ChemWiki - User contributions [en]

Rep:Mod:ly2112

2016-12-16T14:04:31Z

Ly2112: /* The orbital interaction */

== Abstract ==
The Gaussian 09W and Gaussview 5.0 was used to modified and calculate the transition state of reactions involves Diels-Alder cycloaddition and cheletropic addition. The MO diagram and the activation energies were presented and analysed for different geometry of products and to obtained a preferred path way for reactions.

== Reaction of Butadiene with Ethylene ==

[[File:2016-12-16 07.58.56.png|thumb|Figure 1. Cycloaddtion of cis-butadiene with Ethylene.]]

The reaction of cis-butadiene with ethylene is a Diels-Alder reaction as a [4+2] cycloaddition reaction. The [4+2] indicates the number of electrons involved in this reaction. A six-membered ring is formed by converting two bond to Two bonds during the reaction.

----

=== Optimise the reactants and TS ===
{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!Point Group
!HOMO
!LUMO
|-
|Butadiene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2BUTENE.LOG)
|
[[File: Butpickk.PNG|300px]]
|0.09923
|C2
|[[File:2016-12-16 08.09.06.png|200px]]
|[[File:2016-12-16 08.11.19.png|200px]]

|-
|Ethylene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:1ETHENE.LOG)
|
[[File:Dienepickk.PNG|300px]]

|0.049447
|C2
|[[File:2016-12-16 08.12.44.png|200px]]
|[[File:2016-12-16 08.14.12.png|200px]]
|}

|
|

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Cyclo TS (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:5UDKS_5.LOG)
|[[File:TScyclopickk.PNG|300px]]
|0.2126
|[[File:2016-12-16 08.15.56.png|200px]]
|[[File:2016-12-16 08.17.11.png|200px]]
|}

==== MO diagram for the formation of the butadiene/ethene TS====

[[File:2016-12-16 08.25.06.png|400px]]

[[File:2016-12-16 10.58.42.png]]

The MOs of HOMO and LUMO is shown.
The allowed reaction must be followed the rule that the symmetries of the reactants and the transition state must be consistent. By analysing and comparing the MO diagraph of reaction and visualised the MO form the chk. File, the corresponding MO has proved the theory. The symmetric HOMO of ethylene reacts with the symmetric LUMO of butadiene to form the symmetric LUMO of transition state, and the asymmetric LUMO of ethylene reacts with the asymmetric HOMO of butadiene to form the asymmetric HOMO of transition state.

==== The orbital interaction ====

[[File:屏幕快照 2016-12-16 14.03.04.png|600px|center|thumb|Formula]]

The symmetric-symmetric interaction and asymmetric-asymmetric interaction has non-zero overlap integral as their orbitals overlap.

=== Optimise the final product ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Final Product (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:3FINAL_PRODUCT_CYCLOADDTION.LOG)
|[[File:2016-12-16 08.30.24.png|200px]]
|0.105183
|[[File:2016-12-16 08.32.16.png|200px]]
|[[File:2016-12-16 08.33.27.png|200px]]
|}

==== C-C bond length of the TS and product ====

{| class="wikitable" border="1"
|+
|-
| [[File:2016-12-16 08.36.28.png|400px]] || [[File:2016-12-16 08.42.56.png|400px]] || [[File:2016-12-16 08.43.50.png|400px]]

|}

The C,C bond (C1-C2, C3-C4) of butadiene in transition state(TS) is larger than it original value which is larger than the C=C bond and shorter than C-C bond. On the other hand, the C2-C3 bond of butadiene in TS is shorter than the C-C single bond of butadiene. Therefore the appearance of the bond length in transition state gives the evidence of the resonance of electron across the whole structure, and the C5-C6, C6-C1 bond length which is shorter than van Der Waals’ radius and longer than the typical SP3 C-C bond length indicates that the formation of a new C-C single bond between these two reactants. The final product showed a C-C bond length close to the typical SP3 C-C bond, but the two C-C bond(C1-C2), (C3-C4)which close to the double is slightly smaller than the literature value.

{| class="wikitable"
!Bond Length/Å
!C1-C2
!C2-C3
!C3-C4
!C4-C5
!C5-C6
!C6-C1
!Typical SP2 C=C Bond
!Typical SP3 C-C Bond
!Van Der Waals Radius of C,C
|-
|Butadiene
|1.335
|1.468
|1.335
|
|
|
|1.34
|1.54
|1.70
|-
|Ethylene
|1.327
|
|
|
|
|
|
|
|
|-
|TS
|1.395
|1.395
|1.395
|2.200
|1.395
|1.908
|
|
|
|-
|Final Product
|1.500
|1.338
|1.500
|1.540
|1.541
|1.540
|
|
|
|}

==== vibration at the transition state ====

{| class="wikitable" border="1"
|+The formation of two bonds with the first and negative imaginary frequency is synchronous.
! Frequency/cm-1 !! asynchronous
|-
| -948.34 || <jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 7; vibration 1;rotate x -20; </script>
<uploadedFileContents>Kkkk1.log</uploadedFileContents>
</jmolApplet>
</jmol>

|}

{| class="wikitable" border="1"
|+The formation of two bonds with the lowest positive frequency is asynchronous as shown below.
! Frequency/cm-1 !! asynchronous
|-
| 145.04 || <jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 8; vibration 1;rotate x -20; </script>
<uploadedFileContents>Kkkk2.log</uploadedFileContents>
</jmolApplet>
</jmol>

|}

== Reaction of Cyclohexadiene and 1,3-Dioxole ==

This reaction is a Diels Alder reaction with regio-selectivity. The transition state is optimised on both Semi-empirical/PM6 level and B3LYP/6-31G(d). Both reactants are optimised first on Semi-empirical/PM6 level to get a better geometry, followed by freezing the bond distances between reactive points of both reactants. 1,3-Dioxole is an electron poor dienophile due to the presence of two electrons withdrawing Oxygen therefore lower energy level for this reactant. In this case, the reaction is possibly to happened between the LUMO of 1,3-Dioxole and the HOMO of the Cyclohexadiene to undergo the normal Diels-Alder reaction. There are two conformation for the products, which are endo and exo form.

[[File:2016-12-16 09.29.14.png|800px|center|thumb|Fig 3. Reaction of Cyclohexadiene and 1,3-Dioxole to form Endo and Exo product]]

----

=== Optimise the reactants ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Cyclohexadiene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:CYCLODIENE_PM6_3.LOG)
|[[File:2016-12-16 09.36.26.png|200px]]
|0.118064
|[[File:Cyclo reactant HOMO.PNG|200px]]
|[[File:Cyclo reactant LUMO.PNG|200px]]
|}

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|1,3-Dioxole (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2DIO_ENE_NEWEST.LOG)
|[[File:2016-12-16 09.40.20.png|200px]]
| -0.052279
|[[File:2016-12-16 09.41.06.png|200px]]
|[[File:2016-12-16 09.41.54.png|200px]]
|}

=== Optimise the ENDO form ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Endo(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_10.48.49.png)(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:ENDO_TS_B3LYP631G_D.LOG)
|[[File:2016-12-16 10.48.49.png|200px]]
|0.137941
|[[File:2016-12-16 10.52.21.png|200px]]
|[[File:2016-12-16 10.53.37.png|200px]]
|}

=== Optimise the EXO form ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Exo(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_10.55.07.png)
|[[File:2016-12-16 10.55.07.png|200px]]
|0.138906
|[[File:2016-12-16 10.55.54.png|200px]]
|[[File:2016-12-16 10.57.09.png|200px]]
|}

[[File:18.54.png|center|600px|thumb|Inverse Demand of DA reaction]]

By comprising the MO diagrams of both TS, the reaction is happened between the LUMO of Cyclohexadiene and the HOMO of the 1,3-Dioxole to undergo the Inverse Diels-Alder reaction. This result indicates 1,3-Dioxole is an electron rich dienophile since it performs an inverse Diels-Alder reaction. The C=C bond of 1,3-Dioxole is possibly benefited from the donating of electron cloud density of Oxygen. This electro-donating effect raise the energy level of 1,3-Dioxole so the HOMO orbital of it is more close to the LUMO orbital of Diene.

