ChemWiki - User contributions [en]

User:Xv114

2016-12-16T11:50:03Z

Xv114:

== Introduction ==
A transition state is a transient species with the highest energy in the reaction profile that cannot be isolated or detected by spectroscopic methods. As a result it is the maximum point in the potential energy surface with zero gradient. This wiki page would discuss about transition states of cycloaddition reaction between different reactants using Gaussview for transition state optimisation followed by IRC and frequency calculation to determine the energy of reactants, transition states and products to determine favourable reaction route.

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:Xv114 new HOMO AND LUMO OF TS.JPG|700px|thumb|centre|Figure 2 Molecular orbitals of transition state with MO2 and MO3 being the transition state HOMO and LUMO respectively]]

From the MO diagram, it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 3: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure 2 and 3, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.<ref>J.Clayden, N.Greeves, S. Warren, ''Organic Chemistry'', OUP, New York, 2012, 2nd. ed,</ref>

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length <ref>Fox, Marye Anne; Whitesell, James K. (1995). Organische Chemie: Grundlagen, Mechanismen, Bioorganische Anwendungen. Springer. ISBN 978-3-86025-249-9. </ref>
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å <ref>A. Bondi. "Van der Waals Volumes and Radii". J. Phys. Chem. ,1964, 68 (3): 441–51.</ref>

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure 4 correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond is asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 7: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

The MO diagram for reaction between cyclohexadiene and 1,3-dioxole in Figure 8 below:

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 8: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

The three dimensional transition state orbitals visualised in Gaussview in Figure 10-13 correlate with those in the MO diagram, Figure 8. The presence of oxygen lone pair would raise the energy levels of dioxole, including its HOMO. As a result energetically the HOMO of dioxole would interact better with LUMO of cyclohexadiene.<ref>J.Clayden, N.Greeves, S. Warren, ''Organic Chemistry'', OUP, New York, 2012, 2nd. ed, pg. 887 </ref> Furthermore presence of mirror plane extending along the length of the transition state is consistent with that for a cycloaddition reaction with an inverse electron demand as illustrated in Figure 14 confirming that the reaction has an inverse electron demand.

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 9: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 10: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 11: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 12: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 13: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Symmetry plane 1.JPG|600px|thumb|centre|Figure 14: Symmetry plane, indicated by red dash line, is present only in the transition state that correspond with an inverse electron demand interaction which correlates. The presence of symmetry plane in the transition state MO confirms that it is an inverse electron demand cycloaddition]]

{| class="wikitable"
|+ Table 2: Activation energy and Gibbs free energy for both endo- and exo- Diels Alder reactio between 1,3-dioxole and cyclohexadiene
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 15: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is observed in the circled region between oxygen lone pair and π* orbital as shown in Figure 16. The presence of secondary and primary orbital interactions, as shown in Figure 16 and 15, and from the lower activation energy and Gibbs free energy calculated in Table 2 means the endo-Diels Alder reaction is both the thermodynamic and kinetic product. This also suggests that there is a lower steric interaction in endo- than exo-Diels Alder reaction.

[[File:Xv114 Secondary orbital new one.JPG|600px|thumb|centre|Figure 16:On the left diagram the orbitals coloured in red within the circled region are overlapped with each other indicating secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure 17-19, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:Xv114 newone Exo reaction profile.JPG|700px|thumb|centre|Figure 17: Reaction profile of exo-Diels Alder reaction]]

[[File:Endo reaction profile newone.JPG|700px|thumb|centre|Figure 18: Reaction profile of endo-Diels Alder reaction]]

[[File:Xv114 Cheletropic reaction profile newone.JPG|700px|thumb|centre|Figure 19: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 20: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 21: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 22: Endo IRC]]

For all three IRC calculations shown above in Figure 21-22, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure 21 shown is different from Figure 20 and 22 by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

==Reference==

User:Xv114

2016-12-16T11:48:23Z

Xv114:

== Introduction ==
A transition state is a transient species with the highest energy in the reaction profile that cannot be isolated or detected by spectroscopic methods. As a result it is the maximum point in the potential energy surface with zero gradient. This wiki page would discuss about transition states of cycloaddition reaction between different reactants using Gaussview for transition state optimisation followed by IRC and frequency calculation to determine the energy of reactants, transition states and products to determine favourable reaction route.

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:Xv114 new HOMO AND LUMO OF TS.JPG|700px|thumb|centre|Figure 2 Molecular orbitals of transition state with MO2 and MO3 being the transition state HOMO and LUMO respectively]]

From the MO diagram, it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 3: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure 2 and 3, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.<ref>J.Clayden, N.Greeves, S. Warren, ''Organic Chemistry'', OUP, New York, 2012, 2nd. ed,</ref>

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length <ref>Fox, Marye Anne; Whitesell, James K. (1995). Organische Chemie: Grundlagen, Mechanismen, Bioorganische Anwendungen. Springer. ISBN 978-3-86025-249-9. </ref>
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å <ref>A. Bondi. "Van der Waals Volumes and Radii". J. Phys. Chem. ,1964, 68 (3): 441–51.</ref>

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure 4 correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond is asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 7: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

The MO diagram for reaction between cyclohexadiene and 1,3-dioxole in Figure 8 below:

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 8: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

The three dimensional transition state orbitals visualised in Gaussview in Figure 10-13 correlate with those in the MO diagram, Figure 8. The presence of oxygen lone pair would raise the energy levels of dioxole, including its HOMO. As a result energetically the HOMO of dioxole would interact better with LUMO of cyclohexadiene.<ref>J.Clayden, N.Greeves, S. Warren, ''Organic Chemistry'', OUP, New York, 2012, 2nd. ed, pg. 887 </ref> Furthermore presence of mirror plane extending along the length of the transition state is consistent with that for a cycloaddition reaction with an inverse electron demand as illustrated in Figure 14 confirming that the reaction has an inverse electron demand.

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 9: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 10: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 11: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 12: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 13: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Symmetry plane 1.JPG|600px|thumb|centre|Figure 14: Symmetry plane, indicated by red dash line, is present only in the transition state that correspond with an inverse electron demand interaction which correlates. The presence of symmetry plane in the transition state MO confirms that it is an inverse electron demand cycloaddition]]

{| class="wikitable"
|+ Table 2: Activation energy and Gibbs free energy for both endo- and exo- Diels Alder reactio between 1,3-dioxole and cyclohexadiene
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 15: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is observed in the circled region between oxygen lone pair and π* orbital as shown in Figure 16. The presence of secondary and primary orbital interactions, as shown in Figure 16 and 15, and from the lower activation energy and Gibbs free energy calculated in Table 2 means the endo-Diels Alder reaction is both the thermodynamic and kinetic product. This also suggests that there is a lower steric interaction in endo- than exo-Diels Alder reaction.

