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Rep:Gcw114: Transition States and Reactivity

2017-02-10T11:48:57Z

Gcw114: /* Conclusion */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is an inverse demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

=== MO Diagram ===
[[File:GcwEx1 MO.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="8"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== MO Diagram ===
[[File:GcwEx2 MO.png|thumb|centre|500px|Diagram 8:MO diagram of Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole.]]

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Reaction Energies==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]

The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

[[File:Gcw114E2 2ndorbital 02.png|thumb|centre|500px|Diagram 10: Secondary orbital interaction between Cyclohexadiene and 1,3-Dioxole ]]

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Reaction Energies==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEX3 energy profile 05.png|thumb|centre|500px|Diagram 11: Energy Profile of reaction between Xylylene and sulphur dioxide.]]

From the energy profile, The Exo product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is exo product. Endo product is kinectically favorable.

Rep:Gcw114: Transition States and Reactivity

2017-02-10T11:47:54Z

Gcw114: /* Reaction Energies */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is an inverse demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

=== MO Diagram ===
[[File:GcwEx1 MO.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="8"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== MO Diagram ===
[[File:GcwEx2 MO.png|thumb|centre|500px|Diagram 8:MO diagram of Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole.]]

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Reaction Energies==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]

The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

[[File:Gcw114E2 2ndorbital 02.png|thumb|centre|500px|Diagram 10: Secondary orbital interaction between Cyclohexadiene and 1,3-Dioxole ]]

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Reaction Energies==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEX3 energy profile 05.png|thumb|centre|500px|Diagram 11: Energy Profile of reaction between Xylylene and sulphur dioxide.]]

From the energy profile, The Exo product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is chelatropic. Endo product is kinectically favorable.

File:GcwEX3 energy profile 05.png

2017-02-10T11:47:11Z

Gcw114:

Rep:Gcw114: Transition States and Reactivity

2017-02-10T11:37:56Z

Gcw114: /* Reaction Energies */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is an inverse demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

=== MO Diagram ===
[[File:GcwEx1 MO.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="8"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== MO Diagram ===
[[File:GcwEx2 MO.png|thumb|centre|500px|Diagram 8:MO diagram of Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole.]]

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Reaction Energies==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]

The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

[[File:Gcw114E2 2ndorbital 02.png|thumb|centre|500px|Diagram 10: Secondary orbital interaction between Cyclohexadiene and 1,3-Dioxole ]]

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Reaction Energies==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 11: Energy Profile of reaction between Xylylene and sulphur dioxide.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is chelatropic. Endo product is kinectically favorable.

Rep:Gcw114: Transition States and Reactivity

2017-02-10T11:37:33Z

Gcw114: /* Reaction Energies */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is an inverse demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

=== MO Diagram ===
[[File:GcwEx1 MO.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="8"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== MO Diagram ===
[[File:GcwEx2 MO.png|thumb|centre|500px|Diagram 8:MO diagram of Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole.]]

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Reaction Energies==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]

The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

[[File:Gcw114E2 2ndorbital 02.png|thumb|centre|500px|Diagram 10: Secondary orbital interaction between Cyclohexadiene and 1,3-Dioxole ]]

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Reaction Energies==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 10: Energy Profile of reaction between Xylylene and sulphur dioxide.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is chelatropic. Endo product is kinectically favorable.

Rep:Gcw114: Transition States and Reactivity

2017-02-10T11:37:05Z

Gcw114: /* Reaction Energies */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is an inverse demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

=== MO Diagram ===
[[File:GcwEx1 MO.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="8"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== MO Diagram ===
[[File:GcwEx2 MO.png|thumb|centre|500px|Diagram 8:MO diagram of Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole.]]

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Reaction Energies==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]

The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 10: Secondary orbital interaction between Cyclohexadiene and 1,3-Dioxole ]]

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Reaction Energies==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 10: Energy Profile of reaction between Xylylene and sulphur dioxide.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is chelatropic. Endo product is kinectically favorable.

File:Gcw114E2 2ndorbital 02.png

2017-02-10T11:36:07Z

Gcw114:

Rep:Gcw114: Transition States and Reactivity

2017-02-10T11:19:08Z

Gcw114: /* Reaction Energies */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is an inverse demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

=== MO Diagram ===
[[File:GcwEx1 MO.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="8"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== MO Diagram ===
[[File:GcwEx2 MO.png|thumb|centre|500px|Diagram 8:MO diagram of Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole.]]