=== Compare The reaction path of two products ===
[[File:2016-12-16 12.57.24.png]]

=== Secondary orbital interaction ===
[[File:Second thermo.PNG|center]]

The p-orbitals of Oxygen in endo conformation react with C=C bond and stabilise the transition state.

Therefore, there is a secondary reaction at HOMO for the endo form which lowered the reaction barrier, and stabilised the TS as well.

[[File:2016-12-16 12.58.47.png|center|400px]]

Endo has smaller activation energy and it is kinetically controlled, and less thermodynamically stable
Exo has slightly higher activation energy but more thermodynamically stable.
Overall, Exo conformation is preferred for this reaction.

The bonding of the 6-membered ring could be distorted during the reaction.

== Diels-Alder vs Cheletropic ==

[[File:2016-12-16 13.56.21.png]]

=== Optimise the TSs for the endo- and exo- Diels-Alder reaction ===

{| class="wikitable"
!Molecule
!Structure
!HOMO
!LUMO
|-
|XYLYLENE DIELS ALDER ENDO TS PM6 1(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:XYLYLENE_DIELS_ALDER_ENDO_TS_PM6_1.LOG)
|[[File:Xylylene TS endo.PNG|200px]]
|[[File:Xylylene TS endo HOMO.PNG|200px]]
|[[File:Xylylene TS endo LUMO.PNG|200px]]
|}

{| class="wikitable"
!Molecule
!Structure
!HOMO
!LUMO
|-
|XYLYLENE DIELS ALDER TS PM6 1(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:XYLYLENE_DIELS_ALDER_TS_PM6_1.LOG)
|[[File:Xylylene TS exo.PNG|200px]]
|[[File:Xylylene TS exo HOMO.PNG|200px]]
|[[File:Xylylene TS exo LUMO.PNG|200px]]
|}

=== Optimise the TSs for the heletropic reactions ===

{| class="wikitable"
!Molecule
!Structure
!HOMO
!LUMO
|-
|REACTANTS(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:REACTANTS_NEW.LOG)
|[[File:Xylylene TS chelate.PNG|200px]]
|[[File:Cyclo reactant HOMO.PNG|200px]]
|[[File:Cyclo reactant LUMO.PNG|200px]]
|}

=== IRC calculation for each path ===

[[File:Exo.PNG|600px|thumb|center|IRC/DA EXO]]
[[File:Irc chelate.PNG|600px|thumb|center|IRC/DA Chelate]]
[[File:Irc endo.PNG|600px|thumb|center|IRC/DA ENDO]]

=== The activation and reaction energies for each step ===

=== relative heights of the energy levels of the reactants ===

== Reference ==

1. Clayden, J., Greeves, N. and Warren, S. (2012). Organic chemistry. 2nd ed. Oxford: Oxford University Press.PP,P145

File:屏幕快照 2016-12-16 14.03.04.png

2016-12-16T14:03:35Z

Ly2112:

Rep:Mod:ly2112

2016-12-16T13:57:58Z

Ly2112: /* Diels-Alder vs Cheletropic */

== Abstract ==
The Gaussian 09W and Gaussview 5.0 was used to modified and calculate the transition state of reactions involves Diels-Alder cycloaddition and cheletropic addition. The MO diagram and the activation energies were presented and analysed for different geometry of products and to obtained a preferred path way for reactions.

== Reaction of Butadiene with Ethylene ==

[[File:2016-12-16 07.58.56.png|thumb|Figure 1. Cycloaddtion of cis-butadiene with Ethylene.]]

The reaction of cis-butadiene with ethylene is a Diels-Alder reaction as a [4+2] cycloaddition reaction. The [4+2] indicates the number of electrons involved in this reaction. A six-membered ring is formed by converting two bond to Two bonds during the reaction.

----

=== Optimise the reactants and TS ===
{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!Point Group
!HOMO
!LUMO
|-
|Butadiene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2BUTENE.LOG)
|
[[File: Butpickk.PNG|300px]]
|0.09923
|C2
|[[File:2016-12-16 08.09.06.png|200px]]
|[[File:2016-12-16 08.11.19.png|200px]]

|-
|Ethylene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:1ETHENE.LOG)
|
[[File:Dienepickk.PNG|300px]]

|0.049447
|C2
|[[File:2016-12-16 08.12.44.png|200px]]
|[[File:2016-12-16 08.14.12.png|200px]]
|}

|
|

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Cyclo TS (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:5UDKS_5.LOG)
|[[File:TScyclopickk.PNG|300px]]
|0.2126
|[[File:2016-12-16 08.15.56.png|200px]]
|[[File:2016-12-16 08.17.11.png|200px]]
|}

==== MO diagram for the formation of the butadiene/ethene TS====

[[File:2016-12-16 08.25.06.png|400px]]

[[File:2016-12-16 10.58.42.png]]

The MOs of HOMO and LUMO is shown.
The allowed reaction must be followed the rule that the symmetries of the reactants and the transition state must be consistent. By analysing and comparing the MO diagraph of reaction and visualised the MO form the chk. File, the corresponding MO has proved the theory. The symmetric HOMO of ethylene reacts with the symmetric LUMO of butadiene to form the symmetric LUMO of transition state, and the asymmetric LUMO of ethylene reacts with the asymmetric HOMO of butadiene to form the asymmetric HOMO of transition state.

==== The orbital interaction ====

The formula for overlap integral S is: S =
S0 , orbital do not overlap;
S0, orbitals overlap.

The symmetric-symmetric interaction and asymmetric-asymmetric interaction has non-zero overlap integral as their orbitals overlap.

=== Optimise the final product ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Final Product (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:3FINAL_PRODUCT_CYCLOADDTION.LOG)
|[[File:2016-12-16 08.30.24.png|200px]]
|0.105183
|[[File:2016-12-16 08.32.16.png|200px]]
|[[File:2016-12-16 08.33.27.png|200px]]
|}

==== C-C bond length of the TS and product ====

{| class="wikitable" border="1"
|+
|-
| [[File:2016-12-16 08.36.28.png|400px]] || [[File:2016-12-16 08.42.56.png|400px]] || [[File:2016-12-16 08.43.50.png|400px]]

|}

The C,C bond (C1-C2, C3-C4) of butadiene in transition state(TS) is larger than it original value which is larger than the C=C bond and shorter than C-C bond. On the other hand, the C2-C3 bond of butadiene in TS is shorter than the C-C single bond of butadiene. Therefore the appearance of the bond length in transition state gives the evidence of the resonance of electron across the whole structure, and the C5-C6, C6-C1 bond length which is shorter than van Der Waals’ radius and longer than the typical SP3 C-C bond length indicates that the formation of a new C-C single bond between these two reactants. The final product showed a C-C bond length close to the typical SP3 C-C bond, but the two C-C bond(C1-C2), (C3-C4)which close to the double is slightly smaller than the literature value.