[[File:Xv114 Secondary orbital new one.JPG|600px|thumb|centre|Figure 16:On the left diagram the orbitals coloured in red within the circled region are overlapped with each other indicating secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure 17-19, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:Xv114 newone Exo reaction profile.JPG|700px|thumb|centre|Figure 17: Reaction profile of exo-Diels Alder reaction]]

[[File:Endo reaction profile newone.JPG|700px|thumb|centre|Figure 18: Reaction profile of endo-Diels Alder reaction]]

[[File:File:Xv114 Cheletropic reaction profile newone.JPG|700px|thumb|centre|Figure 19: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 20: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 21: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 22: Endo IRC]]

For all three IRC calculations shown above in Figure 21-22, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure 21 shown is different from Figure 20 and 22 by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

==Reference==

User:Xv114

2016-12-16T11:46:58Z

Xv114:

== Introduction ==
A transition state is a transient species with the highest energy in the reaction profile that cannot be isolated or detected by spectroscopic methods. As a result it is the maximum point in the potential energy surface with zero gradient. This wiki page would discuss about transition states of cycloaddition reaction between different reactants using Gaussview for transition state optimisation followed by IRC and frequency calculation to determine the energy of reactants, transition states and products to determine favourable reaction route.

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:Xv114 new HOMO AND LUMO OF TS.JPG|700px|thumb|centre|Figure 2 Molecular orbitals of transition state with MO2 and MO3 being the transition state HOMO and LUMO respectively]]

From the MO diagram, it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 3: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure 2 and 3, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.<ref>J.Clayden, N.Greeves, S. Warren, ''Organic Chemistry'', OUP, New York, 2012, 2nd. ed,</ref>

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length <ref>Fox, Marye Anne; Whitesell, James K. (1995). Organische Chemie: Grundlagen, Mechanismen, Bioorganische Anwendungen. Springer. ISBN 978-3-86025-249-9. </ref>
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å <ref>A. Bondi. "Van der Waals Volumes and Radii". J. Phys. Chem. ,1964, 68 (3): 441–51.</ref>

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure 4 correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond is asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 7: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

The MO diagram for reaction between cyclohexadiene and 1,3-dioxole in Figure 8 below:

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 8: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

The three dimensional transition state orbitals visualised in Gaussview in Figure 10-13 correlate with those in the MO diagram, Figure 8. The presence of oxygen lone pair would raise the energy levels of dioxole, including its HOMO. As a result energetically the HOMO of dioxole would interact better with LUMO of cyclohexadiene.<ref>J.Clayden, N.Greeves, S. Warren, ''Organic Chemistry'', OUP, New York, 2012, 2nd. ed, pg. 887 </ref> Furthermore presence of mirror plane extending along the length of the transition state is consistent with that for a cycloaddition reaction with an inverse electron demand as illustrated in Figure 14 confirming that the reaction has an inverse electron demand.

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 9: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 10: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 11: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 12: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 13: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Symmetry plane 1.JPG|600px|thumb|centre|Figure 14: Symmetry plane, indicated by red dash line, is present only in the transition state that correspond with an inverse electron demand interaction which correlates. The presence of symmetry plane in the transition state MO confirms that it is an inverse electron demand cycloaddition]]

{| class="wikitable"
|+ Table 2: Activation energy and Gibbs free energy for both endo- and exo- Diels Alder reactio between 1,3-dioxole and cyclohexadiene
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 15: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is observed in the circled region between oxygen lone pair and π* orbital as shown in Figure 16. The presence of secondary and primary orbital interactions, as shown in Figure 16 and 15, and from the lower activation energy and Gibbs free energy calculated in Table 2 means the endo-Diels Alder reaction is both the thermodynamic and kinetic product. This also suggests that there is a lower steric interaction in endo- than exo-Diels Alder reaction.

[[File:Xv114 Xv114 Secondary orbital new one.JPG|600px|thumb|centre|Figure 16:On the left diagram the orbitals coloured in red within the circled region are overlapped with each other indicating secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure 17-19, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:Xv114 newone Exo reaction profile.JPG|700px|thumb|centre|Figure 17: Reaction profile of exo-Diels Alder reaction]]

[[File:Endo reaction profile newone.JPG|700px|thumb|centre|Figure 18: Reaction profile of endo-Diels Alder reaction]]

[[File:File:Xv114 Cheletropic reaction profile newone.JPG|700px|thumb|centre|Figure 19: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 20: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 21: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 22: Endo IRC]]

For all three IRC calculations shown above in Figure 21-22, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure 21 shown is different from Figure 20 and 22 by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

==Reference==

File:Xv114 Secondary orbital new one.JPG

2016-12-16T11:44:45Z

Xv114:

File:Xv114 Cheletropic reaction profile newone.JPG

2016-12-16T11:40:55Z

Xv114:

File:Endo reaction profile newone.JPG

2016-12-16T11:39:43Z

Xv114:

File:Xv114 newone Exo reaction profile.JPG

2016-12-16T11:38:19Z

Xv114:

User:Xv114

2016-12-16T11:35:40Z

Xv114:

== Introduction ==
A transition state is a transient species with the highest energy in the reaction profile that cannot be isolated or detected by spectroscopic methods. As a result it is the maximum point in the potential energy surface with zero gradient. This wiki page would discuss about transition states of cycloaddition reaction between different reactants using Gaussview for transition state optimisation followed by IRC and frequency calculation to determine the energy of reactants, transition states and products to determine favourable reaction route.

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:Xv114 new HOMO AND LUMO OF TS.JPG|700px|thumb|centre|Figure 2 Molecular orbitals of transition state with MO2 and MO3 being the transition state HOMO and LUMO respectively]]

From the MO diagram, it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 3: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure 2 and 3, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.<ref>J.Clayden, N.Greeves, S. Warren, ''Organic Chemistry'', OUP, New York, 2012, 2nd. ed,</ref>

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length <ref>Fox, Marye Anne; Whitesell, James K. (1995). Organische Chemie: Grundlagen, Mechanismen, Bioorganische Anwendungen. Springer. ISBN 978-3-86025-249-9. </ref>
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å <ref>A. Bondi. "Van der Waals Volumes and Radii". J. Phys. Chem. ,1964, 68 (3): 441–51.</ref>

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure 4 correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond is asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 7: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

The MO diagram for reaction between cyclohexadiene and 1,3-dioxole in Figure 8 below:

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 8: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

The three dimensional transition state orbitals visualised in Gaussview in Figure 10-13 correlate with those in the MO diagram, Figure 8. The presence of oxygen lone pair would raise the energy levels of dioxole, including its HOMO. As a result energetically the HOMO of dioxole would interact better with LUMO of cyclohexadiene.<ref>J.Clayden, N.Greeves, S. Warren, ''Organic Chemistry'', OUP, New York, 2012, 2nd. ed, pg. 887 </ref> Furthermore presence of mirror plane extending along the length of the transition state is consistent with that for a cycloaddition reaction with an inverse electron demand as illustrated in Figure 14 confirming that the reaction has an inverse electron demand.