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Reaction Energies==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]

The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Reaction Energies==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 10: Energy Profile of reaction between Xylylene and sulphur dioxide.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is chelatropic. Endo product is kinectically favorable.

Rep:Gcw114: Transition States and Reactivity

2017-02-10T11:18:42Z

Gcw114: /* Reaction Energies */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is an inverse demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

=== MO Diagram ===
[[File:GcwEx1 MO.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="8"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== MO Diagram ===
[[File:GcwEx2 MO.png|thumb|centre|500px|Diagram 8:MO diagram of Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole.]]

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Reaction Energies==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]

The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Reaction Energies==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 10: Energy Profile of reaction between Xylylene and sulphur dioxide.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is chelatropic. Endo product is kinectically favorable.

Rep:Gcw114: Transition States and Reactivity

2017-02-10T11:18:17Z

Gcw114: /* Bond Length Analysis */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is an inverse demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

=== MO Diagram ===
[[File:GcwEx1 MO.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="8"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== MO Diagram ===
[[File:GcwEx2 MO.png|thumb|centre|500px|Diagram 8:MO diagram of Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole.]]

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Reaction Energies==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]
The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Reaction Energies==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 10: Energy Profile of reaction between Xylylene and sulphur dioxide.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is chelatropic. Endo product is kinectically favorable.

Rep:Gcw114: Transition States and Reactivity

2017-02-10T11:17:44Z

Gcw114: /* Thermochemistry data */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is an inverse demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

=== MO Diagram ===
[[File:GcwEx1 MO.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== MO Diagram ===
[[File:GcwEx2 MO.png|thumb|centre|500px|Diagram 8:MO diagram of Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole.]]

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Reaction Energies==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]
The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Reaction Energies==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 10: Energy Profile of reaction between Xylylene and sulphur dioxide.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is chelatropic. Endo product is kinectically favorable.

Rep:Gcw114: Transition States and Reactivity

2017-02-10T11:17:23Z

Gcw114: /* Energy data */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is an inverse demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

=== MO Diagram ===
[[File:GcwEx1 MO.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== MO Diagram ===
[[File:GcwEx2 MO.png|thumb|centre|500px|Diagram 8:MO diagram of Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole.]]

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Reaction Energies==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]
The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 10: Energy Profile of reaction between Xylylene and sulphur dioxide.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is chelatropic. Endo product is kinectically favorable.

Rep:Gcw114: Transition States and Reactivity

2017-02-10T11:16:10Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is an inverse demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

=== MO Diagram ===
[[File:GcwEx1 MO.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== MO Diagram ===
[[File:GcwEx2 MO.png|thumb|centre|500px|Diagram 8:MO diagram of Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole.]]

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Energy data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]
The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 10: Energy Profile of reaction between Xylylene and sulphur dioxide.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is chelatropic. Endo product is kinectically favorable.

File:GcwEx2 MO.png

2017-02-10T11:13:54Z

Gcw114:

Rep:Gcw114: Transition States and Reactivity

2017-02-10T11:04:07Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is an inverse demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

=== MO Diagram ===
[[File:GcwEx1 MO.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Energy data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 8: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]
The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is chelatropic. Endo product is kinectically favorable.

Rep:Gcw114: Transition States and Reactivity

2017-02-10T10:57:00Z

Gcw114: /* MO Diagram */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of S,AS,AS and S.

=== MO Diagram ===
[[File:GcwEx1 MO.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Energy data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 8: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]
The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is chelatropic. Endo product is kinectically favorable.

File:GcwEx1 MO.png

2017-02-10T10:56:31Z

Gcw114:

Rep:Gcw114: Transition States and Reactivity

2017-02-10T04:35:34Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of S,AS,AS and S.

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Energy data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 8: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]
The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.

Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.

Exercise 3: Xylylene and sulphur dioxide can be reacted through Diels-Alder or Cheletropic pathway. The thermodynamically favored product is chelatropic. Endo product is kinectically favorable.

Rep:Gcw114: Transition States and Reactivity

2017-02-10T04:32:44Z

Gcw114: /* Exercise 3: Diels-Alder vs Cheletropic */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of S,AS,AS and S.

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Energy data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 8: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]
The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

Intrinsic reaction coordinate is used to determine the reaction profile from reactant to product. The successful IRC will shows the reaction profiles as above. Xylylene is unstable. From the IRC, it can be observed that when the 6-membered ring is formed the electrons quickly delocalised.The bond is delocalised and it is more reactive.

