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Rep:YNX19950213

2016-12-16T11:42:59Z

Ynx14:

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state. And discus the relationships between molecular symmetries and reactivity. Investigate how does '''Endo''' and '''Exo''' pathway in '''Diels-Alder reaction''' differ in energy profile. Which reaction pathway is more favorable in thermodynamic aspect and kinetic aspect. Is there any potential secondary orbital interactions happened during the reactions? If do, is it true for both Endo and Exo pathway? And finally how does Cheletropic reaction differ from '''Diels-Alder reaction''' in every aspect.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===
In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The HOMO) and ethene (The LUMO) are both symmetric (denoted as s), thus the interaction is allowed. And the interactions between an Anti-symmetric (a) and a Symmetric (s) orbital is forbidden due to their different orbital symmetry.

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|1000px|thumb|left| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|1000px|thumb|center| The Reaction process visualised]]

==Reaction of Cyclohexadiene and 1,3-Dioxole==
===Reaction Scheme===
The reaction have two different pathway, namely '''Endo''' and '''Exo'''. Which are shown below
[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]

===Molecular Orbitals===
This is an inverse demand DA reaction because there are two new chemical bonds and a six-membered ring are formed and is between an electron-rich dienophile, namely cyclohexadiene, and an electron-poor diene, namely dioxole.
The Dioxole is electron-poor due to the two electron withdrawing Oxygen atom in adjacent to the double bond.
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
| The energies of the Reaction Profile
!Endo(KJ/mol)
!Exo(KJ/mol)
|-
|Reactant
|<nowiki>-1511893.671</nowiki>
|<nowiki>-1511877.126</nowiki>
|-
|Transition State
|<nowiki>-1511963.779</nowiki>
|<nowiki>-1511970.525</nowiki>
|-
|Product
|<nowiki>-1511921.323</nowiki>
|<nowiki>-1511892.187</nowiki>
|-
|Ea
|70.108
|93.399
|-
|ΔE
|<nowiki>-27.652</nowiki>
|<nowiki>-15.061</nowiki>
|}

The Endo pathway having both a more stable product (a bigger ΔE) and a smaller activation energy (Ea), which means that the '''Endo pathway''' is '''both thermodynamically and knetically favoured.'''

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene. The '''Endo''' pathway experienced the Secondary Orbital Interactions, however,the '''Exo''' reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the '''distance''' between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.

==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using '''GaussView''', one can simply realized that the reaction energies are really important and useful for confirming hypothetical '''transition state'''. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of '''reaction mechanism''' and '''molecular symmetries'''.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the '''PM6''' was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T11:41:03Z

Ynx14: /* Visualization of the Transition State */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state. And discus the relationships between molecular symmetries and reactivity. Investigate how does '''Endo''' and '''Exo''' pathway in '''Diels-Alder reaction''' differ in energy profile. Which reaction pathway is more favorable in thermodynamic aspect and kinetic aspect. Is there any potential secondary orbital interactions happened during the reactions? If do, is it true for both Endo and Exo pathway? And finally how does Cheletropic reaction differ from '''Diels-Alder reaction''' in every aspect.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===
In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The HOMO) and ethene (The LUMO) are both symmetric (denoted as s), thus the interaction is allowed. And the interactions between an Anti-symmetric (a) and a Symmetric (s) orbital is forbidden due to their different orbital symmetry.

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|1000px|thumb|left| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|1000px|thumb|right| The Reaction process visualised]]

==Reaction of Cyclohexadiene and 1,3-Dioxole==
===Reaction Scheme===
The reaction have two different pathway, namely '''Endo''' and '''Exo'''. Which are shown below
[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]

===Molecular Orbitals===
This is an inverse demand DA reaction because there are two new chemical bonds and a six-membered ring are formed and is between an electron-rich dienophile, namely cyclohexadiene, and an electron-poor diene, namely dioxole.
The Dioxole is electron-poor due to the two electron withdrawing Oxygen atom in adjacent to the double bond.
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
| The energies of the Reaction Profile
!Endo(KJ/mol)
!Exo(KJ/mol)
|-
|Reactant
|<nowiki>-1511893.671</nowiki>
|<nowiki>-1511877.126</nowiki>
|-
|Transition State
|<nowiki>-1511963.779</nowiki>
|<nowiki>-1511970.525</nowiki>
|-
|Product
|<nowiki>-1511921.323</nowiki>
|<nowiki>-1511892.187</nowiki>
|-
|Ea
|70.108
|93.399
|-
|ΔE
|<nowiki>-27.652</nowiki>
|<nowiki>-15.061</nowiki>
|}

The Endo pathway having both a more stable product (a bigger ΔE) and a smaller activation energy (Ea), which means that the '''Endo pathway''' is '''both thermodynamically and knetically favoured.'''

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene. The '''Endo''' pathway experienced the Secondary Orbital Interactions, however,the '''Exo''' reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the '''distance''' between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.