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 9: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 10: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 11: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 12: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 13: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Symmetry plane 1.JPG|600px|thumb|centre|Figure 14: Symmetry plane, indicated by red dash line, is present only in the transition state that correspond with an inverse electron demand interaction which correlates. The presence of symmetry plane in the transition state MO confirms that it is an inverse electron demand cycloaddition]]

{| class="wikitable"
|+ Table 2: Activation energy and Gibbs free energy for both endo- and exo- Diels Alder reactio between 1,3-dioxole and cyclohexadiene
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 15: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in endo- Diels Alder transition state in Figure 15 the orbital did not overlap despite both being in correct geometry and are in close proximity to each other. The presence of secondary and primary orbital interactions, as shown in Figure 16, and from the lower activation energy and Gibbs free energy calculated in Table 2 means the endo-Diels Alder reaction is both the thermodynamic and kinetic product. This also suggests that there is a lower steric interaction in endo- than exo-Diels Alder reaction.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 16:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure 17-19, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 17: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 18: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 19: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 20: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 21: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 22: Endo IRC]]

For all three IRC calculations shown above in Figure 21-22, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure 21 shown is different from Figure 20 and 22 by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

==Reference==

User:Xv114

2016-12-16T11:24:23Z

Xv114:

== Introduction ==
A transition state is a transient species with the highest energy in the reaction profile that cannot be isolated or detected by spectroscopic methods. As a result it is the maximum point in the potential energy surface with zero gradient. This wiki page would discuss about transition states of cycloaddition reaction between different reactants using Gaussview for transition state optimisation followed by IRC and frequency calculation to determine the energy of reactants, transition states and products to determine favourable reaction route.

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:Xv114 new HOMO AND LUMO OF TS.JPG|700px|thumb|centre|Figure 2 Molecular orbitals of transition state with MO2 and MO3 being the transition state HOMO and LUMO respectively]]

From the MO diagram, it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 3: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure 2 and 3, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length <ref>Fox, Marye Anne; Whitesell, James K. (1995). Organische Chemie: Grundlagen, Mechanismen, Bioorganische Anwendungen. Springer. ISBN 978-3-86025-249-9. </ref>
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure 4 correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond is asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 7: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

The MO diagram for reaction between cyclohexadiene and 1,3-dioxole in Figure 8 below:

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 8: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

The three dimensional transition state orbitals visualised in Gaussview in Figure 10-13 correlate with those in the MO diagram, Figure 8. The presence of oxygen lone pair would raise the energy levels of dioxole, including its HOMO. As a result energetically the HOMO of dioxole would interact better with LUMO of cyclohexadiene. Furthermore presence of mirror plane extending along the length of the transition state is consistent with that for a cycloaddition reaction with an inverse electron demand as illustrated in Figure 14 confirming that the reaction has an inverse electron demand.

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 9: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 10: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 11: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 12: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 13: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Symmetry plane 1.JPG|600px|thumb|centre|Figure 14: Symmetry plane, indicated by red dash line, is present only in the transition state that correspond with an inverse electron demand interaction which correlates. The presence of symmetry plane in the transition state MO confirms that it is an inverse electron demand cycloaddition]]

{| class="wikitable"
|+ Table 2: Activation energy and Gibbs free energy for both endo- and exo- Diels Alder reactio between 1,3-dioxole and cyclohexadiene
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 15: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in endo- Diels Alder transition state in Figure 15 the orbital did not overlap despite both being in correct geometry and are in close proximity to each other. The presence of secondary and primary orbital interactions, as shown in Figure 16, and from the lower activation energy and Gibbs free energy calculated in Table 2 means the endo-Diels Alder reaction is both the thermodynamic and kinetic product. This also suggests that there is a lower steric interaction in endo- than exo-Diels Alder reaction.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 16:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure 17-19, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 17: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 18: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 19: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 20: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 21: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 22: Endo IRC]]

For all three IRC calculations shown above in Figure 21-22, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure 21 shown is different from Figure 20 and 22 by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

==Reference==

User:Xv114

2016-12-16T11:19:17Z

Xv114:

== Introduction ==
A transition state is a transient species with the highest energy in the reaction profile that cannot be isolated or detected by spectroscopic methods. As a result it is the maximum point in the potential energy surface with zero gradient. This wiki page would discuss about transition states of cycloaddition reaction between different reactants using Gaussview for transition state optimisation followed by IRC and frequency calculation to determine the energy of reactants, transition states and products to determine favourable reaction route.

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:Xv114 new HOMO AND LUMO OF TS.JPG|700px|thumb|centre|Figure 2 Molecular orbitals of transition state with MO2 and MO3 being the transition state HOMO and LUMO respectively]]

From the MO diagram, it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 3: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure 2 and 3, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length <ref name="C-C bond length" />
<references>
<ref name="C-C bond length">Fox, Marye Anne; Whitesell, James K. (1995). Organische Chemie: Grundlagen, Mechanismen, Bioorganische Anwendungen. Springer. ISBN 978-3-86025-249-9.</ref>
</references>
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure 4 correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond is asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 7: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

The MO diagram for reaction between cyclohexadiene and 1,3-dioxole in Figure 8 below:

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 8: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

The three dimensional transition state orbitals visualised in Gaussview in Figure 10-13 correlate with those in the MO diagram, Figure 8. The presence of oxygen lone pair would raise the energy levels of dioxole, including its HOMO. As a result energetically the HOMO of dioxole would interact better with LUMO of cyclohexadiene. Furthermore presence of mirror plane extending along the length of the transition state is consistent with that for a cycloaddition reaction with an inverse electron demand as illustrated in Figure 14 confirming that the reaction has an inverse electron demand.