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.
Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.
Exercise 3:

Rep:Gcw114: Transition States and Reactivity

2017-02-10T04:23:05Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel-Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. This is determined by looking at the position of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of S,AS,AS and S.

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Energy data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 8: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]
The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinetic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to the secondary interaction between carbon and oxygen.

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram 9: Energy Profile of reaction between.]]

From the energy profile, The Cheletropic product is a thermodynamically favored product, while the endo product is a kinetically favorable product.

== Conclusion==
Exercise 1: The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. The C-C bond length changes from reactant to product.
Exercise 2: The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. Endo product is the kinetic product with secondary orbital interaction which lowers the activation energies barrier.
Exercise 3:

Rep:Gcw114: Transition States and Reactivity

2017-02-10T04:09:29Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of S,AS,AS and S.

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

==Energy data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 8: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]
The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinetically favorable product. The kinectic product forms much quicker than endo product. The Exo product is a thermodynamically favorable product and there is less steric interaction.

From the HOMO of transition states, there is secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting between non-bonding atoms. From the energy profile, endo has lower activation energy due to secondary interaction between carbon and oxygen.

== Exercise 3: Diels-Alder vs Cheletropic ==
In the exercise, xylylene and sulphur dioxide is react through Diels-Alder or Cheletropic pathway.
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 9: Structure of xylylene and sulphur dioxide
|-
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 10: Transition state and product of Xylylene and sulphur dioxide through Diels-Alder.
|-
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 11: Transition state and product of Xylylene and sulphur dioxide through Cheletropic.
|-
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="2"|Table 12: GIF of reaction between Xylylene and sulphur dioxide and its IRC reaction profile.
|-
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T03:47:17Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method. The frontier orbital of reaction is shown in the diagram below.

The Diels-Alder reaction between butadiene and ethene is a normal demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of S,AS,AS and S.

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

==Energy data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="5"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}
The Diels-Alder reaction between Cyclohexadiene and 1,3-Dioxole is an inverse demand reaction. This is determined by looking at the postion of the transition state of MO symmetry order. The symmetry of HOMO-1, HOMO , LUMO and LUMO-1 are in the order of AS,S,S and AS.

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 8: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]
The Endo pathway has slightly lower activation energy barrier which makes the endo product as a kinectically favourable product. The kinectic product forms much quicker than endo product. The Exo product is a thermodynamically favourable product and becasue there is less steric interaction.

From the HOMO of transition states, there are secondary orbital interaction in Endo pathway. The secondary orbital interaction has lowered the activation energy barrier by interacting betwwen non-bonding orbital.

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T02:45:17Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method.The frontier orbital of reaction is shown in the diagram below.
=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 2: Frontier Orbitals of transition state of reaction s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 3: C-C bonds length from reactant to product
|-
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 4: Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 5: Transition state and product of the Endo and Exo pathway.
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 6: Frontier Orbitals of Transition State of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

==Energy data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 7: Energy data obtained from the reaction of Cyclohexadiene and 1,3-Dioxole.
|-
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 8: Activation Energies and Reaction energies of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 8: Energy Profile of reaction between Cyclohexadiene and 1,3-Dioxole ]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T02:34:52Z

Gcw114: /* Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method.The frontier orbital of reaction is shown in the diagram below.
=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Bonding Interaction
| AntiBonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
| AntiBonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (LUMO cyclohexadiene & HOMO 1,3-Dioxole)
| Bonding (HOMO cyclohexadiene & LUMO 1,3-Dioxole)
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T02:21:49Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|600px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction, the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product, the reactant has to overcome a barrier to the reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is known as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result in the formation of the product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional space, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which give the PES.

The transition states can be obtained by taking the first and second derivative. In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight into the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimized using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimized using the same method.The frontier orbital of reaction is shown in the diagram below.
=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== Frontier Orbitals of s-cis butadiene and ethene ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero, the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"| 1.48
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthened.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shorten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with the same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram 6: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram 7: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

The reaction of cyclohexadiene and 1,3-dioxole can undergo two reaction pathway: Endo an Exo. The 1,3-Dioxole approaches the cyclohexadiene at different orientations to forms two transition states as shown in diagram 7. Both starting reactants cyclohexadiene and 1,3-dioxole are first optimized using semi-empirical method with PM6 basis set then higher DFT method with B3LYP631Gd basis set. The optimized reactants are used to from a proposed structure of TS where it also undergoes the same optimization process as before. The IRC is run to determine the reaction coordinate of the Endo and Exo pathway. The results are discussed in the session below.