==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using '''GaussView''', one can simply realized that the reaction energies are really important and useful for confirming hypothetical '''transition state'''. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of '''reaction mechanism''' and '''molecular symmetries'''.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the '''PM6''' was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T11:39:06Z

Ynx14: /* Visualization of the Transition State */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state. And discus the relationships between molecular symmetries and reactivity. Investigate how does '''Endo''' and '''Exo''' pathway in '''Diels-Alder reaction''' differ in energy profile. Which reaction pathway is more favorable in thermodynamic aspect and kinetic aspect. Is there any potential secondary orbital interactions happened during the reactions? If do, is it true for both Endo and Exo pathway? And finally how does Cheletropic reaction differ from '''Diels-Alder reaction''' in every aspect.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===
In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The HOMO) and ethene (The LUMO) are both symmetric (denoted as s), thus the interaction is allowed. And the interactions between an Anti-symmetric (a) and a Symmetric (s) orbital is forbidden due to their different orbital symmetry.

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|left| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|right| The Reaction process visualised]]

==Reaction of Cyclohexadiene and 1,3-Dioxole==
===Reaction Scheme===
The reaction have two different pathway, namely '''Endo''' and '''Exo'''. Which are shown below
[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]

===Molecular Orbitals===
This is an inverse demand DA reaction because there are two new chemical bonds and a six-membered ring are formed and is between an electron-rich dienophile, namely cyclohexadiene, and an electron-poor diene, namely dioxole.
The Dioxole is electron-poor due to the two electron withdrawing Oxygen atom in adjacent to the double bond.
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
| The energies of the Reaction Profile
!Endo(KJ/mol)
!Exo(KJ/mol)
|-
|Reactant
|<nowiki>-1511893.671</nowiki>
|<nowiki>-1511877.126</nowiki>
|-
|Transition State
|<nowiki>-1511963.779</nowiki>
|<nowiki>-1511970.525</nowiki>
|-
|Product
|<nowiki>-1511921.323</nowiki>
|<nowiki>-1511892.187</nowiki>
|-
|Ea
|70.108
|93.399
|-
|ΔE
|<nowiki>-27.652</nowiki>
|<nowiki>-15.061</nowiki>
|}

The Endo pathway having both a more stable product (a bigger ΔE) and a smaller activation energy (Ea), which means that the '''Endo pathway''' is '''both thermodynamically and knetically favoured.'''

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene. The '''Endo''' pathway experienced the Secondary Orbital Interactions, however,the '''Exo''' reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the '''distance''' between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.

==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using '''GaussView''', one can simply realized that the reaction energies are really important and useful for confirming hypothetical '''transition state'''. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of '''reaction mechanism''' and '''molecular symmetries'''.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the '''PM6''' was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T11:38:35Z

Ynx14: /* Introduction */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state. And discus the relationships between molecular symmetries and reactivity. Investigate how does '''Endo''' and '''Exo''' pathway in '''Diels-Alder reaction''' differ in energy profile. Which reaction pathway is more favorable in thermodynamic aspect and kinetic aspect. Is there any potential secondary orbital interactions happened during the reactions? If do, is it true for both Endo and Exo pathway? And finally how does Cheletropic reaction differ from '''Diels-Alder reaction''' in every aspect.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===
In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The HOMO) and ethene (The LUMO) are both symmetric (denoted as s), thus the interaction is allowed. And the interactions between an Anti-symmetric (a) and a Symmetric (s) orbital is forbidden due to their different orbital symmetry.

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

==Reaction of Cyclohexadiene and 1,3-Dioxole==
===Reaction Scheme===
The reaction have two different pathway, namely '''Endo''' and '''Exo'''. Which are shown below
[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]

===Molecular Orbitals===
This is an inverse demand DA reaction because there are two new chemical bonds and a six-membered ring are formed and is between an electron-rich dienophile, namely cyclohexadiene, and an electron-poor diene, namely dioxole.
The Dioxole is electron-poor due to the two electron withdrawing Oxygen atom in adjacent to the double bond.
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
| The energies of the Reaction Profile
!Endo(KJ/mol)
!Exo(KJ/mol)
|-
|Reactant
|<nowiki>-1511893.671</nowiki>
|<nowiki>-1511877.126</nowiki>
|-
|Transition State
|<nowiki>-1511963.779</nowiki>
|<nowiki>-1511970.525</nowiki>
|-
|Product
|<nowiki>-1511921.323</nowiki>
|<nowiki>-1511892.187</nowiki>
|-
|Ea
|70.108
|93.399
|-
|ΔE
|<nowiki>-27.652</nowiki>
|<nowiki>-15.061</nowiki>
|}

The Endo pathway having both a more stable product (a bigger ΔE) and a smaller activation energy (Ea), which means that the '''Endo pathway''' is '''both thermodynamically and knetically favoured.'''

