View source for Rep:Mod:cjc415 jmol

==Exercise 1==

{| class="wikitable"
|-
| colspan="3"|'''Butadiene'''
|-
! Optimised molecule
! HOMO
! LUMO
|-
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 34</script>
 <uploadedFileContents>CJC415 Ex1 BUTADIENE MINIMISED UPDATED.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 34; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex1 BUTADIENE MINIMISED UPDATED.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 34; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex1 BUTADIENE MINIMISED UPDATED.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|}
It is to be noted that the trans-butadiene form is the lowest global energy minimum.  However, it is the cis conformation that is reacting with ethene. 

{| class="wikitable"
|-
| colspan="3"|'''Ethene'''
|-
! Optimised molecule
! HOMO
! LUMO
|-
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 12</script>
 <uploadedFileContents>CJC415 ETHENE MINIMISED.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 12; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 ETHENE MINIMISED.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 12; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 ETHENE MINIMISED.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|}

{| class="wikitable"
|-
| colspan="5"|'''Transition state'''
|-
! Optimised TS
! MO 16 
! MO 17 (HOMO)
! MO 18 (LUMO)
! MO 19
|-
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 26</script>
 <uploadedFileContents>CJC415 Ex1 CORRECT PRODUCT MINIMISEDTS.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 108; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex1 CORRECT PRODUCT MINIMISEDTS.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 108; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex1 CORRECT PRODUCT MINIMISEDTS.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 108; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex1 CORRECT PRODUCT MINIMISEDTS.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 108; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex1 CORRECT PRODUCT MINIMISEDTS.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|}

==Exercise 2==
{| class="wikitable"
|-
| colspan="3"|'''Cyclohexadiene'''
|-
! Optimised molecule
! HOMO
! LUMO
|-
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 20</script>
 <uploadedFileContents>CJC415 Ex2 CORRECT CYCLOHEXADIENE B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 20; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex2 CORRECT CYCLOHEXADIENE B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 20; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex2 CORRECT CYCLOHEXADIENE B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|}


{| class="wikitable"
|-
| colspan="3"|'''1,3 dioxole'''
|-
! Optimised molecule
! HOMO
! LUMO
|-
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 12</script>
 <uploadedFileContents>CJC415 Ex2 DIOXOLE B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex2 DIOXOLE B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex2 DIOXOLE B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|}

{| class="wikitable"
|-
| colspan="2"|'''Optimised products'''
|-
! Exo product
! Endo product
|-
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 20</script>
 <uploadedFileContents>CJC415 Ex2 EXO PRODUCT MINIMISED B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 20</script>
 <uploadedFileContents>CJC415 Ex2 ENDO PRODUCT MINIMISED B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|}


{| class="wikitable"
|-
| colspan="5"|'''Transition State MOs - Exo product'''
|-
! Optimised molecule
! MO 40
! MO 41 (HOMO)
! MO 42 (LUMO)
! MO 43
|-
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 12</script>
 <uploadedFileContents>CJC415 Ex2 EXO TS B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 54; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex2 EXO TS B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 54; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex2 EXO TS B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 54; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex2 EXO TS B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 54; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex2 EXO TS B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|}


{| class="wikitable"
|-
| colspan="5"|'''Transition State MOs - Endo product'''
|-
! Optimised molecule
! MO 40
! MO 41 (HOMO)
! MO 42 (LUMO)
! MO 43
|-
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 12</script>
 <uploadedFileContents>CJC415 Ex2 ENDO TS B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 52; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex2 ENDO TS B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 52; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex2 ENDO TS B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 52; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex2 ENDO TS B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
| <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 52; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
 <uploadedFileContents>CJC415 Ex2 ENDO TS B3LYP.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|}

==Exercise 3==

{| class="wikitable"
|-
| colspan="8"|'''Optimised structures at 298K'''
|-
! Xylylene
! SO2
! Endo TS
! Exo TS
! Cheletropic TS
! Endo Product
! Exo Product
! Cheletropic Product
|- 
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 20</script>
 <uploadedFileContents>CJC415 Ex3 XYLYLENE REACTANT.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 20</script>
 <uploadedFileContents>CJC415 Ex3 SO2 REACTANT.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 20</script>
 <uploadedFileContents>CJC415 Ex3 ENDO TS MINIMUM.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 20</script>
 <uploadedFileContents>CJC415 Ex3 EXO TS MINIMUM.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 20</script>
 <uploadedFileContents>CJC415 Ex3 CHELETROPIC TS MINIMUM.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 20</script>
 <uploadedFileContents>CJC415 Ex3 ENDO PRODUCT.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 20</script>
 <uploadedFileContents>CJC415 Ex3 EXO PRODUCT.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|  <jmol>
 <jmolApplet>
 <color>white</color>
 <size>200</size>
 <script>frame 20</script>
 <uploadedFileContents>CJC415 Ex3 CHELETROPIC PRODUCT.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>