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 9: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 10: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 11: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 12: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 13: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Symmetry plane 1.JPG|600px|thumb|centre|Figure 14: Symmetry plane, indicated by red dash line, is present only in the transition state that correspond with an inverse electron demand interaction which correlates. The presence of symmetry plane in the transition state MO confirms that it is an inverse electron demand cycloaddition]]

{| class="wikitable"
|+ Table 2: Activation energy and Gibbs free energy for both endo- and exo- Diels Alder reactio between 1,3-dioxole and cyclohexadiene
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 15: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in endo- Diels Alder transition state in Figure 15 the orbital did not overlap despite both being in correct geometry and are in close proximity to each other. The presence of secondary and primary orbital interactions, as shown in Figure 16, and from the lower activation energy and Gibbs free energy calculated in Table 2 means the endo-Diels Alder reaction is both the thermodynamic and kinetic product. This also suggests that there is a lower steric interaction in endo- than exo-Diels Alder reaction.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 16:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure 17-19, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 17: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 18: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 19: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 20: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 21: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 22: Endo IRC]]

For all three IRC calculations shown above in Figure 21-22, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure 21 shown is different from Figure 20 and 22 by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

User:Xv114

2016-12-16T11:11:40Z

Xv114:

= Introduction =
A transition state is a transient species with the highest energy in the reaction profile that cannot be isolated or detected by spectroscopic methods. As a result it is the maximum point in the potential energy surface with zero gradient. This wiki page would discuss about transition states of cycloaddition reaction between different reactants using Gaussview for transition state optimisation followed by IRC and frequency calculation to determine the energy of reactants, transition states and products to determine favourable reaction route.

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:Xv114 new HOMO AND LUMO OF TS.JPG|700px|thumb|centre|Figure 2 Molecular orbitals of transition state with MO2 and MO3 being the transition state HOMO and LUMO respectively]]

From the MO diagram, it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 3: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure 2 and 3, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure 4 correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond is asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 7: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

The MO diagram for reaction between cyclohexadiene and 1,3-dioxole in Figure 8 below:

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 8: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

The three dimensional transition state orbitals visualised in Gaussview in Figure 10-13 correlate with those in the MO diagram, Figure 8. The presence of oxygen lone pair would raise the energy levels of dioxole, including its HOMO. As a result energetically the HOMO of dioxole would interact better with LUMO of cyclohexadiene. Furthermore presence of mirror plane extending along the length of the transition state is consistent with that for a cycloaddition reaction with an inverse electron demand as illustrated in Figure 14 confirming that the reaction has an inverse electron demand.

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 9: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 10: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 11: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 12: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 13: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Symmetry plane 1.JPG|600px|thumb|centre|Figure 14: Symmetry plane, indicated by red dash line, is present only in the transition state that correspond with an inverse electron demand interaction which correlates. The presence of symmetry plane in the transition state MO confirms that it is an inverse electron demand cycloaddition]]

{| class="wikitable"
|+ Table 2: Activation energy and Gibbs free energy for both endo- and exo- Diels Alder reactio between 1,3-dioxole and cyclohexadiene
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 15: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in endo- Diels Alder transition state in Figure 15 the orbital did not overlap despite both being in correct geometry and are in close proximity to each other. The presence of secondary and primary orbital interactions, as shown in Figure 16, and from the lower activation energy and Gibbs free energy calculated in Table 2 means the endo-Diels Alder reaction is both the thermodynamic and kinetic product. This also suggests that there is a lower steric interaction in endo- than exo-Diels Alder reaction.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 16:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure 17-19, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 17: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 18: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 19: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 20: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 21: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 22: Endo IRC]]

For all three IRC calculations shown above in Figure 21-22, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure 21 shown is different from Figure 20 and 22 by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

User:Xv114

2016-12-16T11:02:38Z

Xv114:

= Introduction =
A transition state is a transient species with the highest energy in the reaction profile that cannot be isolated or detected by spectroscopic methods. As a result it is the maximum point in the potential energy surface with zero gradient. This wiki page would discuss about transition states of cycloaddition reaction between different reactants using Gaussview for transition state optimisation followed by IRC and frequency calculation to determine the energy of reactants, transition states and products to determine favourable reaction route.

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:Xv114 new HOMO AND LUMO OF TS.JPG|700px|thumb|centre|Figure 2 Molecular orbitals of transition state with MO2 and MO3 being the transition state HOMO and LUMO respectively]]

From the MO diagram, it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure ? and ?, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure ? correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

The MO diagram for reaction between cyclohexadiene and 1,3-dioxole in Figure ? below:

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

The three dimensional orbitals visualised in Gaussview in Figure ? correlate with those in the MO diagram, Figure ?. The presence of oxygen lone pair would raise the energy levels of dioxole, including its HOMO. As a result energetically the HOMO of dioxole would interact better with LUMO of cyclohexadiene. Furthermore presence of mirror plane extending along the length of the transition state is consistent with that for a cycloaddition reaction with an inverse electron demand as illustrated in Figure ? confirming that the reaction has an inverse electron demand.

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Symmetry plane 1.JPG|600px|thumb|centre|Figure 7: Symmetry plane, indicated by red dash line, is present only in the transition state that correspond with an inverse electron demand interaction which correlates. The presence of symmetry plane in the transition state MO confirms that it is an inverse electron demand cycloaddition]]

{| class="wikitable"
|+ Table 2: Activation energy and Gibbs free energy for both endo- and exo- Diels Alder reactio between 1,3-dioxole and cyclohexadiene
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in endo- Diels Alder transition state in Figure ? the orbital did not overlap despite both being in correct geometry and are in close proximity to each other. The presence of secondary and primary orbital interactions, as shown in Figure ?, and from the lower activation energy and Gibbs free energy calculated in Table ? means the endo-Diels Alder reaction is both the thermodynamic and kinetic product. This also suggests that there is a lower steric interaction in endo- than exo-Diels Alder reaction.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

For all three IRC calculations shown above in Figure ?-?, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure ? shown is different from Figure ? and ? by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

User:Xv114

2016-12-16T11:00:55Z

Xv114:

= Introduction =
A transition state is a transient species with the highest energy in the reaction profile that cannot be isolated or detected by spectroscopic methods. As a result it is the maximum point in the potential energy surface with zero gradient. This wiki page would discuss about transition states of cycloaddition reaction between different reactants using Gaussview for transition state optimisation followed by IRC and frequency calculation to determine the energy of reactants, transition states and products to determine favourable reaction route.