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene. The '''Endo''' pathway experienced the Secondary Orbital Interactions, however,the '''Exo''' reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the '''distance''' between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.

==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using '''GaussView''', one can simply realized that the reaction energies are really important and useful for confirming hypothetical '''transition state'''. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of '''reaction mechanism''' and '''molecular symmetries'''.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the '''PM6''' was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T11:32:51Z

Ynx14: /* Conclusion */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===
In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The HOMO) and ethene (The LUMO) are both symmetric (denoted as s), thus the interaction is allowed. And the interactions between an Anti-symmetric (a) and a Symmetric (s) orbital is forbidden due to their different orbital symmetry.

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

==Reaction of Cyclohexadiene and 1,3-Dioxole==
===Reaction Scheme===
The reaction have two different pathway, namely '''Endo''' and '''Exo'''. Which are shown below
[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]

===Molecular Orbitals===
This is an inverse demand DA reaction because there are two new chemical bonds and a six-membered ring are formed and is between an electron-rich dienophile, namely cyclohexadiene, and an electron-poor diene, namely dioxole.
The Dioxole is electron-poor due to the two electron withdrawing Oxygen atom in adjacent to the double bond.
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
| The energies of the Reaction Profile
!Endo(KJ/mol)
!Exo(KJ/mol)
|-
|Reactant
|<nowiki>-1511893.671</nowiki>
|<nowiki>-1511877.126</nowiki>
|-
|Transition State
|<nowiki>-1511963.779</nowiki>
|<nowiki>-1511970.525</nowiki>
|-
|Product
|<nowiki>-1511921.323</nowiki>
|<nowiki>-1511892.187</nowiki>
|-
|Ea
|70.108
|93.399
|-
|ΔE
|<nowiki>-27.652</nowiki>
|<nowiki>-15.061</nowiki>
|}

The Endo pathway having both a more stable product (a bigger ΔE) and a smaller activation energy (Ea), which means that the '''Endo pathway''' is '''both thermodynamically and knetically favoured.'''

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene. The '''Endo''' pathway experienced the Secondary Orbital Interactions, however,the '''Exo''' reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the '''distance''' between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.

==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using '''GaussView''', one can simply realized that the reaction energies are really important and useful for confirming hypothetical '''transition state'''. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of '''reaction mechanism''' and '''molecular symmetries'''.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the '''PM6''' was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T11:31:40Z

Ynx14: /* Secondary orbital interaction */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===
In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The HOMO) and ethene (The LUMO) are both symmetric (denoted as s), thus the interaction is allowed. And the interactions between an Anti-symmetric (a) and a Symmetric (s) orbital is forbidden due to their different orbital symmetry.

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

==Reaction of Cyclohexadiene and 1,3-Dioxole==
===Reaction Scheme===
The reaction have two different pathway, namely '''Endo''' and '''Exo'''. Which are shown below
[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]

===Molecular Orbitals===
This is an inverse demand DA reaction because there are two new chemical bonds and a six-membered ring are formed and is between an electron-rich dienophile, namely cyclohexadiene, and an electron-poor diene, namely dioxole.
The Dioxole is electron-poor due to the two electron withdrawing Oxygen atom in adjacent to the double bond.
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
| The energies of the Reaction Profile
!Endo(KJ/mol)
!Exo(KJ/mol)
|-
|Reactant
|<nowiki>-1511893.671</nowiki>
|<nowiki>-1511877.126</nowiki>
|-
|Transition State
|<nowiki>-1511963.779</nowiki>
|<nowiki>-1511970.525</nowiki>
|-
|Product
|<nowiki>-1511921.323</nowiki>
|<nowiki>-1511892.187</nowiki>
|-
|Ea
|70.108
|93.399
|-
|ΔE
|<nowiki>-27.652</nowiki>
|<nowiki>-15.061</nowiki>
|}

The Endo pathway having both a more stable product (a bigger ΔE) and a smaller activation energy (Ea), which means that the '''Endo pathway''' is '''both thermodynamically and knetically favoured.'''

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene. The '''Endo''' pathway experienced the Secondary Orbital Interactions, however,the '''Exo''' reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the '''distance''' between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.

==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T11:30:19Z

Ynx14: /* Reaction analysis: Energies */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===
In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The HOMO) and ethene (The LUMO) are both symmetric (denoted as s), thus the interaction is allowed. And the interactions between an Anti-symmetric (a) and a Symmetric (s) orbital is forbidden due to their different orbital symmetry.