=== Frontier Orbitals of Cyclohexadiene and 1,3-Dioxole ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" | Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T02:06:51Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====

Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative. In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight for the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]

Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimised using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimised using the same method.The frontier orbital of reaction is shown in the diagram below.
=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero , the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

=== Bond Length Analysis ===
The table below shows the change of length in C-C bonds from reactant to product.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
! Bond
! Bond length (angstrom)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}

From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthen.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shroten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with same length and the internuclear distance reduced.

As for the transition state, the bond length of all bonds is in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T02:02:39Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight for the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]
Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimised using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimised using the same method.The frontier orbital of reaction is shown in the diagram below.
=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethenee
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}

Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero , the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}
From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthen.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shroten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with same length and the internuclear distance reduced.

As for the transiton state, the bond length of all bonds are in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T01:59:17Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight for the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]
Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimised using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimised using the same method.The frontier orbital of reaction is shown in the diagram below.
=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
|}

Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero , the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}
From reactant to product,
1. The C1-C4, C12-C14 and C7-C10 change from double bond to single bond. Hence, the bond is lengthen.
2. The C10-12 changes from a single bond to double bond. Hence, the bond is shroten
3. C1-C7 and C14-4 are the newly formed bonds. These two bonds are with same length and the internuclear distance reduced.

As for the transiton state, the bond length of all bonds are in between their bond length for reactants and products except for C1-C7 and C14-4.
The Van Der Waals radius of C-C is 170pm (1.7 angstrom). For C1-C7 and C14-4, the bond length is in between 3.4 angstrom (two carbon bond length) and 1.54 angstrom (literature value for sp3C-sp3C)

[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T01:33:52Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight for the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]
Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimised using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimised using the same method.The frontier orbital of reaction is shown in the diagram below.
=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
Diagram 4: Transition state of Diels-Alder reaction between butadiene and ethene
|}

Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero , the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T01:30:28Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight for the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]
Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimised using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimised using the same method.The frontier orbital of reaction is shown in the diagram below.
=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<title>Diagram 4: Transition State of the Diel Alders reaction</title>
<align>Centre</align>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

Transition state of the reaction of butadiene and ethene are shown in diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

ALong the reaction coordinate, for reaction to occur, both reactants has to come in the same symmetry.The TS HOMO-1 (bonding) and TS LUMO+1 (antibonding) have resulted from the asymmetrical HOMO of butadiene and asymmetrical LUMO of ethene. On the other hand, the interaction between symmetrical LUMO of butadiene and symmetrical HOMO of ethene has caused the TS HOMO (bonding) and LUMO(antibonding).

The bonding reaction would have a positive integral while the antibonding reaction would have a zero integral. When a symmetrical MO reacts with an asymmetrical MO the overlap integral is zero. Besides that, the stabilising effect of bonding interaction will cancel out the destabilising effect of antibonding interaction.Hence, there are not interaction between symmetrical MO and asymmetrical MO.

For the interaction of symmetrical pair and asymmetrical pair, the overlap integral is non-zero , the bonding one would have a stabilising effect whereas the antibonding will have a destabilising effect.

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram 5: Reactant with numbered atoms.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T01:01:51Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight for the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]
Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimised using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimised using the same method.The frontier orbital of reaction is shown in the diagram below.
=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<title>Diagram 4: Transition State of the Diel Alders reaction</title>
<align>Centre</align>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>

Transition state of the reaction of butadiene and ethene are shown in the diagram 4. The molecular orbitals formed are displayed and we can clearly see the relation between the frontier orbital and TS symmetry.

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T00:53:16Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight for the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]
Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimised using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimised using the same method.The frontier orbital of reaction is shown in the diagram below.
=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
|-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T00:52:23Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight for the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]
Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimised using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimised using the same method.The frontier orbital of reaction is shown in the diagram below.
=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3"|Table 1: Frontier Orbitals of s-cis butadiene and ethene
-
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T00:49:51Z

Gcw114: /* Exercise 1: Reaction of Butadiene with Ethene */

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight for the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram 2:Reaction of butadiene with ethene]]
Diagram 2 shows the pushing arrows diagram for the reaction between butadiene and ethene. Both reactants are optimised using semi empirical method with basis set PM 6. The optimised reactant are used to form a TS structure which is later also optimised using the same method.The frontier orbital of reaction is shown in the diagram below.
=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram 3:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
<title>Table 1: Frontier Orbitals of s-cis butadiene and ethene </title>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-10T00:33:15Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy (EAct). The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product. This will give us a better insight for the reaction happened from reactant to product or vice versa.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram x:Reaction of butadiene with ethene]]

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram x:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

Rep:Gcw114: Transition States and Reactivity

2017-02-09T19:47:23Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram x:Reaction of butadiene with ethene]]

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram x:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

[[File:GcwEx3 enrgy profile.png|thumb|centre|500px|Diagram xx: Energy Profile of reaction between.]]

