Cyclohexa-1,3-diene===

<jmol>
<jmolApplet>
<color>white</color>
<uploadedFileContents>CYCLOHEXADIENE_AM1_OPT_am5713.LOG</uploadedFileContents>
<name>hexadiene</name>
<script>frame 22; center 000;rotate z -90; rotate x 220;zoom 180; abc=0; set antialiasdisplay on</script>
</jmolApplet>
<jmolbutton>
<script>if (abc==0) abc=1; frame 22; mo 16; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; elseif (abc==2) abc=1; frame 22; mo 16; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>hexadiene</target>
<text>Toggle HOMO</text>
</jmolbutton>
<jmolbutton>
<script>if (abc==0) abc=2; frame 22; mo 17; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; elseif (abc==1) abc=2; frame 22; mo 17; mo nodots nomesh fill translucent;mo titleformat "";else; abc=0; mo off; endif</script>
<target>hexadiene</target>
<text>Toggle LUMO</text>
</jmolbutton>
</jmol>

===Exo Transition State===

To view a new MO after one is already loaded, please click the button twice.

<jmol>
<jmolApplet>
<color>white</color>
<uploadedFileContents>EXO_TS_AM1_QST2_am5713.LOG</uploadedFileContents>
<name>exo</name>
<script>frame 68; center 000;rotate z -90; rotate x 180; rotate y 180; zoom 130; abc=0; set antialiasdisplay on</script>
</jmolApplet>
<jmolbutton>
<script>if (abc==0) abc=1; frame 68; mo 33; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>exo</target>
<text>HOMO -1</text>
</jmolbutton>
<jmolbutton>
<script>if (abc==0) abc=2; frame 68; mo 34; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>exo</target>
<text>HOMO</text>
</jmolbutton>
<jmolbutton>
<script>if (abc==0) abc=3; frame 68; mo 35; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>exo</target>
<text>LUMO</text>
</jmolbutton>
<jmolbutton>
<script>if (abc==0) abc=4; frame 68; mo 36; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>exo</target>
<text>LUMO +1</text>
</jmolbutton>
<jmolbutton>
<script>if (abc==0) abc=5; frame 68; mo 37; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>exo</target>
<text>LUMO +2</text>
</jmolbutton>
</jmol>

===Endo Transition State===

To view a new MO after one is already loaded, please click the button twice.

<jmol>
<jmolApplet>
<color>white</color>
<uploadedFileContents>ENDO_TS_QST2_AM1_am5713.LOG</uploadedFileContents>
<name>endo</name>
<script>frame 68; center 000;rotate z -90; rotate x 180; zoom 130; abc=0; set antialiasdisplay on</script>
</jmolApplet>
<jmolbutton>
<script>if (abc==0) abc=1; frame 46; mo 33; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>endo</target>
<text>HOMO -1</text>
</jmolbutton>
<jmolbutton>
<script>if (abc==0) abc=2; frame 46; mo 34; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>endo</target>
<text>HOMO</text>
</jmolbutton>
<jmolbutton>
<script>if (abc==0) abc=3; frame 46; mo 35; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>endo</target>
<text>LUMO</text>
</jmolbutton>
<jmolbutton>
<script>if (abc==0) abc=4; frame 46; mo 36; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>endo</target>
<text>LUMO +1</text>
</jmolbutton>
<jmolbutton>
<script>if (abc==0) abc=5; frame 46; mo 37; mo nodots nomesh fill translucent;mo titleformat ""; mo cutoff 0.02; else; abc=0; mo off; endif</script>
<target>endo</target>
<text>LUMO +2</text>
</jmolbutton>
</jmol>