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

==Reaction of Cyclohexadiene and 1,3-Dioxole==
===Reaction Scheme===
The reaction have two different pathway, namely '''Endo''' and '''Exo'''. Which are shown below
[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]

===Molecular Orbitals===
This is an inverse demand DA reaction because there are two new chemical bonds and a six-membered ring are formed and is between an electron-rich dienophile, namely cyclohexadiene, and an electron-poor diene, namely dioxole.
The Dioxole is electron-poor due to the two electron withdrawing Oxygen atom in adjacent to the double bond.
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
| The energies of the Reaction Profile
!Endo(KJ/mol)
!Exo(KJ/mol)
|-
|Reactant
|<nowiki>-1511893.671</nowiki>
|<nowiki>-1511877.126</nowiki>
|-
|Transition State
|<nowiki>-1511963.779</nowiki>
|<nowiki>-1511970.525</nowiki>
|-
|Product
|<nowiki>-1511921.323</nowiki>
|<nowiki>-1511892.187</nowiki>
|-
|Ea
|70.108
|93.399
|-
|ΔE
|<nowiki>-27.652</nowiki>
|<nowiki>-15.061</nowiki>
|}

The Endo pathway having both a more stable product (a bigger ΔE) and a smaller activation energy (Ea), which means that the '''Endo pathway''' is '''both thermodynamically and knetically favoured.'''

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T11:29:36Z

Ynx14: /* Molecular Orbitals */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===
In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The HOMO) and ethene (The LUMO) are both symmetric (denoted as s), thus the interaction is allowed. And the interactions between an Anti-symmetric (a) and a Symmetric (s) orbital is forbidden due to their different orbital symmetry.

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

==Reaction of Cyclohexadiene and 1,3-Dioxole==
===Reaction Scheme===
The reaction have two different pathway, namely '''Endo''' and '''Exo'''. Which are shown below
[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]

===Molecular Orbitals===
This is an inverse demand DA reaction because there are two new chemical bonds and a six-membered ring are formed and is between an electron-rich dienophile, namely cyclohexadiene, and an electron-poor diene, namely dioxole.
The Dioxole is electron-poor due to the two electron withdrawing Oxygen atom in adjacent to the double bond.
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
| The energies of the Reaction Profile
!Endo(KJ/mol)
!Exo(KJ/mol)
|-
|Reactant
|<nowiki>-1511893.671</nowiki>
|<nowiki>-1511877.126</nowiki>
|-
|Transition State
|<nowiki>-1511963.779</nowiki>
|<nowiki>-1511970.525</nowiki>
|-
|Product
|<nowiki>-1511921.323</nowiki>
|<nowiki>-1511892.187</nowiki>
|-
|Ea
|70.108
|93.399
|-
|ΔE
|<nowiki>-27.652</nowiki>
|<nowiki>-15.061</nowiki>
|}

The Endo pathway having both a more stable product (a bigger ΔE) and a smaller activation energy (Ea), which means that the Endo pathway is both thermodynamically and knetically favoured.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T11:23:16Z

Ynx14: /* Reaction Scheme */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===
In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The HOMO) and ethene (The LUMO) are both symmetric (denoted as s), thus the interaction is allowed. And the interactions between an Anti-symmetric (a) and a Symmetric (s) orbital is forbidden due to their different orbital symmetry.

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

==Reaction of Cyclohexadiene and 1,3-Dioxole==
===Reaction Scheme===
The reaction have two different pathway, namely '''Endo''' and '''Exo'''. Which are shown below
[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]

===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
| The energies of the Reaction Profile
!Endo(KJ/mol)
!Exo(KJ/mol)
|-
|Reactant
|<nowiki>-1511893.671</nowiki>
|<nowiki>-1511877.126</nowiki>
|-
|Transition State
|<nowiki>-1511963.779</nowiki>
|<nowiki>-1511970.525</nowiki>
|-
|Product
|<nowiki>-1511921.323</nowiki>
|<nowiki>-1511892.187</nowiki>
|-
|Ea
|70.108
|93.399
|-
|ΔE
|<nowiki>-27.652</nowiki>
|<nowiki>-15.061</nowiki>
|}

The Endo pathway having both a more stable product (a bigger ΔE) and a smaller activation energy (Ea), which means that the Endo pathway is both thermodynamically and knetically favoured.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T11:18:56Z

Ynx14: /* Molecular Orbitals */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===
In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The HOMO) and ethene (The LUMO) are both symmetric (denoted as s), thus the interaction is allowed. And the interactions between an Anti-symmetric (a) and a Symmetric (s) orbital is forbidden due to their different orbital symmetry.