File:GcwEx3 enrgy profile.png

2017-02-09T19:46:22Z

Gcw114:

Rep:Gcw114: Transition States and Reactivity

2017-02-09T19:19:23Z

Gcw114:

== Introduction ==
=== Transition state ===
[[File:GcwEnergy profile 3.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram x:Reaction of butadiene with ethene]]

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram x:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

[[File:GcwEx2 energy profile 5.png|thumb|centre|500px|Diagram 1: Energy Profile of a chemical reaction.]]

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

File:GcwEx2 energy profile 5.png

2017-02-09T19:18:25Z

Gcw114:

File:GcwEx2- energy profile.png

2017-02-09T19:14:13Z

Gcw114:

File:GcwEnergy profile 3.png

2017-02-09T18:28:58Z

Gcw114:

File:Gcw314px-GcwEnergy profile 2.png

2017-02-09T18:25:01Z

Gcw114:

File:GcwEnergy profile 1.png

2017-02-09T18:24:11Z

Gcw114:

Rep:Gcw114: Transition States and Reactivity

2017-02-09T17:45:16Z

Gcw114: /* HOMO and LUMO */

== Introduction ==
=== Transition state ===
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram x:Reaction of butadiene with ethene]]

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram x:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.540
|-
|C7-C10
|1.335
|C7-C10
|1.380
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.380
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.540
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

Rep:Gcw114: Transition States and Reactivity

2017-02-09T17:44:08Z

Gcw114: /* Thermochemistry data */

== Introduction ==
=== Transition state ===
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram x:Reaction of butadiene with ethene]]

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram x:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.54
|-
|C7-C10
|1.335
|C7-C10
|1.38
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.38
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.54
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
|160.1756
| -100.1728
|140.2570
| -124.4464

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 154.2320
| -108.1756
|141.5336
| -124.5400

|-
|}

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

Rep:Gcw114: Transition States and Reactivity

2017-02-09T17:42:53Z

Gcw114: /* Thermochemistry data */

== Introduction ==
=== Transition state ===
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram x:Reaction of butadiene with ethene]]

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram x:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.54
|-
|C7-C10
|1.335
|C7-C10
|1.38
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.38
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.54
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
| 0.061606
| 0.038528
| 0.053945
| 0.047864
|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 0.059320
| 0.041606
| 0.054436
| 0.047900
|-
|}

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
| -101.5066
|29.1356
| -156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
| -184.5844
|51.3448
| -208.6526

|}

Rep:Gcw114: Transition States and Reactivity

2017-02-09T17:41:59Z

Gcw114: /* Thermochemistry data */

== Introduction ==
=== Transition state ===
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram x:Reaction of butadiene with ethene]]

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram x:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.54
|-
|C7-C10
|1.335
|C7-C10
|1.38
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.38
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.54
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
| 0.061606
| 0.038528
| 0.053945
| 0.047864
|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 0.059320
| 0.041606
| 0.054436
| 0.047900
|-
|}

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
| 58.8354
| -120.2032
| 30.6488
| -148.9774

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 82.1106
|-101.5066
|29.1356
|-156.832

|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
| 72.9794
|-184.5844
|51.3448
|-208.6526

|}

Rep:Gcw114: Transition States and Reactivity

2017-02-09T17:28:22Z

Gcw114: /* Thermochemistry data */

== Introduction ==
=== Transition state ===
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram x:Reaction of butadiene with ethene]]

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram x:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.54
|-
|C7-C10
|1.335
|C7-C10
|1.38
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.38
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.54
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
| 0.061606
| 0.038528
| 0.053945
| 0.047864
|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 0.059320
| 0.041606
| 0.054436
| 0.047900
|-
|}

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;"|Endo reactants
|0.067932
|0.114802
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.090561
|0.126590
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.021700
|0.057503
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.060496
|0.116965
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.092077
|0.128171
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.021455
|0.056645
|-
! style="background: #0D4F8B; color: white;" |Cheletropic reactants
|0.070992
|0.114807
|-
! style="background: #0D4F8B; color: white;" |Cheletropic TS
|0.099061
|0.095059
|-
! style="background: #0D4F8B; color: white;" |Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;" |Endo pathway
|
|
|
|

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
|
|
|
|
|-
! style="background: #0D4F8B; color: white;" |Cheletropic pathway
|
|
|
|
|}

Rep:Gcw114: Transition States and Reactivity

2017-02-09T17:25:12Z

Gcw114: /* Thermochemistry data */

== Introduction ==
=== Transition state ===
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram x:Reaction of butadiene with ethene]]

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram x:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.54
|-
|C7-C10
|1.335
|C7-C10
|1.38
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.38
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.54
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
! style="background: #0D4F8B; color: white;" |Endo reactants
|0.076335
|0.118543
|-
! style="background: #0D4F8B; color: white;" |Endo TS
|0.137941
|0.172488
|-
! style="background: #0D4F8B; color: white;" |Endo Product
|0.037807
|0.070679
|-
! style="background: #0D4F8B; color: white;" |Exo reactants
|0.079583
|0.118829
|-
! style="background: #0D4F8B; color: white;" |Exo TS
|0.138903
|0.173265
|-
! style="background: #0D4F8B; color: white;" |Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
| 0.061606
| 0.038528
| 0.053945
| 0.047864
|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 0.059320
| 0.041606
| 0.054436
| 0.047900
|-
|}

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
|Endo reactants
|0.067932
|0.114802
|-
|Endo TS
|0.090561
|0.126590
|-
|Endo Product
|0.021700
|0.057503
|-
|Exo reactants
|0.060496
|0.116965
|-
|Exo TS
|0.092077
|0.128171
|-
|Exo Product
|0.021455
|0.056645
|-
|Cheletropic reactants
|0.070992
|0.114807
|-
|Cheletropic TS
|0.099061
|0.095059
|-
|Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white; colspan="2"|Endo pathway
|
|
|
|

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
|
|
|
|
|-
|Cheletropic pathway
|
|
|
|
|}

Rep:Gcw114: Transition States and Reactivity

2017-02-09T17:24:27Z

Gcw114: /* Thermochemistry data */

== Introduction ==
=== Transition state ===
For a chemical reaction,the energy profile diagram can be drawn in Figure 1 to show the reaction coordinate as the reactant is transformed into product. The product is more stable than the reactant. However, in order to form the product,the reactant has to overcome a barrier to reaction which is the activation energy The highest point of this barrier must correspond to some structure which is know as the transition state. The transition state is the highest energy structure with partially formed or broken bond. Transition state cannot be isolated and it is very unstable. Any small change in displacement will result to the formation of product.

==== Potential Energy Surface====
Using the concept of potential energy surface, we can describe the geometry optimization and transition state in computational and mathematical ways. Each atom would have defined in three coordinates,x,y,and z. Thus, a single atom has 3N coordinates. (N is the number of atoms)After removing the t three rotational and three translational coordinates, the final structure would have 3N-6 coordinates. Due to the complexity in visualizing large dimensional sapce, we can only normally draw in 3D which at most to be able to picture two of the 3N-6 dimensions which gives the PES.

The transition states can be obtained by taking first and second derivative

In this lab, we will investigate the transition states of the Diel Alder reaction using GAUSSIAN. We will run a series of optimization of structure to look for transition state and frequency analysis which gives us the second derivative. The Intrinsic Reaction Coordinate (IRC) analysis can ensure that the transition state connects a particular reactant and product.

== Exercise 1: Reaction of Butadiene with Ethene ==
[[File:GcwExercise 1 DA reaction.png|thumb|500px|centre|Diagram x:Reaction of butadiene with ethene]]

=== MO Diagram ===
[[File:GcwButadiene02.png|thumb|centre|500px|Diagram x:MO diagram of Diels-Alder reaction between butadiene and ethene.]]

=== HOMO and LUMO ===

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>s-cis butadiene</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gcw114 BUTADINE OPT.LOG</uploadedFileContents>
<script>frame 6</script>
</jmolApplet></jmol>

|[[File:Gcw114 Butadiene opt 02.png|200px|]]
Asymmetric

|[[File:LUMO butadiene opt pm6.gcw114.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>ethene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Gcw114ETHENE OPT 2.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114Homo 03 butadinee.png|200px|]]
Symmetric

| [[File:Gcw114Lumo 03 ethene pm6.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" colspan="3" | Transition state
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 14</script>
<uploadedFileContents>GcwOPT TS 02 AFTER PROPOSED STRUCTURE.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|-
! style="background: #0D4F8B; color: white;" |Molecular Orbital
! style="background: #0D4F8B; color: white;" |LUMO +1
! style="background: #0D4F8B; color: white;" |LUMO
! style="background: #0D4F8B; color: white;" |HUMO
! style="background: #0D4F8B; color: white;" |HUMO-1

|-
! style="background: #0D4F8B; color: white;" |Bonding
| [[File:Gcw114LUMO+1 02 TS.png|200px|]]
| [[File:Gcw114TS LUMO 01 pm6.png|200px|]]
| [[File:Gcw114TS HOMO 01 pm6.png|200px|]]
| [[File:Gcw114HOMO-1 pm6 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric

|}

[[File:GcwReactant with atom number01.png|thumb|centre|600px|Diagram: Diels-Alder reaction between a butadiene and an ethene.]]

{| class="wikitable"
<table border=1 align=center>
! colspan="2"| Reactant
! colspan="2"| TS
! colspan="2"| Product
! rowspan="2" colspan= "2"| Literature Values for C-C bond length <ref name="carbon bond length" />
|-
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
! Bond
! Bond length (Armstrong)
|-
|C1-C4
|1.327
|C1-C4
|1.382
|C1-C4
|1.541
|rowspan="2"|sp<sup>3</sup>C-sp<sup>3</sup>C
|rowspan="2"|1.54
|-
|C1-C7
|N/A
|C1-C7
|2.114
|C1-C7
|1.54
|-
|C7-C10
|1.335
|C7-C10
|1.38
|C7-C10
|1.501
|rowspan="2"|sp<sup>3</sup>C-sp<sup>2</sup>C
|rowspan="2"|1.50
|-
|C10-C12
|1.468
|C10-C12
|1.411
|C10-C12
|1.338
|-
|C12-C14
|1.335
|C12-C14
|1.38
|C12-C14
|1.501
|rowspan="2"|sp<sup>2</sup>C-sp<sup>2</sup>C
|rowspan="2"|
|-
|C14-C4
|N/A
|C14-C4
|2.115
|C14-C4
|1.54
|}
[[File:GcwEx1 04 internuclear distance.png|600px|thumb|centre|Diagram xx: Internuclear distance VS Reaction Coordinate]]

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==
=== Reaction Mechanism:Exo and Endo ===
[[File:GcwDA ex2 02 endoexo.png|thumb|600px|centre|Diagram xx: Endo and Exo reaction between Cyclohexadiene and 1,3-Dioxole]]

=== HOMO and LUMO ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Species
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114CYCLOHEXADIENE B3LYP 02 OPT 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>

|[[File:Gcw114HOMO c7yclohexaidne 03.png|200px|]]
Asymmetric

|[[File:GcwLUMO 03 cyclohexadiene.png|200px|]]
Symmetric

|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw11413 DIOXOLE B3LYP 01 3001.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Gcw114a HOMO 01 1,2 dioxole.png|200px|]]
Symmetric

| [[File:Gcw114LUMO 01 1,3dixole.png|200px|]]
Asymmetric
|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" |Gif

|-
! style="background: #0D4F8B; color: white;" |Exo
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 16</script>
<uploadedFileContents>GcwEXO TS B3LYP E2 02 3101.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwEX2 EXO PM6 PRODUCT OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx2 exo movie 01.gif|centre|500px]]

|-
! style="background: #0D4F8B; color: white;" |Endo
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 42</script>
<uploadedFileContents>GcwENDO TS 03 EX2 B3LYP.LOG</uploadedFileContents>
</jmolApplet></jmol>

| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<align>center</align>
<script>frame 12</script>
<uploadedFileContents>GcwE2 ENDO OPT PM6 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

| [[File:GcwEx endo movie01.gif|centre]|500px]]

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Pathway
! style="background: #0D4F8B; color: white;" | LUMO +1
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | HOMO -1

|-
! style="background: #0D4F8B; color: white;" |Exo
| [[File:GvwExolumo+1 01.png|200px|]]
| [[File:GcwLUMO exo 01.png|200px|]]
| [[File:GcwHOMO exo 01.png|200px|]]
| [[File:Gcw1HOMO-1 01 exo.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
! style="background: #0D4F8B; color: white;" |Endo
| [[File:GcwLUMO+1 02.png|200px|]]
| [[File:Gcw11LUMO 01.png|200px|]]
| [[File:Gcw11Homo 01.png|200px|]]
| [[File:HOMO-1 01.png|200px|]]
|-
! style="background: #0D4F8B; color: white;" |Symmetry
| Asymmetric
| Symmetric
| Symmetric
| Asymmetric
|-
|}

==Thermochemistry data==
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
|Endo reactants
|0.076335
|0.118543
|-
|Endo TS
|0.137941
|0.172488
|-
|Endo Product
|0.037807
|0.070679
|-
|Exo reactants
|0.079583
|0.118829
|-
|Exo TS
|0.138903
|0.173265
|-
|Exo Product
|0.037977
|0.070929

|}

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white;"|Endo pathway
| 0.061606
| 0.038528
| 0.053945
| 0.047864
|-
! style="background: #0D4F8B; color: white;"|Exo pathway
| 0.059320
| 0.041606
| 0.054436
| 0.047900
|-
|}

== Exercise 3: Diels-Alder vs Cheletropic ==
=== Reactant ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Xylylene
! style="background: #0D4F8B; color: white;" |Sulphur Dioxide
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>GcwREACTANT XYELNE PM6 OPT 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Gcw114REACTANT SO2 OPT PM6 01.LOG</uploadedFileContents>
</jmolApplet></jmol>

|}
=== Diels-Alder ===
Transition state

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Exo
! style="background: #0D4F8B; color: white;" | Endo
|-
| <jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw EXO DA XYELENE 02.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Transition State</title>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw114 ENDO DA PM6 OPT 02 BREAKSYM.LOG</uploadedFileContents>
</jmolApplet></jmol>

|-
| <jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>GcwEXO PRODUCT 01 PM6 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<title>Product</title>
<color>white</color>
<size>200</size>
<script>frame 40</script>
<uploadedFileContents>Gcw114ENDO PRODUCT 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Cheletropic ===
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" | Transition State
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>Gcw CHELAT TS 01 OPT PM6.LOG</uploadedFileContents>
</jmolApplet></jmol>

|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 12</script>
<uploadedFileContents>GcwCHELATE PRODUCT OPT 02.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
<table border=1 align=center>
|+ <b>: Gif file of IRC output </b>
! Reaction Pathway (reactant to product)
! Intrinsic Reaction Coordinate

|-
|[[File:Gcw114Endo movie 01 pm6.gif]]
::::::::'''Endo Pathway (reactant to product)'''
|[[File:Gcw114PlotISC 01 endo.png]]
|-
| [[File:GcwExo movie 02.gif]]
::::::::'''Exo Pathway (product to reactant)'''
|[[File:Gcw114Plot EXO ISC 01.png]]
|-
| [[File:GcwMovie 2.gif|centre]]
::::::::'''Cheletropic Pathway (reactant to product)'''
|[[File:GcwPlot irc chelate.png]]
|}

==Thermochemistry data==
The data is calculated from semi-empirical PM6 optimised reactant, product, TS from IRC output except exo reactants

{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |Temperature/ K
! style="background: #0D4F8B; color: white;" |298.150 Kelvin
Sum of electronic and thermal free Energies (Hartree/Particle)
! style="background: #0D4F8B; color: white;" |0 Kelvin
Sum of electronic and zero-point energies (Hartree/Particle)
|-
|Endo reactants
|0.067932
|0.114802
|-
|Endo TS
|0.090561
|0.126590
|-
|Endo Product
|0.021700
|0.057503
|-
|Exo reactants
|0.060496
|0.116965
|-
|Exo TS
|0.092077
|0.128171
|-
|Exo Product
|0.021455
|0.056645
|-
|Cheletropic reactants
|0.070992
|0.114807
|-
|Cheletropic TS
|0.099061
|0.095059
|-
|Cheletropic Product
| -0.000002
|0.034556
|-
|}
{| class="wikitable"
<table border=1 align=center>
! style="background: #0D4F8B; color: white;" |
! style="background: #0D4F8B; color: white;" colspan="2"|298.150 Kelvin
! style="background: #0D4F8B; color: white;" colspan="2"|O Kelvin
|-
! style="background: #0D4F8B; color: white;" |Reaction Pathway
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
! style="background: #0D4F8B; color: white;" |Activation barrier(kJ/mol)
! style="background: #0D4F8B; color: white;" |Reaction energy(kJ/mol)
|-
! style="background: #0D4F8B; color: white; colspan="2"|Endo pathway
|
|
|
|

|-
! style="background: #0D4F8B; color: white;"|Exo pathway
|
|
|
|
|-
|Cheletropic pathway
|
|
|
|
|}