{| class="wikitable"
!Bond Length/Å
!C1-C2
!C2-C3
!C3-C4
!C4-C5
!C5-C6
!C6-C1
!Typical SP2 C=C Bond
!Typical SP3 C-C Bond
!Van Der Waals Radius of C,C
|-
|Butadiene
|1.335
|1.468
|1.335
|
|
|
|1.34
|1.54
|1.70
|-
|Ethylene
|1.327
|
|
|
|
|
|
|
|
|-
|TS
|1.395
|1.395
|1.395
|2.200
|1.395
|1.908
|
|
|
|-
|Final Product
|1.500
|1.338
|1.500
|1.540
|1.541
|1.540
|
|
|
|}

==== vibration at the transition state ====

{| class="wikitable" border="1"
|+The formation of two bonds with the first and negative imaginary frequency is synchronous.
! Frequency/cm-1 !! asynchronous
|-
| -948.34 || <jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 7; vibration 1;rotate x -20; </script>
<uploadedFileContents>Kkkk1.log</uploadedFileContents>
</jmolApplet>
</jmol>

|}

{| class="wikitable" border="1"
|+The formation of two bonds with the lowest positive frequency is asynchronous as shown below.
! Frequency/cm-1 !! asynchronous
|-
| 145.04 || <jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 8; vibration 1;rotate x -20; </script>
<uploadedFileContents>Kkkk2.log</uploadedFileContents>
</jmolApplet>
</jmol>

|}

== Reaction of Cyclohexadiene and 1,3-Dioxole ==

This reaction is a Diels Alder reaction with regio-selectivity. The transition state is optimised on both Semi-empirical/PM6 level and B3LYP/6-31G(d). Both reactants are optimised first on Semi-empirical/PM6 level to get a better geometry, followed by freezing the bond distances between reactive points of both reactants. 1,3-Dioxole is an electron poor dienophile due to the presence of two electrons withdrawing Oxygen therefore lower energy level for this reactant. In this case, the reaction is possibly to happened between the LUMO of 1,3-Dioxole and the HOMO of the Cyclohexadiene to undergo the normal Diels-Alder reaction. There are two conformation for the products, which are endo and exo form.

[[File:2016-12-16 09.29.14.png|800px|center|thumb|Fig 3. Reaction of Cyclohexadiene and 1,3-Dioxole to form Endo and Exo product]]

----

=== Optimise the reactants ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Cyclohexadiene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:CYCLODIENE_PM6_3.LOG)
|[[File:2016-12-16 09.36.26.png|200px]]
|0.118064
|[[File:Cyclo reactant HOMO.PNG|200px]]
|[[File:Cyclo reactant LUMO.PNG|200px]]
|}

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|1,3-Dioxole (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2DIO_ENE_NEWEST.LOG)
|[[File:2016-12-16 09.40.20.png|200px]]
| -0.052279
|[[File:2016-12-16 09.41.06.png|200px]]
|[[File:2016-12-16 09.41.54.png|200px]]
|}

=== Optimise the ENDO form ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Endo(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_10.48.49.png)(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:ENDO_TS_B3LYP631G_D.LOG)
|[[File:2016-12-16 10.48.49.png|200px]]
|0.137941
|[[File:2016-12-16 10.52.21.png|200px]]
|[[File:2016-12-16 10.53.37.png|200px]]
|}

=== Optimise the EXO form ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Exo(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_10.55.07.png)
|[[File:2016-12-16 10.55.07.png|200px]]
|0.138906
|[[File:2016-12-16 10.55.54.png|200px]]
|[[File:2016-12-16 10.57.09.png|200px]]
|}

[[File:18.54.png|center|600px|thumb|Inverse Demand of DA reaction]]

By comprising the MO diagrams of both TS, the reaction is happened between the LUMO of Cyclohexadiene and the HOMO of the 1,3-Dioxole to undergo the Inverse Diels-Alder reaction. This result indicates 1,3-Dioxole is an electron rich dienophile since it performs an inverse Diels-Alder reaction. The C=C bond of 1,3-Dioxole is possibly benefited from the donating of electron cloud density of Oxygen. This electro-donating effect raise the energy level of 1,3-Dioxole so the HOMO orbital of it is more close to the LUMO orbital of Diene.

=== Compare The reaction path of two products ===
[[File:2016-12-16 12.57.24.png]]

=== Secondary orbital interaction ===
[[File:Second thermo.PNG|center]]

The p-orbitals of Oxygen in endo conformation react with C=C bond and stabilise the transition state.

Therefore, there is a secondary reaction at HOMO for the endo form which lowered the reaction barrier, and stabilised the TS as well.

[[File:2016-12-16 12.58.47.png|center|400px]]

Endo has smaller activation energy and it is kinetically controlled, and less thermodynamically stable
Exo has slightly higher activation energy but more thermodynamically stable.
Overall, Exo conformation is preferred for this reaction.

The bonding of the 6-membered ring could be distorted during the reaction.

== Diels-Alder vs Cheletropic ==

[[File:2016-12-16 13.56.21.png]]

=== Optimise the TSs for the endo- and exo- Diels-Alder reaction ===

{| class="wikitable"
!Molecule
!Structure
!HOMO
!LUMO
|-
|XYLYLENE DIELS ALDER ENDO TS PM6 1(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:XYLYLENE_DIELS_ALDER_ENDO_TS_PM6_1.LOG)
|[[File:Xylylene TS endo.PNG|200px]]
|[[File:Xylylene TS endo HOMO.PNG|200px]]
|[[File:Xylylene TS endo LUMO.PNG|200px]]
|}

{| class="wikitable"
!Molecule
!Structure
!HOMO
!LUMO
|-
|XYLYLENE DIELS ALDER TS PM6 1(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:XYLYLENE_DIELS_ALDER_TS_PM6_1.LOG)
|[[File:Xylylene TS exo.PNG|200px]]
|[[File:Xylylene TS exo HOMO.PNG|200px]]
|[[File:Xylylene TS exo LUMO.PNG|200px]]
|}

=== Optimise the TSs for the heletropic reactions ===

{| class="wikitable"
!Molecule
!Structure
!HOMO
!LUMO
|-
|REACTANTS(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:REACTANTS_NEW.LOG)
|[[File:Xylylene TS chelate.PNG|200px]]
|[[File:Cyclo reactant HOMO.PNG|200px]]
|[[File:Cyclo reactant LUMO.PNG|200px]]
|}

=== IRC calculation for each path ===

[[File:Exo.PNG|600px|thumb|center|IRC/DA EXO]]
[[File:Irc chelate.PNG|600px|thumb|center|IRC/DA Chelate]]
[[File:Irc endo.PNG|600px|thumb|center|IRC/DA ENDO]]

=== The activation and reaction energies for each step ===

=== relative heights of the energy levels of the reactants ===

== Reference ==

1. Clayden, J., Greeves, N. and Warren, S. (2012). Organic chemistry. 2nd ed. Oxford: Oxford University Press.PP,P145

Rep:Mod:ly2112

2016-12-16T13:57:05Z

Ly2112: /* Optimise the TSs for the heletropic reactions */

== Abstract ==
The Gaussian 09W and Gaussview 5.0 was used to modified and calculate the transition state of reactions involves Diels-Alder cycloaddition and cheletropic addition. The MO diagram and the activation energies were presented and analysed for different geometry of products and to obtained a preferred path way for reactions.

== Reaction of Butadiene with Ethylene ==

[[File:2016-12-16 07.58.56.png|thumb|Figure 1. Cycloaddtion of cis-butadiene with Ethylene.]]

The reaction of cis-butadiene with ethylene is a Diels-Alder reaction as a [4+2] cycloaddition reaction. The [4+2] indicates the number of electrons involved in this reaction. A six-membered ring is formed by converting two bond to Two bonds during the reaction.