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
| The energies of the Reaction Profile
!Endo(KJ/mol)
!Exo(KJ/mol)
|-
|Reactant
|<nowiki>-1511893.671</nowiki>
|<nowiki>-1511877.126</nowiki>
|-
|Transition State
|<nowiki>-1511963.779</nowiki>
|<nowiki>-1511970.525</nowiki>
|-
|Product
|<nowiki>-1511921.323</nowiki>
|<nowiki>-1511892.187</nowiki>
|-
|Ea
|70.108
|93.399
|-
|ΔE
|<nowiki>-27.652</nowiki>
|<nowiki>-15.061</nowiki>
|}

The Endo pathway having both a more stable product (a bigger ΔE) and a smaller activation energy (Ea), which means that the Endo pathway is both thermodynamically and knetically favoured.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T11:17:51Z

Ynx14:

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
| The energies of the Reaction Profile
!Endo(KJ/mol)
!Exo(KJ/mol)
|-
|Reactant
|<nowiki>-1511893.671</nowiki>
|<nowiki>-1511877.126</nowiki>
|-
|Transition State
|<nowiki>-1511963.779</nowiki>
|<nowiki>-1511970.525</nowiki>
|-
|Product
|<nowiki>-1511921.323</nowiki>
|<nowiki>-1511892.187</nowiki>
|-
|Ea
|70.108
|93.399
|-
|ΔE
|<nowiki>-27.652</nowiki>
|<nowiki>-15.061</nowiki>
|}

The Endo pathway having both a more stable product (a bigger ΔE) and a smaller activation energy (Ea), which means that the Endo pathway is both thermodynamically and knetically favoured.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T11:05:16Z

Ynx14: /* Reaction analysis: Energies */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| align="center" , class = "wikitable"
|+ Table 1: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|523.375
|436.789
|<nowiki>-1313895.059</nowiki>
|-
|Exo
|524.068
|438.136
|<nowiki>-1313891.573</nowiki>
|}

From the Table 1 we can conclude that the Endo product is a little more negative in sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class = "wikitable"
|+ Table 2: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|540.906
|449.987
|<nowiki>-1297035.117</nowiki>
|-
|Exo
|372.461
|279.264
|<nowiki>-1296125.026</nowiki>
|}

From the table 2 , the endo path has a more negative sum of electronic and thermal Free of Energies, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T10:53:13Z

Ynx14: /* Reaction analysis: Energies */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| align="center" , class = "wikitable"
|+ Table 1: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table 1 we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class = "wikitable"
|+ Table 2: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table 2 , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T10:51:26Z

Ynx14: /* Reaction analysis: Energies */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| align="center"
|+ Table 1: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table 1 we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| align="center"
|+ Table 2: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table 2 , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T10:50:59Z

Ynx14: /* Molecular Orbitals */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg|center]]
{| align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
|+ Table 1: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table 1 we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class="wikitable" align="center"
|+ Table 2: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table 2 , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T10:50:36Z

Ynx14: /* Molecular Orbitals */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{|align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{|align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg|center]]
{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
|+ Table 1: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table 1 we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class="wikitable" align="center"
|+ Table 2: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table 2 , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T10:49:06Z

Ynx14: /* Molecular Orbitals */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{| align="center" class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg|center]]
{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
|+ Table 1: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table 1 we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class="wikitable" align="center"
|+ Table 2: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table 2 , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T10:48:33Z

Ynx14:

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{| align="center" class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre| The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre| The Reaction process visualised]]

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg]]
{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
|+ Table 1: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table 1 we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class="wikitable" align="center"
|+ Table 2: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table 2 , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T10:46:17Z

Ynx14:

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]
{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre|Figure ?: The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre|Figure ?: The Reaction process visualised]]

<jmol>
<jmolApplet>
<color>white</color>
<size>500</size>
<script>frame 78; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>EX1_PRODUCT_OPTIMISATION_PM6_WITH_KEY_WORD.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg]]
{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| class="wikitable" align="center"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable" align="center"
|+ Table 1: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table 1 we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class="wikitable" align="center"
|+ Table 2: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table 2 , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==

===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|ΔE
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

From the Reaction Profile and the data, it can be conclude that the '''Endo''' pathway is the most '''Kinetically''' favoured as it has the lowest activation energy (Ea), thus having the fastest reaction rate. The Cheletropic pathway on the other hand, although having the highest activation energy, but has the biggest ΔE and lowest product energy. The product's free energy is almost zero, which will be extremely stable (irreversible) and thus will be the thermodynamically favourable pathway.

Below are IRC of each reaction pathway, the energy was in '''Hatree'''.(1 Hatree = 2625.5 KJ/mol)

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

==Conclusion==
With all the studies of the three Ring forming reactions using GaussView, one can simply realized that the reaction energies are really important and useful for confirming hypothetical transition state. And being able to visualize reaction process via animation and generate actual MO lobes are also extremely helpful in the study of reaction mechanism and symmetries.

With the help of computational portal, more accurate '''6-31G''' calculation can be utilized, however, in practice the PM6 was much more commonly used thanks to it's fast processing. The most useful and unique feature of computational chemistry is that it costs nothing, and you have the result almost immediately, one can thus quickly get feedback and redesign his/her experiment.