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:Xv114 new HOMO AND LUMO OF TS.JPG|700px|thumb|centre|Figure 2 Molecular orbitals of transition state with MO2 and MO3 being the transition state HOMO and LUMO respectively]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure ? and ?, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure ? correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

The MO diagram for reaction between cyclohexadiene and 1,3-dioxole in Figure ? below:

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

The three dimensional orbitals visualised in Gaussview in Figure ? correlate with those in the MO diagram, Figure ?. The presence of oxygen lone pair would raise the energy levels of dioxole, including its HOMO. As a result energetically the HOMO of dioxole would interact better with LUMO of cyclohexadiene. Furthermore presence of mirror plane extending along the length of the transition state is consistent with that for a cycloaddition reaction with an inverse electron demand as illustrated in Figure ? confirming that the reaction has an inverse electron demand.

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Symmetry plane 1.JPG|600px|thumb|centre|Figure 7: Symmetry plane, indicated by red dash line, is present only in the transition state that correspond with an inverse electron demand interaction which correlates. The presence of symmetry plane in the transition state MO confirms that it is an inverse electron demand cycloaddition]]

{| class="wikitable"
|+ Table 2: Activation energy and Gibbs free energy for both endo- and exo- Diels Alder reactio between 1,3-dioxole and cyclohexadiene
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in endo- Diels Alder transition state in Figure ? the orbital did not overlap despite both being in correct geometry and are in close proximity to each other. The presence of secondary and primary orbital interactions, as shown in Figure ?, and from the lower activation energy and Gibbs free energy calculated in Table ? means the endo-Diels Alder reaction is both the thermodynamic and kinetic product. This also suggests that there is a lower steric interaction in endo- than exo-Diels Alder reaction.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

For all three IRC calculations shown above in Figure ?-?, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure ? shown is different from Figure ? and ? by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

File:Xv114 new HOMO AND LUMO OF TS.JPG

2016-12-16T10:59:05Z

Xv114:

File:XV114 HOMO AND LUMO OF TS.JPG

2016-12-16T10:56:30Z

Xv114:

User:Xv114

2016-12-16T10:49:24Z

Xv114:

= Introduction =
A transition state is a transient species with the highest energy in the reaction profile that cannot be isolated or detected by spectroscopic methods. As a result it is the maximum point in the potential energy surface with zero gradient. This wiki page would discuss about transition states of cycloaddition reaction between different reactants using Gaussview for transition state optimisation followed by IRC and frequency calculation to determine the energy of reactants, transition states and products to determine favourable reaction route.

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure ? and ?, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure ? correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

The MO diagram for reaction between cyclohexadiene and 1,3-dioxole in Figure ? below:

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

The three dimensional orbitals visualised in Gaussview in Figure ? correlate with those in the MO diagram, Figure ?. The presence of oxygen lone pair would raise the energy levels of dioxole, including its HOMO. As a result energetically the HOMO of dioxole would interact better with LUMO of cyclohexadiene. Furthermore presence of mirror plane extending along the length of the transition state is consistent with that for a cycloaddition reaction with an inverse electron demand as illustrated in Figure ? confirming that the reaction has an inverse electron demand.

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Symmetry plane 1.JPG|600px|thumb|centre|Figure 7: Symmetry plane, indicated by red dash line, is present only in the transition state that correspond with an inverse electron demand interaction which correlates. The presence of symmetry plane in the transition state MO confirms that it is an inverse electron demand cycloaddition]]

{| class="wikitable"
|+ Table 2: Activation energy and Gibbs free energy for both endo- and exo- Diels Alder reactio between 1,3-dioxole and cyclohexadiene
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in endo- Diels Alder transition state in Figure ? the orbital did not overlap despite both being in correct geometry and are in close proximity to each other. The presence of secondary and primary orbital interactions, as shown in Figure ?, and from the lower activation energy and Gibbs free energy calculated in Table ? means the endo-Diels Alder reaction is both the thermodynamic and kinetic product. This also suggests that there is a lower steric interaction in endo- than exo-Diels Alder reaction.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

For all three IRC calculations shown above in Figure ?-?, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure ? shown is different from Figure ? and ? by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

User:Xv114

2016-12-16T10:33:50Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure ? and ?, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure ? correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

The MO diagram for reaction between cyclohexadiene and 1,3-dioxole in Figure ? below:

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

The three dimensional orbitals visualised in Gaussview in Figure ? correlate with those in the MO diagram, Figure ?. The presence of oxygen lone pair would raise the energy levels of dioxole, including its HOMO. As a result energetically the HOMO of dioxole would interact better with LUMO of cyclohexadiene. Furthermore presence of mirror plane extending along the length of the transition state is consistent with that for a cycloaddition reaction with an inverse electron demand as illustrated in Figure ? confirming that the reaction has an inverse electron demand.

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Symmetry plane 1.JPG|600px|thumb|centre|Figure 7: Symmetry plane, indicated by red dash line, is present only in the transition state that correspond with an inverse electron demand interaction which correlates. The presence of symmetry plane in the transition state MO confirms that it is an inverse electron demand cycloaddition]]

{| class="wikitable"
|+ Table 2: Activation energy and Gibbs free energy for both endo- and exo- Diels Alder reactio between 1,3-dioxole and cyclohexadiene
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in endo- Diels Alder transition state in Figure ? the orbital did not overlap despite both being in correct geometry and are in close proximity to each other. The presence of secondary and primary orbital interactions, as shown in Figure ?, and from the lower activation energy and Gibbs free energy calculated in Table ? means the endo-Diels Alder reaction is both the thermodynamic and kinetic product. This also suggests that there is a lower steric interaction in endo- than exo-Diels Alder reaction.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

For all three IRC calculations shown above in Figure ?-?, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure ? shown is different from Figure ? and ? by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

File:Xv114 Symmetry plane 1.JPG

2016-12-16T10:31:15Z

Xv114:

File:Xv114 Symmetry plane.JPG

2016-12-16T10:25:24Z

Xv114:

User:Xv114

2016-12-16T09:55:11Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure ? and ?, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure ? correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

{| class="wikitable"
|+ Table 2: Activation energy and Gibbs free energy for both endo- and exo- Diels Alder reactio between 1,3-dioxole and cyclohexadiene
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in endo- Diels Alder transition state in Figure ? the orbital did not overlap despite both being in correct geometry and are in close proximity to each other. The presence of secondary and primary orbital interactions, as shown in Figure ?, and low steric interaction means the endo-Diels Alder reaction is both the thermodynamic and kinetic product.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

For all three IRC calculations shown above in Figure ?-?, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure ? shown is different from Figure ? and ? by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

User:Xv114

2016-12-16T09:53:01Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure ? and ?, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure ? correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