----

=== Optimise the reactants and TS ===
{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!Point Group
!HOMO
!LUMO
|-
|Butadiene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2BUTENE.LOG)
|
[[File: Butpickk.PNG|300px]]
|0.09923
|C2
|[[File:2016-12-16 08.09.06.png|200px]]
|[[File:2016-12-16 08.11.19.png|200px]]

|-
|Ethylene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:1ETHENE.LOG)
|
[[File:Dienepickk.PNG|300px]]

|0.049447
|C2
|[[File:2016-12-16 08.12.44.png|200px]]
|[[File:2016-12-16 08.14.12.png|200px]]
|}

|
|

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Cyclo TS (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:5UDKS_5.LOG)
|[[File:TScyclopickk.PNG|300px]]
|0.2126
|[[File:2016-12-16 08.15.56.png|200px]]
|[[File:2016-12-16 08.17.11.png|200px]]
|}

==== MO diagram for the formation of the butadiene/ethene TS====

[[File:2016-12-16 08.25.06.png|400px]]

[[File:2016-12-16 10.58.42.png]]

The MOs of HOMO and LUMO is shown.
The allowed reaction must be followed the rule that the symmetries of the reactants and the transition state must be consistent. By analysing and comparing the MO diagraph of reaction and visualised the MO form the chk. File, the corresponding MO has proved the theory. The symmetric HOMO of ethylene reacts with the symmetric LUMO of butadiene to form the symmetric LUMO of transition state, and the asymmetric LUMO of ethylene reacts with the asymmetric HOMO of butadiene to form the asymmetric HOMO of transition state.

==== The orbital interaction ====

The formula for overlap integral S is: S =
S0 , orbital do not overlap;
S0, orbitals overlap.

The symmetric-symmetric interaction and asymmetric-asymmetric interaction has non-zero overlap integral as their orbitals overlap.

=== Optimise the final product ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Final Product (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:3FINAL_PRODUCT_CYCLOADDTION.LOG)
|[[File:2016-12-16 08.30.24.png|200px]]
|0.105183
|[[File:2016-12-16 08.32.16.png|200px]]
|[[File:2016-12-16 08.33.27.png|200px]]
|}

==== C-C bond length of the TS and product ====

{| class="wikitable" border="1"
|+
|-
| [[File:2016-12-16 08.36.28.png|400px]] || [[File:2016-12-16 08.42.56.png|400px]] || [[File:2016-12-16 08.43.50.png|400px]]

|}

The C,C bond (C1-C2, C3-C4) of butadiene in transition state(TS) is larger than it original value which is larger than the C=C bond and shorter than C-C bond. On the other hand, the C2-C3 bond of butadiene in TS is shorter than the C-C single bond of butadiene. Therefore the appearance of the bond length in transition state gives the evidence of the resonance of electron across the whole structure, and the C5-C6, C6-C1 bond length which is shorter than van Der Waals’ radius and longer than the typical SP3 C-C bond length indicates that the formation of a new C-C single bond between these two reactants. The final product showed a C-C bond length close to the typical SP3 C-C bond, but the two C-C bond(C1-C2), (C3-C4)which close to the double is slightly smaller than the literature value.

{| class="wikitable"
!Bond Length/Å
!C1-C2
!C2-C3
!C3-C4
!C4-C5
!C5-C6
!C6-C1
!Typical SP2 C=C Bond
!Typical SP3 C-C Bond
!Van Der Waals Radius of C,C
|-
|Butadiene
|1.335
|1.468
|1.335
|
|
|
|1.34
|1.54
|1.70
|-
|Ethylene
|1.327
|
|
|
|
|
|
|
|
|-
|TS
|1.395
|1.395
|1.395
|2.200
|1.395
|1.908
|
|
|
|-
|Final Product
|1.500
|1.338
|1.500
|1.540
|1.541
|1.540
|
|
|
|}

==== vibration at the transition state ====

{| class="wikitable" border="1"
|+The formation of two bonds with the first and negative imaginary frequency is synchronous.
! Frequency/cm-1 !! asynchronous
|-
| -948.34 || <jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 7; vibration 1;rotate x -20; </script>
<uploadedFileContents>Kkkk1.log</uploadedFileContents>
</jmolApplet>
</jmol>

|}

{| class="wikitable" border="1"
|+The formation of two bonds with the lowest positive frequency is asynchronous as shown below.
! Frequency/cm-1 !! asynchronous
|-
| 145.04 || <jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 8; vibration 1;rotate x -20; </script>
<uploadedFileContents>Kkkk2.log</uploadedFileContents>
</jmolApplet>
</jmol>

|}

== Reaction of Cyclohexadiene and 1,3-Dioxole ==

This reaction is a Diels Alder reaction with regio-selectivity. The transition state is optimised on both Semi-empirical/PM6 level and B3LYP/6-31G(d). Both reactants are optimised first on Semi-empirical/PM6 level to get a better geometry, followed by freezing the bond distances between reactive points of both reactants. 1,3-Dioxole is an electron poor dienophile due to the presence of two electrons withdrawing Oxygen therefore lower energy level for this reactant. In this case, the reaction is possibly to happened between the LUMO of 1,3-Dioxole and the HOMO of the Cyclohexadiene to undergo the normal Diels-Alder reaction. There are two conformation for the products, which are endo and exo form.

[[File:2016-12-16 09.29.14.png|800px|center|thumb|Fig 3. Reaction of Cyclohexadiene and 1,3-Dioxole to form Endo and Exo product]]

----

=== Optimise the reactants ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Cyclohexadiene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:CYCLODIENE_PM6_3.LOG)
|[[File:2016-12-16 09.36.26.png|200px]]
|0.118064
|[[File:Cyclo reactant HOMO.PNG|200px]]
|[[File:Cyclo reactant LUMO.PNG|200px]]
|}

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|1,3-Dioxole (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2DIO_ENE_NEWEST.LOG)
|[[File:2016-12-16 09.40.20.png|200px]]
| -0.052279
|[[File:2016-12-16 09.41.06.png|200px]]
|[[File:2016-12-16 09.41.54.png|200px]]
|}

=== Optimise the ENDO form ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Endo(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_10.48.49.png)(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:ENDO_TS_B3LYP631G_D.LOG)
|[[File:2016-12-16 10.48.49.png|200px]]
|0.137941
|[[File:2016-12-16 10.52.21.png|200px]]
|[[File:2016-12-16 10.53.37.png|200px]]
|}

=== Optimise the EXO form ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Exo(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_10.55.07.png)
|[[File:2016-12-16 10.55.07.png|200px]]
|0.138906
|[[File:2016-12-16 10.55.54.png|200px]]
|[[File:2016-12-16 10.57.09.png|200px]]
|}

[[File:18.54.png|center|600px|thumb|Inverse Demand of DA reaction]]

By comprising the MO diagrams of both TS, the reaction is happened between the LUMO of Cyclohexadiene and the HOMO of the 1,3-Dioxole to undergo the Inverse Diels-Alder reaction. This result indicates 1,3-Dioxole is an electron rich dienophile since it performs an inverse Diels-Alder reaction. The C=C bond of 1,3-Dioxole is possibly benefited from the donating of electron cloud density of Oxygen. This electro-donating effect raise the energy level of 1,3-Dioxole so the HOMO orbital of it is more close to the LUMO orbital of Diene.

=== Compare The reaction path of two products ===
[[File:2016-12-16 12.57.24.png]]

=== Secondary orbital interaction ===
[[File:Second thermo.PNG|center]]

The p-orbitals of Oxygen in endo conformation react with C=C bond and stabilise the transition state.

Therefore, there is a secondary reaction at HOMO for the endo form which lowered the reaction barrier, and stabilised the TS as well.

[[File:2016-12-16 12.58.47.png|center|400px]]

Endo has smaller activation energy and it is kinetically controlled, and less thermodynamically stable
Exo has slightly higher activation energy but more thermodynamically stable.
Overall, Exo conformation is preferred for this reaction.

The bonding of the 6-membered ring could be distorted during the reaction.

== Diels-Alder vs Cheletropic ==

=== Optimise the TSs for the endo- and exo- Diels-Alder reaction ===

{| class="wikitable"
!Molecule
!Structure
!HOMO
!LUMO
|-
|XYLYLENE DIELS ALDER ENDO TS PM6 1(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:XYLYLENE_DIELS_ALDER_ENDO_TS_PM6_1.LOG)
|[[File:Xylylene TS endo.PNG|200px]]
|[[File:Xylylene TS endo HOMO.PNG|200px]]
|[[File:Xylylene TS endo LUMO.PNG|200px]]
|}

{| class="wikitable"
!Molecule
!Structure
!HOMO
!LUMO
|-
|XYLYLENE DIELS ALDER TS PM6 1(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:XYLYLENE_DIELS_ALDER_TS_PM6_1.LOG)
|[[File:Xylylene TS exo.PNG|200px]]
|[[File:Xylylene TS exo HOMO.PNG|200px]]
|[[File:Xylylene TS exo LUMO.PNG|200px]]
|}

=== Optimise the TSs for the heletropic reactions ===

{| class="wikitable"
!Molecule
!Structure
!HOMO
!LUMO
|-
|REACTANTS(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:REACTANTS_NEW.LOG)
|[[File:Xylylene TS chelate.PNG|200px]]
|[[File:Cyclo reactant HOMO.PNG|200px]]
|[[File:Cyclo reactant LUMO.PNG|200px]]
|}

=== IRC calculation for each path ===

[[File:Exo.PNG|600px|thumb|center|IRC/DA EXO]]
[[File:Irc chelate.PNG|600px|thumb|center|IRC/DA Chelate]]
[[File:Irc endo.PNG|600px|thumb|center|IRC/DA ENDO]]

=== The activation and reaction energies for each step ===

=== relative heights of the energy levels of the reactants ===
== Reference ==

1. Clayden, J., Greeves, N. and Warren, S. (2012). Organic chemistry. 2nd ed. Oxford: Oxford University Press.PP,P145

File:2016-12-16 13.56.21.png

2016-12-16T13:56:51Z

Ly2112:

File:Cyclo reactant LUMO.PNG

2016-12-16T13:55:29Z

Ly2112: Ly2112 uploaded a new version of File:Cyclo reactant LUMO.PNG

File:Cyclo reactant HOMO.PNG

2016-12-16T13:55:02Z

Ly2112: Ly2112 uploaded a new version of File:Cyclo reactant HOMO.PNG

File:Xylylene TS chelate.PNG

2016-12-16T13:54:22Z

Ly2112:

File:REACTANTS NEW.LOG

2016-12-16T13:53:23Z

Ly2112: Ly2112 uploaded a new version of File:REACTANTS NEW.LOG

Rep:Mod:ly2112

2016-12-16T13:51:30Z

File:XYLYLENE DIELS ALDER ENDO TS PM6 1.LOG

2016-12-16T13:46:49Z

Ly2112:

File:Xylylene TS endo LUMO.PNG

2016-12-16T13:45:56Z

Ly2112:

File:Xylylene TS endo HOMO.PNG

2016-12-16T13:45:21Z

Ly2112:

File:Xylylene TS endo.PNG

2016-12-16T13:44:14Z

Ly2112:

Rep:Mod:ly2112

2016-12-16T13:27:24Z

Ly2112: /* Optimise the ENDO form */

== Abstract ==
The Gaussian 09W and Gaussview 5.0 was used to modified and calculate the transition state of reactions involves Diels-Alder cycloaddition and cheletropic addition. The MO diagram and the activation energies were presented and analysed for different geometry of products and to obtained a preferred path way for reactions.

== Reaction of Butadiene with Ethylene ==

[[File:2016-12-16 07.58.56.png|thumb|Figure 1. Cycloaddtion of cis-butadiene with Ethylene.]]

The reaction of cis-butadiene with ethylene is a Diels-Alder reaction as a [4+2] cycloaddition reaction. The [4+2] indicates the number of electrons involved in this reaction. A six-membered ring is formed by converting two bond to Two bonds during the reaction.

----

=== Optimise the reactants and TS ===
{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!Point Group
!HOMO
!LUMO
|-
|Butadiene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2BUTENE.LOG)
|
[[File: Butpickk.PNG|300px]]
|0.09923
|C2
|[[File:2016-12-16 08.09.06.png|200px]]
|[[File:2016-12-16 08.11.19.png|200px]]

|-
|Ethylene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:1ETHENE.LOG)
|
[[File:Dienepickk.PNG|300px]]

|0.049447
|C2
|[[File:2016-12-16 08.12.44.png|200px]]
|[[File:2016-12-16 08.14.12.png|200px]]
|}

|
|

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Cyclo TS (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:5UDKS_5.LOG)
|[[File:TScyclopickk.PNG|300px]]
|0.2126
|[[File:2016-12-16 08.15.56.png|200px]]
|[[File:2016-12-16 08.17.11.png|200px]]
|}

==== MO diagram for the formation of the butadiene/ethene TS====

[[File:2016-12-16 08.25.06.png|400px]]

[[File:2016-12-16 10.58.42.png]]

The MOs of HOMO and LUMO is shown.
The allowed reaction must be followed the rule that the symmetries of the reactants and the transition state must be consistent. By analysing and comparing the MO diagraph of reaction and visualised the MO form the chk. File, the corresponding MO has proved the theory. The symmetric HOMO of ethylene reacts with the symmetric LUMO of butadiene to form the symmetric LUMO of transition state, and the asymmetric LUMO of ethylene reacts with the asymmetric HOMO of butadiene to form the asymmetric HOMO of transition state.

==== The orbital interaction ====

The formula for overlap integral S is: S =
S0 , orbital do not overlap;
S0, orbitals overlap.

The symmetric-symmetric interaction and asymmetric-asymmetric interaction has non-zero overlap integral as their orbitals overlap.

=== Optimise the final product ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Final Product (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:3FINAL_PRODUCT_CYCLOADDTION.LOG)
|[[File:2016-12-16 08.30.24.png|200px]]
|0.105183
|[[File:2016-12-16 08.32.16.png|200px]]
|[[File:2016-12-16 08.33.27.png|200px]]
|}

==== C-C bond length of the TS and product ====

{| class="wikitable" border="1"
|+
|-
| [[File:2016-12-16 08.36.28.png|400px]] || [[File:2016-12-16 08.42.56.png|400px]] || [[File:2016-12-16 08.43.50.png|400px]]

|}

The C,C bond (C1-C2, C3-C4) of butadiene in transition state(TS) is larger than it original value which is larger than the C=C bond and shorter than C-C bond. On the other hand, the C2-C3 bond of butadiene in TS is shorter than the C-C single bond of butadiene. Therefore the appearance of the bond length in transition state gives the evidence of the resonance of electron across the whole structure, and the C5-C6, C6-C1 bond length which is shorter than van Der Waals’ radius and longer than the typical SP3 C-C bond length indicates that the formation of a new C-C single bond between these two reactants. The final product showed a C-C bond length close to the typical SP3 C-C bond, but the two C-C bond(C1-C2), (C3-C4)which close to the double is slightly smaller than the literature value.

{| class="wikitable"
!Bond Length/Å
!C1-C2
!C2-C3
!C3-C4
!C4-C5
!C5-C6
!C6-C1
!Typical SP2 C=C Bond
!Typical SP3 C-C Bond
!Van Der Waals Radius of C,C
|-
|Butadiene
|1.335
|1.468
|1.335
|
|
|
|1.34
|1.54
|1.70
|-
|Ethylene
|1.327
|
|
|
|
|
|
|
|
|-
|TS
|1.395
|1.395
|1.395
|2.200
|1.395
|1.908
|
|
|
|-
|Final Product
|1.500
|1.338
|1.500
|1.540
|1.541
|1.540
|
|
|
|}

==== vibration at the transition state ====

{| class="wikitable" border="1"
|+The formation of two bonds with the first and negative imaginary frequency is synchronous.
! Frequency/cm-1 !! asynchronous
|-
| -948.34 || <jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 7; vibration 1;rotate x -20; </script>
<uploadedFileContents>Kkkk1.log</uploadedFileContents>
</jmolApplet>
</jmol>

|}

{| class="wikitable" border="1"
|+The formation of two bonds with the lowest positive frequency is asynchronous as shown below.
! Frequency/cm-1 !! asynchronous
|-
| 145.04 || <jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 8; vibration 1;rotate x -20; </script>
<uploadedFileContents>Kkkk2.log</uploadedFileContents>
</jmolApplet>
</jmol>

|}

== Reaction of Cyclohexadiene and 1,3-Dioxole ==

This reaction is a Diels Alder reaction with regio-selectivity. The transition state is optimised on both Semi-empirical/PM6 level and B3LYP/6-31G(d). Both reactants are optimised first on Semi-empirical/PM6 level to get a better geometry, followed by freezing the bond distances between reactive points of both reactants. 1,3-Dioxole is an electron poor dienophile due to the presence of two electrons withdrawing Oxygen therefore lower energy level for this reactant. In this case, the reaction is possibly to happened between the LUMO of 1,3-Dioxole and the HOMO of the Cyclohexadiene to undergo the normal Diels-Alder reaction. There are two conformation for the products, which are endo and exo form.

[[File:2016-12-16 09.29.14.png|800px|center|thumb|Fig 3. Reaction of Cyclohexadiene and 1,3-Dioxole to form Endo and Exo product]]

----

=== Optimise the reactants ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Cyclohexadiene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:CYCLODIENE_PM6_3.LOG)
|[[File:2016-12-16 09.36.26.png|200px]]
|0.118064
|[[File:Cyclo reactant HOMO.PNG|200px]]
|[[File:Cyclo reactant LUMO.PNG|200px]]
|}

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|1,3-Dioxole (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2DIO_ENE_NEWEST.LOG)
|[[File:2016-12-16 09.40.20.png|200px]]
| -0.052279
|[[File:2016-12-16 09.41.06.png|200px]]
|[[File:2016-12-16 09.41.54.png|200px]]
|}

=== Optimise the ENDO form ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Endo(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_10.48.49.png)(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:ENDO_TS_B3LYP631G_D.LOG)
|[[File:2016-12-16 10.48.49.png|200px]]
|0.137941
|[[File:2016-12-16 10.52.21.png|200px]]
|[[File:2016-12-16 10.53.37.png|200px]]
|}

=== Optimise the EXO form ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Exo(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_10.55.07.png)
|[[File:2016-12-16 10.55.07.png|200px]]
|0.138906
|[[File:2016-12-16 10.55.54.png|200px]]
|[[File:2016-12-16 10.57.09.png|200px]]
|}

[[File:18.54.png|center|600px|thumb|Inverse Demand of DA reaction]]

By comprising the MO diagrams of both TS, the reaction is happened between the LUMO of Cyclohexadiene and the HOMO of the 1,3-Dioxole to undergo the Inverse Diels-Alder reaction. This result indicates 1,3-Dioxole is an electron rich dienophile since it performs an inverse Diels-Alder reaction. The C=C bond of 1,3-Dioxole is possibly benefited from the donating of electron cloud density of Oxygen. This electro-donating effect raise the energy level of 1,3-Dioxole so the HOMO orbital of it is more close to the LUMO orbital of Diene.

=== Compare The reaction path of two products ===
[[File:2016-12-16 12.57.24.png]]

=== Secondary orbital interaction ===
[[File:Second thermo.PNG|center]]

The p-orbitals of Oxygen in endo conformation react with C=C bond and stabilise the transition state.

Therefore, there is a secondary reaction at HOMO for the endo form which lowered the reaction barrier, and stabilised the TS as well.

[[File:2016-12-16 12.58.47.png|center|400px]]

Endo has smaller activation energy and it is kinetically controlled, and less thermodynamically stable
Exo has slightly higher activation energy but more thermodynamically stable.
Overall, Exo conformation is preferred for this reaction.

The bonding of the 6-membered ring could be distorted during the reaction.

== Diels-Alder vs Cheletropic ==

=== Optimise the TSs for the endo- and exo- Diels-Alder reaction ===
=== Optimise the TSs for the heletropic reactions ===

=== IRC calculation for each path ===

[[File:Exo.PNG|600px|thumb|center|IRC/DA EXO]]
[[File:Irc chelate.PNG|600px|thumb|center|IRC/DA Chelate]]
[[File:Irc endo.PNG|600px|thumb|center|IRC/DA ENDO]]

=== The activation and reaction energies for each step ===

=== relative heights of the energy levels of the reactants ===
== Reference ==

1. Clayden, J., Greeves, N. and Warren, S. (2012). Organic chemistry. 2nd ed. Oxford: Oxford University Press.PP,P145

Rep:Mod:ly2112

Rep:Mod:ly2112

2016-12-16T12:42:51Z

Ly2112: /* Optimise the reactants */

== Abstract ==
The Gaussian 09W and Gaussview 5.0 was used to modified and calculate the transition state of reactions involves Diels-Alder cycloaddition and cheletropic addition. The MO diagram and the activation energies were presented and analysed for different geometry of products and to obtained a preferred path way for reactions.

== Reaction of Butadiene with Ethylene ==

[[File:2016-12-16 07.58.56.png|thumb|Figure 1. Cycloaddtion of cis-butadiene with Ethylene.]]

The reaction of cis-butadiene with ethylene is a Diels-Alder reaction as a [4+2] cycloaddition reaction. The [4+2] indicates the number of electrons involved in this reaction. A six-membered ring is formed by converting two bond to Two bonds during the reaction.

----

=== Optimise the reactants and TS ===
{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!Point Group
!HOMO
!LUMO
|-
|Butadiene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2BUTENE.LOG)
|
[[File: Butpickk.PNG|300px]]
|0.09923
|C2
|[[File:2016-12-16 08.09.06.png|200px]]
|[[File:2016-12-16 08.11.19.png|200px]]

|-
|Ethylene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:1ETHENE.LOG)
|
[[File:Dienepickk.PNG|300px]]

|0.049447
|C2
|[[File:2016-12-16 08.12.44.png|200px]]
|[[File:2016-12-16 08.14.12.png|200px]]
|}

|
|

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Cyclo TS (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:5UDKS_5.LOG)
|[[File:TScyclopickk.PNG|300px]]
|0.2126
|[[File:2016-12-16 08.15.56.png|200px]]
|[[File:2016-12-16 08.17.11.png|200px]]
|}

==== MO diagram for the formation of the butadiene/ethene TS====

[[File:2016-12-16 08.25.06.png|400px]]

The MOs of HOMO and LUMO is shown.
The allowed reaction must be followed the rule that the symmetries of the reactants and the transition state must be consistent. By analysing and comparing the MO diagraph of reaction and visualised the MO form the chk. File, the corresponding MO has proved the theory. The symmetric HOMO of ethylene reacts with the symmetric LUMO of butadiene to form the symmetric LUMO of transition state, and the asymmetric LUMO of ethylene reacts with the asymmetric HOMO of butadiene to form the asymmetric HOMO of transition state.

==== The orbital interaction ====

The formula for overlap integral S is: S =
S0 , orbital do not overlap;
S0, orbitals overlap.

The symmetric-symmetric interaction and asymmetric-asymmetric interaction has non-zero overlap integral as their orbitals overlap.

=== Optimise the final product ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Final Product (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:3FINAL_PRODUCT_CYCLOADDTION.LOG)
|[[File:2016-12-16 08.30.24.png|200px]]
|0.105183
|[[File:2016-12-16 08.32.16.png|200px]]
|[[File:2016-12-16 08.33.27.png|200px]]
|}

==== C-C bond length of the TS and product ====

{| class="wikitable" border="1"
|+
|-
| [[File:2016-12-16 08.36.28.png|400px]] || [[File:2016-12-16 08.42.56.png|400px]] || [[File:2016-12-16 08.43.50.png|400px]]

|}

The C,C bond (C1-C2, C3-C4) of butadiene in transition state(TS) is larger than it original value which is larger than the C=C bond and shorter than C-C bond. On the other hand, the C2-C3 bond of butadiene in TS is shorter than the C-C single bond of butadiene. Therefore the appearance of the bond length in transition state gives the evidence of the resonance of electron across the whole structure, and the C5-C6, C6-C1 bond length which is shorter than van Der Waals’ radius and longer than the typical SP3 C-C bond length indicates that the formation of a new C-C single bond between these two reactants. The final product showed a C-C bond length close to the typical SP3 C-C bond, but the two C-C bond(C1-C2), (C3-C4)which close to the double is slightly smaller than the literature value.

{| class="wikitable"
!Bond Length/Å
!C1-C2
!C2-C3
!C3-C4
!C4-C5
!C5-C6
!C6-C1
!Typical SP2 C=C Bond
!Typical SP3 C-C Bond
!Van Der Waals Radius of C,C
|-
|Butadiene
|1.335
|1.468
|1.335
|
|
|
|1.34
|1.54
|1.70
|-
|Ethylene
|1.327
|
|
|
|
|
|
|
|
|-
|TS
|1.395
|1.395
|1.395
|2.200
|1.395
|1.908
|
|
|
|-
|Final Product
|1.500
|1.338
|1.500
|1.540
|1.541
|1.540
|
|
|
|}

==== vibration at the transition state ====

{| class="wikitable" border="1"
|+The formation of two bonds with the first and negative imaginary frequency is synchronous.
! Frequency/cm-1 !! asynchronous
|-
| -948.34 || <jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 7; vibration 1;rotate x -20; </script>
<uploadedFileContents>Kkkk1.log</uploadedFileContents>
</jmolApplet>
</jmol>

|}

{| class="wikitable" border="1"
|+The formation of two bonds with the lowest positive frequency is asynchronous as shown below.
! Frequency/cm-1 !! asynchronous
|-
| 145.04 || <jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 8; vibration 1;rotate x -20; </script>
<uploadedFileContents>Kkkk2.log</uploadedFileContents>
</jmolApplet>
</jmol>

|}

== Reaction of Cyclohexadiene and 1,3-Dioxole ==

This reaction is a Diels Alder reaction with regio-selectivity. The transition state is optimised on both Semi-empirical/PM6 level and B3LYP/6-31G(d). Both reactants are optimised first on Semi-empirical/PM6 level to get a better geometry, followed by freezing the bond distances between reactive points of both reactants. 1,3-Dioxole is an electron poor dienophile due to the presence of two electrons withdrawing Oxygen therefore lower energy level for this reactant. In this case, the reaction is possibly to happened between the LUMO of 1,3-Dioxole and the HOMO of the Cyclohexadiene to undergo the normal Diels-Alder reaction. There are two conformation for the products, which are endo and exo form.

[[File:2016-12-16 09.29.14.png|800px|center|thumb|Fig 3. Reaction of Cyclohexadiene and 1,3-Dioxole to form Endo and Exo product]]

----

=== Optimise the reactants ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Cyclohexadiene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:CYCLODIENE_PM6_3.LOG)
|[[File:2016-12-16 09.36.26.png|200px]]
|0.118064
|[[File:Cyclo reactant HOMO.PNG|200px]]
|[[File:Cyclo reactant LUMO.PNG|200px]]
|}

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|1,3-Dioxole (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2DIO_ENE_NEWEST.LOG)
|[[File:2016-12-16 09.40.20.png|200px]]
|-0.052279
|[[File:2016-12-16 09.41.06.png|200px]]
|[[File:2016-12-16 09.41.54.png|200px]]
|}

=== Optimise the ENDO form ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Endo(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_10.48.49.png)
|[[File:2016-12-16 10.48.49.png|200px]]
|0.137941
|[[File:2016-12-16 10.52.21.png|200px]]
|[[File:2016-12-16 10.53.37.png|200px]]
|}

=== Optimise the EXO form ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Exo(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_10.55.07.png)
|[[File:2016-12-16 10.55.07.png|200px]]
|0.138906
|[[File:2016-12-16 10.55.54.png|200px]]
|[[File:2016-12-16 10.57.09.png|200px]]
|}

[[File:2016-12-16 10.58.42.png]]

By comprising the MO diagrams of both TS, the reaction is happened between the LUMO of 1,3-Dioxole and the HOMO of the Cyclohexadiene to undergo the normal Diels-Alder reaction. Therefore 1,3-Dioxole is an electron poor dienophile which performs a normal Diels-Alder reaction. The C=C bond of 1,3-Dioxole is possibly affected by the inductive effect of Oxygen which drag electron density away from it, and lowered the energy level of 1,3-Dioxole as well.

=== Compare The reaction path of two products ===

=== Secondary orbital interaction ===
[[File:Second thermo.PNG|center]]

The p-orbitals of Oxygen in endo conformation react with C=C bond and stabilise the transition state.

Therefore, there is a secondary reaction at HOMO for the endo form which lowered the reaction barrier, and stabilised the TS as well.

== Diels-Alder vs Cheletropic ==

=== Optimise the TSs for the endo- and exo- Diels-Alder reaction ===
=== Optimise the TSs for the heletropic reactions ===

=== IRC calculation for each path ===

[[File:Exo.PNG|300px|thumb|center|IRC/DA EXO]]
[[File:Irc chelate.PNG|300px|thumb|center|IRC/DA Chelate]]
[[File:Irc endo.PNG|300px|thumb|center|IRC/DA ENDO]]

=== The activation and reaction energies for each step ===

=== relative heights of the energy levels of the reactants ===
== Reference ==

1. Clayden, J., Greeves, N. and Warren, S. (2012). Organic chemistry. 2nd ed. Oxford: Oxford University Press.PP,P145

File:2DIO ENE NEWEST.LOG

2016-12-16T12:42:36Z

Ly2112:

File:CYCLODIENE PM6 3.LOG

2016-12-16T12:42:02Z

Ly2112:

Rep:Mod:ly2112

2016-12-16T12:09:12Z

Ly2112: /* Optimise the final product */

== Abstract ==
The Gaussian 09W and Gaussview 5.0 was used to modified and calculate the transition state of reactions involves Diels-Alder cycloaddition and cheletropic addition. The MO diagram and the activation energies were presented and analysed for different geometry of products and to obtained a preferred path way for reactions.

== Reaction of Butadiene with Ethylene ==

[[File:2016-12-16 07.58.56.png|thumb|Figure 1. Cycloaddtion of cis-butadiene with Ethylene.]]

The reaction of cis-butadiene with ethylene is a Diels-Alder reaction as a [4+2] cycloaddition reaction. The [4+2] indicates the number of electrons involved in this reaction. A six-membered ring is formed by converting two bond to Two bonds during the reaction.

----

=== Optimise the reactants and TS ===
{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!Point Group
!HOMO
!LUMO
|-
|Butadiene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:Butpickk.PNG)
|
[[File: Butpickk.PNG|300px]]
|0.09923
|C2
|[[File:2016-12-16 08.09.06.png|200px]]
|[[File:2016-12-16 08.11.19.png|200px]]

|-
|Ethylene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:Dienepickk.PNG)
|
[[File:Dienepickk.PNG|300px]]

|0.049447
|C2
|[[File:2016-12-16 08.12.44.png|200px]]
|[[File:2016-12-16 08.14.12.png|200px]]
|}

|
|

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Cyclo TS (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:TScyclopickk.PNG)
|[[File:TScyclopickk.PNG|300px]]
|0.2126
|[[File:2016-12-16 08.15.56.png|200px]]
|[[File:2016-12-16 08.17.11.png|200px]]
|}

==== MO diagram for the formation of the butadiene/ethene TS====

[[File:2016-12-16 08.25.06.png|400px]]

The MOs of HOMO and LUMO is shown.
The allowed reaction must be followed the rule that the symmetries of the reactants and the transition state must be consistent. By analysing and comparing the MO diagraph of reaction and visualised the MO form the chk. File, the corresponding MO has proved the theory. The symmetric HOMO of ethylene reacts with the symmetric LUMO of butadiene to form the symmetric LUMO of transition state, and the asymmetric LUMO of ethylene reacts with the asymmetric HOMO of butadiene to form the asymmetric HOMO of transition state.

==== The orbital interaction ====

The formula for overlap integral S is: S =
S0 , orbital do not overlap;
S0, orbitals overlap.

The symmetric-symmetric interaction and asymmetric-asymmetric interaction has non-zero overlap integral as their orbitals overlap.

=== Optimise the final product ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Final Product (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_08.30.24.png)
|[[File:2016-12-16 08.30.24.png|200px]]
|0.105183
|[[File:2016-12-16 08.32.16.png|200px]]
|[[File:2016-12-16 08.33.27.png|200px]]
|}

==== C-C bond length of the TS and product ====

{| class="wikitable" border="1"
|+
|-
| [[File:2016-12-16 08.36.28.png|400px]] || [[File:2016-12-16 08.42.56.png|400px]] || [[File:2016-12-16 08.43.50.png|400px]]

|}

The C,C bond (C1-C2, C3-C4) of butadiene in transition state(TS) is larger than it original value which is larger than the C=C bond and shorter than C-C bond. On the other hand, the C2-C3 bond of butadiene in TS is shorter than the C-C single bond of butadiene. Therefore the appearance of the bond length in transition state gives the evidence of the resonance of electron across the whole structure, and the C5-C6, C6-C1 bond length which is shorter than van Der Waals’ radius and longer than the typical SP3 C-C bond length indicates that the formation of a new C-C single bond between these two reactants. The final product showed a C-C bond length close to the typical SP3 C-C bond, but the two C-C bond(C1-C2), (C3-C4)which close to the double is slightly smaller than the literature value.

{| class="wikitable"
!Bond Length/Å
!C1-C2
!C2-C3
!C3-C4
!C4-C5
!C5-C6
!C6-C1
!Typical SP2 C=C Bond
!Typical SP3 C-C Bond
!Van Der Waals Radius of C,C
|-
|Butadiene
|1.335
|1.468
|1.335
|
|
|
|1.34
|1.54
|1.70
|-
|Ethylene
|1.327
|
|
|
|
|
|
|
|
|-
|TS
|1.395
|1.395
|1.395
|2.200
|1.395
|1.908
|
|
|
|-
|Final Product
|1.500
|1.338
|1.500
|1.540
|1.541
|1.540
|
|
|
|}

==== vibration at the transition state ====

{| class="wikitable" border="1"
|+The formation of two bonds with the first and negative imaginary frequency is synchronous.
! Frequency/cm-1 !! asynchronous
|-
| -948.34 || <jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 7; vibration 1;rotate x -20; </script>
<uploadedFileContents>Kkkk1.log</uploadedFileContents>
</jmolApplet>
</jmol>

|}

{| class="wikitable" border="1"
|+The formation of two bonds with the lowest positive frequency is asynchronous as shown below.
! Frequency/cm-1 !! asynchronous
|-
| 145.04 || <jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 8; vibration 1;rotate x -20; </script>
<uploadedFileContents>Kkkk2.log</uploadedFileContents>
</jmolApplet>
</jmol>

|}

== Reaction of Cyclohexadiene and 1,3-Dioxole ==

This reaction is a Diels Alder reaction with regio-selectivity. The transition state is optimised on both Semi-empirical/PM6 level and B3LYP/6-31G(d). Both reactants are optimised first on Semi-empirical/PM6 level to get a better geometry, followed by freezing the bond distances between reactive points of both reactants. 1,3-Dioxole is an electron poor dienophile due to the presence of two electrons withdrawing Oxygen therefore lower energy level for this reactant. In this case, the reaction is possibly to happened between the LUMO of 1,3-Dioxole and the HOMO of the Cyclohexadiene to undergo the normal Diels-Alder reaction. There are two conformation for the products, which are endo and exo form.

[[File:2016-12-16 09.29.14.png|800px|center|thumb|Fig 3. Reaction of Cyclohexadiene and 1,3-Dioxole to form Endo and Exo product]]

----

=== Optimise the reactants ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Cyclohexadiene (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_09.36.26.png)
|[[File:2016-12-16 09.36.26.png|200px]]
|
|[[File:Cyclo reactant HOMO.PNG|200px]]
|[[File:Cyclo reactant LUMO.PNG|200px]]
|}

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|1,3-Dioxole (https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_09.40.20.png)
|[[File:2016-12-16 09.40.20.png|200px]]
|
|[[File:2016-12-16 09.41.06.png|200px]]
|[[File:2016-12-16 09.41.54.png|200px]]
|}

=== Optimise the ENDO form ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Endo(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_10.48.49.png)
|[[File:2016-12-16 10.48.49.png|200px]]
|
|[[File:2016-12-16 10.52.21.png|200px]]
|[[File:2016-12-16 10.53.37.png|200px]]
|}

=== Optimise the EXO form ===

{| class="wikitable"
!Molecule
!Structure
!Semi-Emirical Energy (Hartrees)
!HOMO
!LUMO
|-
|Exo(https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:2016-12-16_10.55.07.png)
|[[File:2016-12-16 10.55.07.png|200px]]
|
|[[File:2016-12-16 10.55.54.png|200px]]
|[[File:2016-12-16 10.57.09.png|200px]]
|}

[[File:2016-12-16 10.58.42.png]]

By comprising the MO diagrams of both TS, the reaction is happened between the LUMO of 1,3-Dioxole and the HOMO of the Cyclohexadiene to undergo the normal Diels-Alder reaction. Therefore 1,3-Dioxole is an electron poor dienophile which performs a normal Diels-Alder reaction. The C=C bond of 1,3-Dioxole is possibly affected by the inductive effect of Oxygen which drag electron density away from it, and lowered the energy level of 1,3-Dioxole as well.

=== Compare The reaction path of two products ===

=== Secondary orbital interaction ===
[[File:Second thermo.PNG|center]]

The p-orbitals of Oxygen in endo conformation react with C=C bond and stabilise the transition state.

Therefore, there is a secondary reaction at HOMO for the endo form which lowered the reaction barrier, and stabilised the TS as well.

== Diels-Alder vs Cheletropic ==

=== Optimise the TSs for the endo- and exo- Diels-Alder reaction ===
=== Optimise the TSs for the heletropic reactions ===

=== IRC calculation for each path ===

[[File:Exo.PNG|300px|thumb|center|IRC/DA EXO]]
[[File:Irc chelate.PNG|300px|thumb|center|IRC/DA Chelate]]
[[File:Irc endo.PNG|300px|thumb|center|IRC/DA ENDO]]

=== The activation and reaction energies for each step ===

=== relative heights of the energy levels of the reactants ===
== Reference ==

1. Clayden, J., Greeves, N. and Warren, S. (2012). Organic chemistry. 2nd ed. Oxford: Oxford University Press.PP,P145