Rep:YNX19950213

2016-12-16T10:22:04Z

Ynx14: /* Reaction analysis: Reaction profile */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|left|thumb|Butadiene-Ethene Diels Alder Reaction]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre|Figure ?: The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre|Figure ?: The Reaction process visualised]]

<jmol>
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<color>white</color>
<size>500</size>
<script>frame 78; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>EX1_PRODUCT_OPTIMISATION_PM6_WITH_KEY_WORD.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable"
|+ Table 1: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table 1 we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class="wikitable"
|+ Table 2: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table 2 , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==
===Reaction Scheme===
===Molecular Orbitals===
===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|Change in Energy
|<nowiki>-120.03</nowiki>
|<nowiki>-121.25</nowiki>
|<nowiki>-188.55</nowiki>
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

Rep:YNX19950213

2016-12-16T10:20:46Z

Ynx14: /* Reaction analysis: Reaction profile */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|left|thumb|Butadiene-Ethene Diels Alder Reaction]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre|Figure ?: The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre|Figure ?: The Reaction process visualised]]

<jmol>
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<color>white</color>
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<script>frame 78; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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</jmolApplet>
</jmol>

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable"
|+ Table 1: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table 1 we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class="wikitable"
|+ Table 2: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table 2 , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==
===Reaction Scheme===
===Molecular Orbitals===
===Reaction analysis: Reaction profile===

{| class="wikitable" align="center"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|Change in Energy
|120.03
|121.25
|188.55
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

File:Ash-EX3-Reaction profile.PNG

2016-12-16T10:19:43Z

Ynx14:

Rep:YNX19950213

2016-12-16T10:19:21Z

Ynx14: /* Reaction analysis: Reaction profile */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|left|thumb|Butadiene-Ethene Diels Alder Reaction]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre|Figure ?: The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre|Figure ?: The Reaction process visualised]]

<jmol>
<jmolApplet>
<color>white</color>
<size>500</size>
<script>frame 78; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>EX1_PRODUCT_OPTIMISATION_PM6_WITH_KEY_WORD.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable"
|+ Table 1: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table 1 we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class="wikitable"
|+ Table 2: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table 2 , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==
===Reaction Scheme===
===Molecular Orbitals===
===Reaction analysis: Reaction profile===

{| class="wikitable"
|+ Table 3: The energies of the Reaction Profile
!
!Endo(KJ/mol)
!Exo(KJ/mol)
!Cheletropic(KJ/mol)
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|Change in Energy
|120.03
|121.25
|188.55
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

Rep:YNX19950213

2016-12-16T10:18:33Z

Ynx14:

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|left|thumb|Butadiene-Ethene Diels Alder Reaction]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre|Figure ?: The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre|Figure ?: The Reaction process visualised]]

<jmol>
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<color>white</color>
<size>500</size>
<script>frame 78; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>EX1_PRODUCT_OPTIMISATION_PM6_WITH_KEY_WORD.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable"
|+ Table 1: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table 1 we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class="wikitable"
|+ Table 2: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table 2 , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==
===Reaction Scheme===
===Molecular Orbitals===
===Reaction analysis: Reaction profile===

{| class="wikitable"
|+ Table 3: The energies of the Reaction Profile
!
!Endo
!Exo
!Cheletropic
|-
|Reactant
|176.33
|178.25
|188.56
|-
|Transition State
|241.75
|237.76
|260.07
|-
|Product
|56.3
|57.0
|0.0005
|-
|Ea
|65.42
|59.51
|71.51
|-
|Change in Energy
|120.03
|121.25
|188.55
|}

[[File:Ash-EX3-Reaction_profile.PNG|1000x1000px|thumb|centre|Reaction Profiles]]

[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

Rep:YNX19950213

2016-12-16T09:52:45Z

Ynx14: /* Reaction analysis: Energies */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|left|thumb|Butadiene-Ethene Diels Alder Reaction]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre|Figure ?: The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre|Figure ?: The Reaction process visualised]]

<jmol>
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<color>white</color>
<size>500</size>
<script>frame 78; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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</jmolApplet>
</jmol>

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable"
|+ Table 1: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table 1 we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class="wikitable"
|+ Table 2: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table 2 , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==
===Reaction Scheme===
===Molecular Orbitals===
===Reaction analysis: Reaction profile===
[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

File:Ash-EX2 MO32.PNG

2016-12-16T09:30:17Z

Ynx14:

File:Ash-EX2 MO31.PNG

2016-12-16T09:30:15Z

Ynx14:

File:Ash-EX2 MO30.PNG

2016-12-16T09:30:13Z

Ynx14:

File:Ash-EX2 MO29.PNG

2016-12-16T09:30:10Z

Ynx14:

Rep:YNX19950213

2016-12-16T09:28:13Z

Ynx14: /* Molecular Orbitals */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|left|thumb|Butadiene-Ethene Diels Alder Reaction]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre|Figure ?: The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre|Figure ?: The Reaction process visualised]]

<jmol>
<jmolApplet>
<color>white</color>
<size>500</size>
<script>frame 78; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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</jmol>

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2_MO29.PNG]]
| [[File:Ash-EX2_MO30.PNG]]
| [[File:Ash-EX2_MO31.PNG]]
| [[File:Ash-EX2_MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable"
|+ Table ?: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table ? we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class="wikitable"
|+ Table ?: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table ?? , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==
===Reaction Scheme===
===Molecular Orbitals===
===Reaction analysis: Reaction profile===
[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

File:Ash-EX2-TS-Exo-MO32.PNG

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Rep:YNX19950213

2016-12-16T09:22:45Z

Ynx14: /* Molecular Orbitals */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|left|thumb|Butadiene-Ethene Diels Alder Reaction]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre|Figure ?: The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre|Figure ?: The Reaction process visualised]]

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

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2-MO29.PNG]]
| [[File:Ash-EX2-MO30.PNG]]
| [[File:Ash-EX2-MO31.PNG]]
| [[File:Ash-EX2-MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable"
|+ Table ?: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table ? we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class="wikitable"
|+ Table ?: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table ?? , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==
===Reaction Scheme===
===Molecular Orbitals===
===Reaction analysis: Reaction profile===
[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

File:Ash-EX2-MO32.PNG

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File:Ash-EX2-MO31.PNG

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File:Ash-EX2-MO30.PNG

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File:Ash-EX2-MO29.PNG

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Ynx14: Ynx14 uploaded a new version of File:Ash-EX2-MO29.PNG

Rep:YNX19950213

2016-12-16T09:20:23Z

Ynx14: /* Molecular Orbitals */

'''Investigation of Transition States and Reactivity'''

==Introduction==

The development of computational chemistry and computational programs have provided great tools for study chemical reaction's mechanisms. One namely the study of transition states[https://en.wikipedia.org/wiki/Transition_state], which would be impossible to monitor or simulate with conventional lab experiments. This page is delicate to present some of the most well-known reactions' transition state.

==Reaction of Butadiene and Ethylene==
===Reaction Scheme===
[[Image:Ash-EX1-reaction-scheme.png|700x700px|center|thumb|'''Scheme 1''':Butadiene-Ethene Diels Alder Reaction]]
This is a very typical and simple '''Diels-Alder Reaction'''[https://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction] between Butadiene and Ethene, illustrated as the MO diagram below.

===Molecular Orbitals===

[[Image:Ash-EX1-MO.jpg|700x700px|left|thumb|Butadiene-Ethene Diels Alder Reaction]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 16
! style="background: #0D4F8B; color: white;" | MO 17
! style="background: #0D4F8B; color: white;" | MO 18
! style="background: #0D4F8B; color: white;" | MO 19
|-
| [[File:Ash-MO-16.PNG]]
| [[File:Ash-MO-17.PNG]]
| [[File:Ash-MO-18.PNG]]
| [[File:Ash-MO-19.PNG]]
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Transition state MO16
! style="background: #0D4F8B; color: white;" | Transition state MO17
! style="background: #0D4F8B; color: white;" | Transition state MO18
! style="background: #0D4F8B; color: white;" | Transition state MO19
|-
| [[File:Ash-TS-MO16.PNG]]
| [[File:Ash-TS-MO17.png]]
| [[File:Ash-TS-MO18.PNG]]
| [[File:Ash-TS-MO19.PNG]]
|}
''The corresponding MO lobes were generated by GaussView 5.0.''

===Reaction analysis: Symmetry and Reactivity===
It can be clearly seen that the LUMO of Butadiene interacted with the HOMO of Ethene. In order to have a successful reaction, symmetries of the HOMO and the LUMO orbitals must match, otherwise the reaction is forbidden. Orbitals can only be either symmetric or anti-symmetric, which can be determined by calculation of their wave functions.
As the MO diagram illustrated, the frontier orbitals of butadiene (The '''HOMO''') and ethene (The '''LUMO''') are both symmetric (denoted as '''s'''), thus the interaction is allowed. And the interactions between an Anti-symmetric ('''a''') and a Symmetric ('''s''') orbital is forbidden due to their different orbital symmetry.

[[File:Ash-EX1-IRC.PNG|1000x1000px|thumb|centre| '''Intrinsic Reaction Coordinate''' (IRC) of the Reaction]]

With the help of '''Intrinsic Reaction Coordinate''' calculation, we can trace the minimum energy pathway between the reactant and the product on the '''potential energy surface'''. The highest point of total energy corresponds to the Transition state.

===Visualization of the Transition State===

With the help of computationol programs, we can simulate the molecular interactions during the transition state. By looking at the ''Imaginary Vibrations''' of the '''TS''' we can have a straight forward idea of how Butadiene and Ethene were react to give the '''Cyclohexene''' .

[[File:Ash-EX1_IVibration.gif|750px|thumb|centre|Figure ?: The Imaginary Vibration mode]]
[[File:Ash-EX1_Reaction.gif|750px|thumb|centre|Figure ?: The Reaction process visualised]]

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</jmolApplet>
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==Reaction of Cyclohexadiene and 1,3-Dioxole==
===Reaction Scheme===

[[File:Ash-EX2-Scheme.png|500x500px|thumb|centre| '''Endo and Exo''' pathway of Diels-Alder Reaction]]
===Molecular Orbitals===
[[File:Ash-EX2-MO.jpg]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | MO 29
! style="background: #0D4F8B; color: white;" | MO 30
! style="background: #0D4F8B; color: white;" | MO 31
! style="background: #0D4F8B; color: white;" | MO 32
|-
| [[File:Ash-EX2-MO29.PNG]]
| [[File:Ash-EX2-MO30.PNG]]
| [[File:Ash-EX2-MO31.PNG]]
| [[File:Ash-EX2-MO32.PNG]]
|}

[[File:Ash-EX2-MO.jpg]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Endo Transition State MO29
! style="background: #0D4F8B; color: white;" | Endo Transition State MO30
! style="background: #0D4F8B; color: white;" | Endo Transition State MO31
! style="background: #0D4F8B; color: white;" | Endo Transition State MO32
|-
| [[File:Ash-EX2-TS-Endo-MO29.PNG]]
| [[File:Ash-EX2-TS-Endo-MO30.PNG]]
| [[File:Ash-EX2-TS-Endo-MO31.PNG]]
| [[File:Ash-EX2-TS-Endo-MO32.PNG]]
|}

[[File:Ash-EX2-MO.jpg]]
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Exo Transition State MO29
! style="background: #0D4F8B; color: white;" | Exo Transition State MO30
! style="background: #0D4F8B; color: white;" | Exo Transition State MO31
! style="background: #0D4F8B; color: white;" | Exo Transition State MO32
|-
| [[File:Ash-EX2-TS-Exo-MO29.PNG]]
| [[File:Ash-EX2-TS-Exo-MO30.PNG]]
| [[File:Ash-EX2-TS-Exo-MO31.PNG]]
| [[File:Ash-EX2-TS-Exo-MO32.PNG]]
|}

===Reaction analysis: Energies===

{| class="wikitable"
|+ Table ?: The energies of the Reaction Product
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.199343
|0.166363
|<nowiki>-500.436130</nowiki>
|-
|Exo
|0.199607
|0.166877
|<nowiki>-500.434802</nowiki>
|}

From the Table ? we can conclude that the Endo product has the most negative sum of electronic and thermal Free Energies, which means that the Endo product is the more stable product, thus the thermodynamic product.

{| class="wikitable"
|+ Table ?: The energies of the Transition State
!Reaction Path
!Zero-point correction (Hartree/Particle)/ kJ/mol
!Thermal correction to Gibbs Free Energy/ kJ/mol
!Sum of electronic and thermal Free Energies/ kJ/mol
|-
|Endo
|0.206020
|0.171391
|<nowiki>-494.014518</nowiki>
|-
|Exo
|0.141863
|0.106366
|<nowiki>-858.059518</nowiki>
|}

From the table ?? , there is a huge energy difference between endo and exo, where the exo path has a much more negative sum of electronic and thermal Free of Energies of -858 compare to -494 that of the Endo path, which means that it requires more energy to achieve the Exo TS, in other words, the energy barrier of the whole Exo path is higher, even the product's energy are similar in both pathways. This draws into another conclusion that the Endo pathway is also the more kinetically preferred pathway as it is easier to react/hase a faster reaction rate.

[[File:Ash-EX2-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the EXO path]]
[[File:Ash-EX2-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]

===Secondary orbital interaction===
[[File:Ash-Secondary_Orbital_Interactions.png|600x600px|thumb|centre|Secondary Orbital Interactions: Endo vs. Exo]]
The Secondary Orbital Interactions happends between the two oxygen lone pairs and the π* orbital of the diene.
The Exo reaction pathway can't experience the Secondary Orbital Interactions however, due to the fact that the distance between the two oxygen lone pairs and the π* orbital is too far for the interactions to take place.
==Diels-Alder vs Cheletropic==
===Reaction Scheme===
===Molecular Orbitals===
===Reaction analysis: Reaction profile===
[[File:Ash-EX3-EXO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Exo path]]
[[File:Ash-EX3-ENDO_IRC.PNG|1000x1000px|thumb|centre|IRC of the Endo path]]
[[File:Ash-Cheltropic_IRC.PNG|1000x1000px|thumb|centre|IRC of the Cheltropic path]]

File:Ash-EX1 IVibration.gif

2016-12-16T08:57:24Z

Ynx14:

Rep:YNX19950213

2016-12-16T08:57:05Z

Ynx14: /* Visualization of the Transition State */