{| class="wikitable"
| + Table 2: Activation energy and Gibbs free energy for both endo- and exo- Diels Alder reactio between 1,3-dioxole and cyclohexadiene
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in endo- Diels Alder transition state in Figure ? the orbital did not overlap despite both being in correct geometry and are in close proximity to each other. The presence of secondary and primary orbital interactions, as shown in Figure ?, and low steric interaction means the endo-Diels Alder reaction is both the thermodynamic and kinetic product.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

For all three IRC calculations shown above in Figure ?-?, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure ? shown is different from Figure ? and ? by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

User:Xv114

2016-12-16T09:49:15Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure ? and ?, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure ? correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]
{| class="wikitable"
!Reaction
!Activation energy (kJ/mol)
!Gibbs free energy (kJ/mol)
|-
|Endo-Diels Alder
|151
|<nowiki>-76.2</nowiki>
|-
|Exo-Diels Alder
|159
|<nowiki>-72.3</nowiki>
|}
[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in endo- Diels Alder transition state in Figure ? the orbital did not overlap despite both being in correct geometry and are in close proximity to each other. The presence of secondary and primary orbital interactions, as shown in Figure ?, and low steric interaction means the endo-Diels Alder reaction is both the thermodynamic and kinetic product.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

For all three IRC calculations shown above in Figure ?-?, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure ? shown is different from Figure ? and ? by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

User:Xv114

2016-12-16T09:44:04Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure ? and ?, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure ? correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in endo- Diels Alder transition state in Figure ? the orbital did not overlap despite both being in correct geometry and are in close proximity to each other. The presence of secondary and primary orbital interactions, as shown in Figure ?, and low steric interaction means the endo-Diels Alder reaction is both the thermodynamic and kinetic product.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

For all three IRC calculations shown above in Figure ?-?, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure ? shown is different from Figure ? and ? by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

User:Xv114

2016-12-16T09:34:54Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure ? and ?, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure ? correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in this model the orbital did not overlap despite both being in correct geometry and are in close proximity to each other.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

For all three IRC calculations shown above in Figure ?-?, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure ? shown is different from Figure ? and ? by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

User:Xv114

2016-12-16T09:34:01Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

From Figure ? and ?, it can be concluded that symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|left|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}

The bond lengths in both reactants and product in Figure ? correlate with those in Table 2. However the C=C bonds lengthen in transition state to a length that is between a typical sp3-sp2 and sp2-sp2 C-C bond length before finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in this model the orbital did not overlap despite both being in correct geometry and are in close proximity to each other.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

For all three IRC calculations shown above in Figure ?-?, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure ? shown is different from Figure ? and ? by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

User:Xv114

2016-12-16T09:23:45Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene. The reverse is also possible however due to larger energy difference the orbitals would have poorer overlap.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

Symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}
From Table 2 and Figure 4, C=C bonds lengthen in transition state to a length that is intermediate between typical sp3-sp2 and sp2-sp2 C-C bond length before and finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in this model the orbital did not overlap despite both being in correct geometry and are in close proximity to each other.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|64
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:XV114 EXO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 ENDO-REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:XNV CHELETROPIC REACTION PROFILE.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

For all three IRC calculations shown above in Figure ?-?, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure ? shown is different from Figure ? and ? by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

File:XNV CHELETROPIC REACTION PROFILE.JPG

2016-12-16T09:23:29Z

Xv114:

File:XV114 ENDO-REACTION PROFILE.JPG

2016-12-16T09:22:13Z

Xv114:

File:XV114 EXO-REACTION PROFILE.JPG

2016-12-16T09:19:01Z

Xv114:

User:Xv114

2016-12-16T09:09:38Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene. The reverse is also possible however due to larger energy difference the orbitals would have poorer overlap.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

Symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}
From Table 2 and Figure 4, C=C bonds lengthen in transition state to a length that is intermediate between typical sp3-sp2 and sp2-sp2 C-C bond length before and finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in this model the orbital did not overlap despite both being in correct geometry and are in close proximity to each other.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 3 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|63
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:Xv114 Exo-DA-reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:Xv114 ENDO-DA-reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:Xv114 Cheletropic reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

For all three IRC calculations shown above in Figure ?-?, the energy of IRC is highest when the first partial double bond is formed in the cyclohexadiene ring before the the formation of C-S and C-O sigma bonds, this is then followed by formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring. Figure ? shown is different from Figure ? and ? by starting off with a higher energy, because IRC calculation begin with the exo product and ends with the breaking of 2 sigma bonds to give the reactants.

User:Xv114

2016-12-16T08:54:47Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene. The reverse is also possible however due to larger energy difference the orbitals would have poorer overlap.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

Symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}
From Table 2 and Figure 4, C=C bonds lengthen in transition state to a length that is intermediate between typical sp3-sp2 and sp2-sp2 C-C bond length before and finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in this model the orbital did not overlap despite both being in correct geometry and are in close proximity to each other.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

[[File:Xv114 Exercise 3-reaction scheme.jpg|700px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than that of exo-Diels Alder reaction by 3 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has the greatest activation barrier as well as Gibbs free energy. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|63
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:Xv114 Exo-DA-reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:Xv114 ENDO-DA-reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:Xv114 Cheletropic reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC calculations below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

Before the formation of C-S and C-O sigma bonds, the double bonds in cyclohexadiene are conjugated, as the reactants are approaching closer to each other, the first partial bond formed is in the cyclohexane ring, followed formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring.

User:Xv114

2016-12-16T08:47:17Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene. The reverse is also possible however due to larger energy difference the orbitals would have poorer overlap.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

Symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}
From Table 2 and Figure 4, C=C bonds lengthen in transition state to a length that is intermediate between typical sp3-sp2 and sp2-sp2 C-C bond length before and finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in this model the orbital did not overlap despite both being in correct geometry and are in close proximity to each other.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has greatest activation barrier as well as Gibbs free energy of all the reactions. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

[[File:Xv114 Exercise 3-reaction scheme.jpg|500px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|63
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:Xv114 Exo-DA-reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:Xv114 ENDO-DA-reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:Xv114 Cheletropic reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC energy graphs below were obtained after PM6 optimisation of the transition states for each reaction shown in Scheme 3.

[[File:XV114 Cheletropic IRC.JPG|1000px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|1000px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|1000px|thumb|centre|Figure 7: Endo IRC]]

Before the formation of C-S and C-O sigma bonds, the double bonds in cyclohexadiene are conjugated, as the reactants are approaching closer to each other, the first partial bond formed is in the cyclohexane ring, followed formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring.

User:Xv114

2016-12-16T08:45:50Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene. The reverse is also possible however due to larger energy difference the orbitals would have poorer overlap.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

Symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}
From Table 2 and Figure 4, C=C bonds lengthen in transition state to a length that is intermediate between typical sp3-sp2 and sp2-sp2 C-C bond length before and finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in this model the orbital did not overlap despite both being in correct geometry and are in close proximity to each other.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has greatest activation barrier as well as Gibbs free energy of all the reactions. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

[[File:Xv114 Exercise 3-reaction scheme.jpg|500px|thumb|centre|Scheme 3: Reaction scheme for exo- and endo- Diels Alder and cheletropic reaction of xylene and sulphur dioxide]]

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|63
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:Xv114 Exo-DA-reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:Xv114 ENDO-DA-reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:Xv114 Cheletropic reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

'''IRC'''

The IRC energy graphs below were obtained after PM6 optimisation of the transition states for each respective reaction.

[[File:XV114 Cheletropic IRC.JPG|700px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|700px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|700px|thumb|centre|Figure 7: Endo IRC]]

Before the formation of C-S and C-O sigma bonds, the double bonds in cyclohexadiene are conjugated, as the reactants are approaching closer to each other, the first partial bond formed is in the cyclohexane ring, followed formation of partial bond in the exocyclic double bond and SO2, and full aromaticity is established at the end of the reaction to produce a benzene ring.

File:Xv114 Exercise 3-reaction scheme.jpg

2016-12-16T08:43:19Z

Xv114:

User:Xv114

2016-12-16T01:34:39Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene. The reverse is also possible however due to larger energy difference the orbitals would have poorer overlap.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

Symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}
From Table 2 and Figure 4, C=C bonds lengthen in transition state to a length that is intermediate between typical sp3-sp2 and sp2-sp2 C-C bond length before and finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in this model the orbital did not overlap despite both being in correct geometry and are in close proximity to each other.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has greatest activation barrier as well as Gibbs free energy of all the reactions. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60
|<nowiki>-117</nowiki>
|-
|Exo-Diels Alder
|63
|<nowiki>-120</nowiki>
|-
|Cheletropic
|82
|<nowiki>-176</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:Xv114 Exo-DA-reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:Xv114 ENDO-DA-reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:Xv114 Cheletropic reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

[[File:XV114 Cheletropic IRC.JPG|500px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|500px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|500px|thumb|centre|Figure 7: Endo IRC]]

User:Xv114

2016-12-16T01:32:25Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene. The reverse is also possible however due to larger energy difference the orbitals would have poorer overlap.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

Symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}
From Table 2 and Figure 4, C=C bonds lengthen in transition state to a length that is intermediate between typical sp3-sp2 and sp2-sp2 C-C bond length before and finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in this model the orbital did not overlap despite both being in correct geometry and are in close proximity to each other.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has greatest activation barrier as well as Gibbs free energy of all the reactions. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60.1
|<nowiki>-118</nowiki>
|-
|Exo-Diels Alder
|64.1
|<nowiki>-121</nowiki>
|-
|Cheletropic
|82.4
|<nowiki>-177</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:Xv114 Exo-DA-reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:Xv114 ENDO-DA-reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of endo-Diels Alder reaction]]

[[File:Xv114 Cheletropic reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of cheletropic reaction]]

[[File:XV114 Cheletropic IRC.JPG|500px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|500px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|500px|thumb|centre|Figure 7: Endo IRC]]

File:Xv114 Cheletropic reaction profile.JPG

2016-12-16T01:31:24Z

Xv114:

File:Xv114 ENDO-DA-reaction profile.JPG

2016-12-16T01:23:08Z

Xv114:

User:Xv114

2016-12-16T01:16:46Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene. The reverse is also possible however due to larger energy difference the orbitals would have poorer overlap.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

Symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}
From Table 2 and Figure 4, C=C bonds lengthen in transition state to a length that is intermediate between typical sp3-sp2 and sp2-sp2 C-C bond length before and finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in this model the orbital did not overlap despite both being in correct geometry and are in close proximity to each other.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has greatest activation barrier as well as Gibbs free energy of all the reactions. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60.1
|<nowiki>-118</nowiki>
|-
|Exo-Diels Alder
|64.1
|<nowiki>-121</nowiki>
|-
|Cheletropic
|82.4
|<nowiki>-177</nowiki>
|}

From Figure ? below, it is also evident between the two types of Diels-Alder reactions, the endo-Diels Alder product is the kinetic product and exo product is the thermodynamic product.

[[File:Xv114 Exo-DA-reaction profile.JPG|700px|thumb|centre|Figure 7: Reaction profile of exo-Diels Alder reaction]]

[[File:XV114 Cheletropic IRC.JPG|500px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|500px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|500px|thumb|centre|Figure 7: Endo IRC]]

File:Xv114 Exo-DA-reaction profile.JPG

2016-12-16T01:14:04Z

Xv114:

User:Xv114

2016-12-16T00:46:17Z

Xv114:

= Introduction =

== Exercise 1: Reaction between butadiene and ethylene==
'''Reaction Scheme'''

Butadiene and ethylene react in Diels Alder as shown in Scheme 1:

[[File:XNV_REACTION_SCHEME_FOR_REACTION_1.jpg|500px|thumb|centre|Scheme 1: Reaction between butadiene and ethylene, producing a cyclohexene via a cyclic transition state]]

'''Molecular orbital'''

The highest occupied molecular orbitals (HOMO) and lowest occupied molecular orbitals (LUMO) of both butadiene and ethylene shown in Figure 1, can overlap to a give 4 different transition state MOs, which correlates with those illustrated on the MO diagram, Figure 2.

[[File:XNV Homo-lumo orbitals 2.JPG|700px|thumb|centre|Figure 1: HOMOs and LUMOs of butadiene and ethylene]]

[[File:XV114 HOMO for TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]] [[File: XV114 LUMO FOR TS.JPG|700px|thumb|centre|Figure 2 Transition state HOMO]]

From the MO diagram, it can be seen that it is the LUMO of butadiene that interacts with HOMO of ethylene. The reverse is also possible however due to larger energy difference the orbitals would have poorer overlap.

[[File:XNV_MO_DIAGRAM.jpg|500px|thumb|centre|Figure 2: Molecular orbital for butadiene, ethylene and transition state, symmetry of the orbitals are either symmetric (S) or asymmetric (A)]]

Symmetry of MO of both reactants needs to be the same in order for overlap to occur and in turn the reaction would be 'allowed'. I.e. Only symmetric orbital can overlap with another symmetric orbital, not with asymmetric. This explains why only LUMO of butadiene and HOMO of ethylene can overlap with each other due to both having the same symmetry.Thus, the orbital overlap integral for a symmetric-asymmetric interaction would be zero, whereas that for symmetric-symmetric or asymmetric-asymmetric interaction would be non-zero.

'''Bond Length'''

Changes in bond length can be monitored to determine whether reactants have undergone a reaction.
{| class="wikitable"
|+ Table 1: C-C bond length
!'''Typical carbon-carbon bond length :'''
!'''Å'''
|-
|Sp3-sp3 
|1.54
|-
|Sp3-sp2
|1.50
|-
|Sp2-sp2
|1.34
|}
Van der waal radius for carbon: 1.70 Å

[[File:Xv114 Bond lengths.JPG|700px|thumb|centre|Figure 4:There is a change in bond length as reactant progress through transition state to product]]

{| class="wikitable"
|+ Table 2: Change in C-C bond length (Å) from reactant to transition state and product
!
!Bond length (Å)
!
!
|-
!Bond number
!Reactant
!Transition state
!Product
|-
|1
|1.32
|1.38
|1.54
|-
|2
|0
|2.11
|1.54
|-
|3
|1.33
|1.38
|1.50
|-
|4
|1.47
|1.41
|1.33
|-
|5
|1.33
|1.38
|1.50
|-
|6
|0
|2.11
|1.54
|}
From Table 2 and Figure 4, C=C bonds lengthen in transition state to a length that is intermediate between typical sp3-sp2 and sp2-sp2 C-C bond length before and finally becoming single C-C bond in product.

'''Transition state vibrations'''

According to Figure 5, the vibration of transition state at -949 Hz indicate that the formation of two bonds appear to be synchronous with both carbons of diene and dienophile approaching each other simultaneously. In contrast to vibration at 145 Hz the formation of bond would appear to be asynchronous.

[[File:Xv114 negativeVibrations of TS.gif|500px|thumb|centre|Figure 5: Vibration of transition state at negative frequency]]

[[File:Xv114 Positive vibration of TS.gif|500px|thumb|centre|Figure 6: Vibration of transition state at the lowest positive frequency]]

'''IRC'''

[[File:XNV IRC PM6.JPG|1200px|thumb|centre|Figure 6: IRC for the reaction]]

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==

'''Reaction Scheme'''

Cyclohexadiene and 1,3-dioxole can react with each other in Diels Alder reaction as shown in Scheme 2:

[[File:xv114_Reaction_scheme.jpg|400px|thumb|centre|Scheme 2: Diels Alder reaction between cyclohexadiene and 1,3 dioxole]]

'''Molecular orbitals'''

From the MO diagram :

[[File:Xv114 MO diagram-exercise 2.jpg|500px|thumb|centre|Figure 7: MO diagram of reaction between cyclohexadiene and 1,3-dioxole]]

From Figure , the three dimensional orbitals visualised in Gaussview correlate with those in the MO diagram, Figure . Reaction has an inverse electron demand

[[File:XV114 HOMO-LUMO REACTION 2.JPG|500px|thumb|centre|Figure 7: HOMOs and LUMOs of 1,3-dioxole and cyclohexadiene]]

[[File:Xv114 HOMO of TS exo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in exo-Diels Alder]]

[[File:Xv114 HOMO of TS endo.JPG|500px|thumb|centre|Figure 7: HOMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS endo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in endo-Diels Alder]]

[[File:Xv114 LUMO of TS exo.JPG|500px|thumb|centre|Figure 7: LUMO of transition state in exo-Diels Alder]]

[[File:Xv114 Secondary orbital.jpg|400px|thumb|centre|Figure 7: In the exo Diel Alder there is only primary orbital interaction whereas in endo Diels Alder, the presence of secondary orbital interaction stabilise the transition state]]

Secondary orbital interaction is expected in this region between oxygen lone pair and π* orbital. However in this model the orbital did not overlap despite both being in correct geometry and are in close proximity to each other.

[[File:Xv114 Comparison in secondary orbital overlap.JPG|600px|thumb|centre|Figure 7:On the left diagram the orbitals coloured in red within the circled region is suppose to overlap with each other to indicate secondary orbital overlap, whereas on the right diagram there is no secondary orbital overlap]]

==Exercise 3: Diels Alder vs Cheletropic==

'''Reaction Scheme'''

Xylene and sulphur dioxide can undergo either Diels-Alder or cheletropic reaction, forming six membered ring and a five membered ring respectively, as shown in the scheme below.

From Table 3 and Figure ?, it can be deduced that endo-Diels Alder reaction has an activation barrier that is lower than of exo-Diels Alder reaction by 4 kJ/mol, however the endo-Diels Alder product is higher in energy than its exo counterpart. Cheletropic product on the other hand is has greatest activation barrier as well as Gibbs free energy of all the reactions. This suggests that kinetically endo-Diels Alder is the preferred reaction route but cheletropic reaction produces the most thermodynamically stable product.

{| class="wikitable"
|+ Table 3: The activation energy and Gibbs free energy of different types of reaction listed in Scheme 2
!Reaction type
!Activation barrier (kJ/mol)
!Gibbs Free energy (kJ/mol)
|-
|Endo- Diels Alder
|60.1
|<nowiki>-118</nowiki>
|-
|Exo-Diels Alder
|64.1
|<nowiki>-121</nowiki>
|-
|Cheletropic
|82.4
|<nowiki>-177</nowiki>
|}
[[File:XV114 Cheletropic IRC.JPG|500px|thumb|centre|Figure 7: Cheletropic IRC]]

[[File:XV114 Endo-ex.3 IRC.JPG|500px|thumb|centre|Figure 7: Exo IRC]]

[[File:Xv114 Endo-ex3 IRC 1.JPG|500px|thumb|centre|Figure 7: Endo IRC]]

User:Xv114

2016-12-16T00:36:19Z

Xv114:

User:Xv114

2016-12-15T23:22:25Z

Xv114:

User:Xv114

2016-12-15T21:09:55Z

Xv114:

File:Xv114 Endo-ex3 IRC 1.JPG

2016-12-15T21:07:32Z

Xv114:

File:XV114 Endo-ex.3 IRC.JPG

2016-12-15T21:04:20Z

Xv114:

File:XV114 Cheletropic IRC.JPG

2016-12-15T21:00:35Z

Xv114:

File:Xv114 Comparison in secondary orbital overlap.JPG

2016-12-15T20:36:20Z

Xv114:

File:Xv114 LUMO of TS exo.JPG

2016-12-15T19:55:46Z

Xv114:

File:Xv114 LUMO of TS endo.JPG

2016-12-15T19:48:49Z

Xv114: