ChemWiki - User contributions [en]

Rep:Mod:KMF14TS

2017-03-24T11:04:04Z

Kmf14: /* Reaction of Cyclohexadiene and 1,3-Dioxole */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==
[[File:reaction1KMF14.jpg|center]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

[[File:DAKMF14.gif]]
Woodward Hoffman rules show that the formation of the two bonds are synchronous

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

[[File:reaction2KMF14.jpg|center]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

The HOMO of the endo transition state shows that orbitals on oxygen are also involved in the reaction. It is believed that as a secondary effect the oxygen orbitals may stabilise the transition state with favourable (non bonding)interactions between the two molecules, despite it sterically being less favourable to have the two molecules on top as in an endo transition state.

== Diels Alder vs Chelotropic Reactions ==

[[File:reaction3KMF14.jpg|center]]

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}
IRC of exo transition state
[[File:expt3 IRC exo.jpg]]

IRC of endo transition state
[[File:expt3 IRC endo.jpg]]

IRC of chelotropic transition state
[[File:expt3 IRC chelo.jpg]]

The diagrams should show the IRC of the transition state however they don't. A proper IRC should have a gradient of 0 either side of the peak but I'm am terrible at actually finding the proper transition state so it doesn't (and sort of ran out of time to try)

The endo transition state has the lowest energy and therefore is the most kinetically favoured product while the chelotropic product is the most stable thermodynamically as it has the lowest product energy

[[File:TSKMF14.PNG]]

Xylylenes structure is very close to that of benzene and can easily form an aromatic ring in order to stabilise itself either by reacting with a double bond or in a ring closing metathesis style reaction. During the course of each of the above reactions an aromatic ring is formed stabilising the reaction and making it less likely to be a reversible reaction

Rep:Mod:KMF14TS

2017-03-24T11:03:23Z

Kmf14: /* Reaction of Butadiene and ethylene */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==
[[File:reaction1KMF14.jpg|center]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

[[File:DAKMF14.gif]]
Woodward Hoffman rules show that the formation of the two bonds are synchronous

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

[[File:reaction2KMF14.jpg|center]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

The HOMO of the endo transition state shows that orbitals on oxygen are also involved in the reaction. It is believed that as a secondary effect the oxygen orbitals may stabilise the transition state with favourable (non bonding)interactions between the two molecules, despite it sterically being less favourable to have the two molecules on top as in an endo transition state.
Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

== Diels Alder vs Chelotropic Reactions ==

[[File:reaction3KMF14.jpg|center]]

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}
IRC of exo transition state
[[File:expt3 IRC exo.jpg]]

IRC of endo transition state
[[File:expt3 IRC endo.jpg]]

IRC of chelotropic transition state
[[File:expt3 IRC chelo.jpg]]

The diagrams should show the IRC of the transition state however they don't. A proper IRC should have a gradient of 0 either side of the peak but I'm am terrible at actually finding the proper transition state so it doesn't (and sort of ran out of time to try)

The endo transition state has the lowest energy and therefore is the most kinetically favoured product while the chelotropic product is the most stable thermodynamically as it has the lowest product energy

[[File:TSKMF14.PNG]]

Xylylenes structure is very close to that of benzene and can easily form an aromatic ring in order to stabilise itself either by reacting with a double bond or in a ring closing metathesis style reaction. During the course of each of the above reactions an aromatic ring is formed stabilising the reaction and making it less likely to be a reversible reaction

File:DAKMF14.gif

2017-03-24T11:02:21Z

Kmf14:

Rep:Mod:KMF14TS

2017-03-24T10:35:21Z

Kmf14: /* Diels Alder vs Chelotropic Reactions */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==
[[File:reaction1KMF14.jpg|center]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?
Woodward Hoffman rules show that the formation of the two bonds are synchronous

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

[[File:reaction2KMF14.jpg|center]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

The HOMO of the endo transition state shows that orbitals on oxygen are also involved in the reaction. It is believed that as a secondary effect the oxygen orbitals may stabilise the transition state with favourable (non bonding)interactions between the two molecules, despite it sterically being less favourable to have the two molecules on top as in an endo transition state.
Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

== Diels Alder vs Chelotropic Reactions ==

[[File:reaction3KMF14.jpg|center]]

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}
IRC of exo transition state
[[File:expt3 IRC exo.jpg]]

IRC of endo transition state
[[File:expt3 IRC endo.jpg]]

IRC of chelotropic transition state
[[File:expt3 IRC chelo.jpg]]

The diagrams should show the IRC of the transition state however they don't. A proper IRC should have a gradient of 0 either side of the peak but I'm am terrible at actually finding the proper transition state so it doesn't (and sort of ran out of time to try)

The endo transition state has the lowest energy and therefore is the most kinetically favoured product while the chelotropic product is the most stable thermodynamically as it has the lowest product energy

[[File:TSKMF14.PNG]]

Xylylenes structure is very close to that of benzene and can easily form an aromatic ring in order to stabilise itself either by reacting with a double bond or in a ring closing metathesis style reaction. During the course of each of the above reactions an aromatic ring is formed stabilising the reaction and making it less likely to be a reversible reaction

Rep:Mod:KMF14TS

2017-03-24T10:26:06Z

Kmf14: /* Reaction of Cyclohexadiene and 1,3-Dioxole */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==
[[File:reaction1KMF14.jpg|center]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?
Woodward Hoffman rules show that the formation of the two bonds are synchronous

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

[[File:reaction2KMF14.jpg|center]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

The HOMO of the endo transition state shows that orbitals on oxygen are also involved in the reaction. It is believed that as a secondary effect the oxygen orbitals may stabilise the transition state with favourable (non bonding)interactions between the two molecules, despite it sterically being less favourable to have the two molecules on top as in an endo transition state.
Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

== Diels Alder vs Chelotropic Reactions ==

[[File:reaction3KMF14.jpg|center]]

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}
IRC of exo transition state
[[File:expt3 IRC exo.jpg]]

IRC of endo transition state
[[File:expt3 IRC endo.jpg]]

IRC of chelotropic transition state
[[File:expt3 IRC chelo.jpg]]

The diagrams should show the IRC of the transition state however they don't. A proper IRC should have a gradient of 0 either side of the peak but I'm am terrible at actually finding the proper transition state so it doesn't (and sort of ran out of time to try)

The endo transition state has the lowest energy and therefore is the most kinetically favoured product while the chelotropic product is the most stable thermodynamically as it has the lowest product energy

[[File:TSKMF14.PNG]]

Rep:Mod:KMF14TS

2017-03-24T10:15:47Z

Kmf14: /* Diels Alder vs Chelotropic Reactions */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==
[[File:reaction1KMF14.jpg|center]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?
Woodward Hoffman rules show that the formation of the two bonds are synchronous

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

[[File:reaction2KMF14.jpg|center]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

== Diels Alder vs Chelotropic Reactions ==

[[File:reaction3KMF14.jpg|center]]

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}
IRC of exo transition state
[[File:expt3 IRC exo.jpg]]

IRC of endo transition state
[[File:expt3 IRC endo.jpg]]

IRC of chelotropic transition state
[[File:expt3 IRC chelo.jpg]]

The diagrams should show the IRC of the transition state however they don't. A proper IRC should have a gradient of 0 either side of the peak but I'm am terrible at actually finding the proper transition state so it doesn't (and sort of ran out of time to try)

The endo transition state has the lowest energy and therefore is the most kinetically favoured product while the chelotropic product is the most stable thermodynamically as it has the lowest product energy

[[File:TSKMF14.PNG]]

File:TSKMF14.PNG

2017-03-24T10:13:48Z

Kmf14:

Rep:Mod:KMF14TS

2017-03-24T09:37:32Z

Kmf14: /* Diels Alder vs Chelotropic Reactions */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==
[[File:reaction1KMF14.jpg|center]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?
Woodward Hoffman rules show that the formation of the two bonds are synchronous

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

[[File:reaction2KMF14.jpg|center]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

== Diels Alder vs Chelotropic Reactions ==

[[File:reaction3KMF14.jpg|center]]

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}
IRC of exo transition state
[[File:expt3 IRC exo.jpg]]

IRC of endo transition state
[[File:expt3 IRC endo.jpg]]

IRC of chelotropic transition state
[[File:expt3 IRC chelo.jpg]]

The diagrams should show the IRC of the transition state however they don't. A proper IRC should have a gradient of 0 either side of the peak but I'm am terrible at actually finding the proper transition state so it doesn't (and sort of ran out of time to try)

The endo transition state has the lowest energy and therefore is the most kinetically favoured product while the chelotropic product is the most stable thermodynamically as it has the lowest product energy

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

File:Expt3 IRC chelo.jpg

2017-03-24T09:23:48Z

Kmf14:

File:Expt3 IRC endo.jpg

2017-03-24T09:23:34Z

Kmf14:

File:Expt3 IRC exo.jpg

2017-03-24T09:23:24Z

Kmf14:

Rep:Mod:KMF14TS

2017-03-24T09:23:05Z

Kmf14: /* Diels Alder vs Chelotropic Reactions */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==
[[File:reaction1KMF14.jpg|center]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?
Woodward Hoffman rules show that the formation of the two bonds are synchronous

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

[[File:reaction2KMF14.jpg|center]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

== Diels Alder vs Chelotropic Reactions ==

[[File:reaction3KMF14.jpg|center]]

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

[[File:Example.jpg]]

The endo transition state has the lowest energy and therefore is the most kinetically favoured product while the chelotropic product is the most stable thermodynamically as it has the lowest product energy

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Rep:Mod:KMF14TS

2017-03-24T09:22:06Z

Kmf14: /* Diels Alder vs Chelotropic Reactions */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==
[[File:reaction1KMF14.jpg|center]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?
Woodward Hoffman rules show that the formation of the two bonds are synchronous

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

[[File:reaction2KMF14.jpg|center]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

== Diels Alder vs Chelotropic Reactions ==

[[File:reaction3KMF14.jpg|center]]

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

The endo transition state has the lowest energy and therefore is the most kinetically favoured product while the chelotropic product is the most stable thermodynamically as it has the lowest product energy

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

File:Expt3 ts endo.PNG

2017-03-24T08:39:15Z

Kmf14:

Rep:Mod:KMF14TS

2017-03-24T08:38:54Z

Kmf14: /* Reaction of Butadiene and ethylene */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==
[[File:reaction1KMF14.jpg|center]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?
Woodward Hoffman rules show that the formation of the two bonds are synchronous

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

[[File:reaction2KMF14.jpg|center]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

== Diels Alder vs Chelotropic Reactions ==

[[File:reaction3KMF14.jpg|center]]

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

The endo transition state has the lowest energy and therefore is the most kinetically favoured product while the chelotropic product is the most stable thermodynamically as it has the lowest product energy

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-24T01:59:28Z

Kmf14:

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==
[[File:reaction1KMF14.jpg|center]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|center]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

== Diels Alder vs Chelotropic Reactions ==

[[File:reaction3KMF14.jpg|center]]

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

{| class="wikitable" border="1"
|+
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

The endo transition state has the lowest energy and therefore is the most kinetically favoured product while the chelotropic product is the most stable thermodynamically as it has the lowest product energy

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-24T01:09:11Z

Kmf14:

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==
[[File:reaction1KMF14.jpg|center]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|center]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

== Diels Alder vs Chelotropic Reactions ==

[[File:reaction3KMF14.jpg|center]]

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

The endo transition state has the lowest energy and therefore is the most kinetically favoured product while the chelotropic product is the most stable thermodynamically as it has the lowest product energy

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-24T01:03:00Z

Kmf14: /* Diels Alder vs Cheotropic Reactions */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

== Diels Alder vs Chelotropic Reactions ==

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

The endo transition state has the lowest energy and therefore is the most kinetically favoured product while the chelotropic product is the most stable thermodynamically as it has the lowest product energy

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-24T00:54:05Z

Kmf14: /* Reaction of Cyclohexadiene and 1,3-Dioxole */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

== Diels Alder vs Cheotropic Reactions ==

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-24T00:53:28Z

Kmf14: /* Reaction of Cyclohexadiene and 1,3-Dioxole */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

A normal diels alder reaction requires an electron rich diene and an electron poor dienophile. The electron rich dienes molecular orbitals are higher in energy to that of the electron poor dienophile. The HOMO of the diene and the LUMO of the dienophile are more similar in energy than the HOMO dienophile and the LUMO of the diene.

The inverse demand diels alder reaction requires an electron-poor diene and an electron rich dienophile. This changes the orbital diagram somewhat so that the LUMO of the diene and HOMO of the diene are most similar in energy.

Given that the HOMO diene and LUMO dienophile gap is smaller than the LUMO diene HOMO dienophile gap, this is a nomal diels alder reaction.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable as it is lowest in enegy and the endo product is also more stable making this reaction both thermodynamically and kinetically favouring the endo product.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

== Diels Alder vs Cheotropic Reactions ==

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-24T00:18:48Z

Kmf14: /* Reaction of Butadiene and ethylene */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. This can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram. This coresponds well with the molecular orbital diagrams as shown below of the transition state which show u-u and g-g overlap but not u-g overlap.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Reactants Bonds !! Bond Length !! Transition States Bonds !! Bond Length !! Products Bonds !! Bond Length !!
|-
| ethene || 1.32731 A || ethene || 1.35580 A || ethene || 1.53460 A
|-
| diene C=C || 1.33533 A || diene C=C || 1.35663 A || diene C-C || 1.50084 A
|-
| diene C-C || 1.46837 A || diene C-C || 1.46837 A || diene C=C || 1.33694 A
|-
| || || forming C-C bond || 2.20723 A|| New C-C bond || 1.53714 A
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable
Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-24T00:01:48Z

Kmf14: /* Introduction */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum energy the potential energy diagram has a gradient of zero and at either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the lowest energy pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model where the frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to the positions of the nuclei.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable
Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T23:47:20Z

Kmf14: /* Reaction of Cyclohexadiene and 1,3-Dioxole */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

This shows that the endo transition state is kinetically favourable
Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T22:44:32Z

Kmf14: /* Diels Alder vs Cheotropic Reactions */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T22:40:26Z

Kmf14: /* Diels Alder vs Cheotropic Reactions */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:expt3 ts chelo.PNG|thumb|Chelotropic transition state.]]
[[File:expt3 ts exo.PNG|thumb|Exo transition state.]]
[[File:expt3 ts endo.PNG|thumb|Endo transition state.]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T22:30:52Z

Kmf14: /* Reaction of Cyclohexadiene and 1,3-Dioxole */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Endo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt2 endo homo.png]] || style="background: white;"|[[File:expt2 endo lumo.png]]
|-
|colspan="2" style="text-align: center;"| Exo Transition State
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:expt 2 exo homo.png]] || style="background: white;"|[[File:expt2 exo lumo.png]]
|}

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T22:21:56Z

Kmf14:

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|MO diagrams of butadiene and ethene transition state
|-
! style="background: #89CFF0;"| 2nd LUMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:expt1 high.png]] || style="background: white;"|[[File:expt1 lumo.png]]
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| 2nd HOMO
|-
|style="background: white;" align=”center”| [[File:expt1 homo.png]] || style="background: white;"|[[File:expt1 low.png]]
|}

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

File:Expt3 ts exo.PNG

2017-03-23T22:06:48Z

Kmf14:

File:Expt3 ts chelo.PNG

2017-03-23T22:06:27Z

Kmf14:

File:Expt2 exo lumo.png

2017-03-23T22:06:05Z

Kmf14:

File:Expt2 endo lumo.png

2017-03-23T22:05:43Z

Kmf14:

File:Expt2 endo homo.png

2017-03-23T22:05:25Z

Kmf14:

File:Expt1 lumo.png

2017-03-23T22:05:09Z

Kmf14:

File:Expt1 low.png

2017-03-23T22:03:32Z

Kmf14:

File:Expt1 homo.png

2017-03-23T22:03:03Z

Kmf14:

File:Expt1 high.png

2017-03-23T22:02:43Z

Kmf14:

File:Expt 2 exo homo.png

2017-03-23T22:02:20Z

Kmf14:

Rep:Mod:KMF14TS

2017-03-23T17:28:13Z

Kmf14: /* Reaction of Butadiene and ethylene */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Transition state 4 orbital diagrams

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T17:25:41Z

Kmf14: /* Reaction of Cyclohexadiene and 1,3-Dioxole */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Transition state 4 orbital diagrams

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || -67.65
|-
| Exo || 0 || 165.98 || -63.24
|}

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T17:25:29Z

Kmf14: /* Diels Alder vs Cheotropic Reactions */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Transition state 4 orbital diagrams

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || 67.65
|-
| Exo || 0 || 165.98 || 63.24
|}

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || -134.17
|-
| Exo || 0 || 50.19 || -130.23
|-
| Chelotropic || 0 || 64.39 || -188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T17:24:43Z

Kmf14: /* Diels Alder vs Cheotropic Reactions */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Transition state 4 orbital diagrams

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || 67.65
|-
| Exo || 0 || 165.98 || 63.24
|}

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1!! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 46.34 || 134.17
|-
| Exo || 0 || 50.19 || 130.23
|-
| Chelotropic || 0 || 64.39 || 188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T17:24:24Z

Kmf14: /* Reaction of Cyclohexadiene and 1,3-Dioxole */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Transition state 4 orbital diagrams

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy kJ mol-1 !! TS energy kJ mol-1!! Product Energy kJ mol-1
|-
| Endo || 0 || 157.63 || 67.65
|-
| Exo || 0 || 165.98 || 63.24
|}

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy!! TS energy!! Product Energy
|-
| Endo || 0 || 46.34 || 134.17
|-
| Exo || 0 || 50.19 || 130.23
|-
| Chelotropic || 0 || 64.39 || 188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T17:23:29Z

Kmf14: /* Reaction of Cyclohexadiene and 1,3-Dioxole */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Transition state 4 orbital diagrams

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy!! TS energy!! Product Energy
|-
| Endo || 0 || 157.63 || 67.65
|-
| Exo || 0 || 165.98 || 63.24
|}

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy!! TS energy!! Product Energy
|-
| Endo || 0 || 46.34 || 134.17
|-
| Exo || 0 || 50.19 || 130.23
|-
| Chelotropic || 0 || 64.39 || 188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T17:23:00Z

Kmf14: /* Diels Alder vs Cheotropic Reactions */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Transition state 4 orbital diagrams

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy!! TS energy!! Product Energy
|-
| Endo || 0 || 157.63 || x
|-
| Exo || 0 || 165.98 || x
|}

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy!! TS energy!! Product Energy
|-
| Endo || 0 || 46.34 || 134.17
|-
| Exo || 0 || 50.19 || 130.23
|-
| Chelotropic || 0 || 64.39 || 188.02
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T17:11:46Z

Kmf14:

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Transition state 4 orbital diagrams

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy!! TS energy!! Product Energy
|-
| Endo || 0 || 157.63 || x
|-
| Exo || 0 || 165.98 || x
|}

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy!! TS energy!! Product Energy
|-
| Endo || 0 || 46.34 || x
|-
| Exo || 0 || 50.19 || x
|-
| Chelotropic || 0 || 64.39 || x
|}

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T17:09:23Z

Kmf14:

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Transition state 4 orbital diagrams

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Reaction type !! Reactant Energy!! TS energy!! Product Energy
|-
| Endo || 0 || 157.63 || x
|-
| Exo || 0 || 165.98 || x
|}

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T15:57:40Z

Kmf14: /* Reaction of Butadiene and ethylene */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Transition state 4 orbital diagrams

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-
|}

In general the bond lengths increase from reactants to transition states to products. Exceptions being the single bond in the diene (starting material)and the newly formed carbon carbon bonds
The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T15:43:44Z

Kmf14: /* Reaction of Butadiene and ethylene */

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;" align=”center”| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;" align=”center”| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Transition state 4 orbital diagrams
What can you conclude about the requirements for symmetry for a reaction (when is a reaction 'allowed' and when is it 'forbidden')? Write whether the orbital overlap integral is zero or non-zero for the case of a symmetric-antisymmetric interaction, a symmetric-symmetric interaction and an antisymmetric-antisymmetric interaction.

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-

|}

Include measurements of the 4 C-C bond lengths of the reactants and the 6 C-C bond lengths of the TS and products. How do the bond lengths change as the reaction progresses? What are typical sp3 and sp2 C-C bond lengths? What is the Van der Waals radius of the C atom? How does this compare with the length of the partly formed C-C bonds in the TS.

The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T15:32:13Z

Kmf14:

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;" style="background:#89CFF0;"|Butadiene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
| style="background: white;"| [[File:dienehomoKMF14.jpg]] || style="background: white;"|[[File:dienelumoKMF14.jpg]]
|-
|colspan="2" style="text-align: center;" style="background: #89CFF0;"| Ethene
|-
! style="background: #89CFF0;"|HOMO!!style="background: #89CFF0;"| LUMO
|-
|style="background: white;"| [[File:ethenehomoKMF14.jpg]] || style="background: white;"|[[File:ethenelumoKMF14.jpg]]
|}

Transition state 4 orbital diagrams
What can you conclude about the requirements for symmetry for a reaction (when is a reaction 'allowed' and when is it 'forbidden')? Write whether the orbital overlap integral is zero or non-zero for the case of a symmetric-antisymmetric interaction, a symmetric-symmetric interaction and an antisymmetric-antisymmetric interaction.

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-

|}

Include measurements of the 4 C-C bond lengths of the reactants and the 6 C-C bond lengths of the TS and products. How do the bond lengths change as the reaction progresses? What are typical sp3 and sp2 C-C bond lengths? What is the Van der Waals radius of the C atom? How does this compare with the length of the partly formed C-C bonds in the TS.

The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo

Rep:Mod:KMF14TS

2017-03-23T15:05:32Z

Kmf14:

== Transition States of Diels Alder Reactions ==

=== Introduction ===

Minima are calculated on gaussian by varying the position of each nucleus to find the lowest energy arangement of the molecule. At the minimum has a gradient of zero and either side of the minimum the gradient increases.

Transition states are calculated by finding the maximum energy on the pathway between the reactants and the products on a potential energy surface.

Gaussian calculates frequencies using a harmonic oscillator model. The frequency is proportional to the square root of the force constant. The force constant is equal to the second derivative of the energy with respect to nuclear positions.

A frequency calculation at the minimum should provide no imaginary frequencies as the second derivative of the energy is positive.
A frequency calculation at the transition state should provide an imaginary frequency as given it must curve downwarrds and therefore have a negative second derivative and the square root of a negative number is imaginary.

== Reaction of Butadiene and ethylene ==

[[File:reaction1KMF14.jpg|centre]]

[[File:da3KMF14.jpg|left]]

[[File:dienehomoKMF14.jpg|thumb|The HOMO of butadiene]]
[[File:dienelumoKMF14.jpg|thumb|The LUMO of butadiene]]

[[File:ethenehomoKMF14.jpg|thumb|The HOMO of ethene]]
[[File:ethenelumoKMF14.jpg|thumb|The LUMO of ethene]]

Transition state 4 orbital diagrams
What can you conclude about the requirements for symmetry for a reaction (when is a reaction 'allowed' and when is it 'forbidden')? Write whether the orbital overlap integral is zero or non-zero for the case of a symmetric-antisymmetric interaction, a symmetric-symmetric interaction and an antisymmetric-antisymmetric interaction.

Any MOs of the same symmetry may overlap but orbitals of different symmetries may not. Symmetries are shown by the parity labels g and u where 'g and g' interactions and 'u and u' interactions have a non zero overlap integral but the overlap integral for 'g and u' interactions is 0. this can be shown in the transition state diagrams which show the diene HOMO reacting with the ethene LUMO and vice versa as the orbitals are clearly labelled in the above orbital diagram.

{| class="wikitable" border="1"
|+ Starting Material Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.32731 A
|-
| diene C=C || 1.33533 A
|-
| diene C-C || 1.46837 A
|-
|}

{| class="wikitable" border="1"
|+ Transition State Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.35580 A
|-
| diene C=C || 1.35663 A
|-
| diene C-C || 1.44068 A
|-
| forming C-C bond || 2.20723 A
|-
|}

{| class="wikitable" border="1"
|+ Product Bond Lengths
! Bond !! Bond Length
|-
| ethene || 1.53460 A
|-
| diene C-C || 1.50084 A
|-
| diene C=C || 1.33694 A
|-
| New C-C bond || 1.53714 A
|-

|}

Include measurements of the 4 C-C bond lengths of the reactants and the 6 C-C bond lengths of the TS and products. How do the bond lengths change as the reaction progresses? What are typical sp3 and sp2 C-C bond lengths? What is the Van der Waals radius of the C atom? How does this compare with the length of the partly formed C-C bonds in the TS.

The van der Waals radius of carbon is 1.7 A and so two carbon atoms purely interacting through van der Waals forces should have a distance of 3.4 A. The partly formed C-C bonds therefore have overlapping van der Waals radii.
The average sp3 C-C bond length is 1.54 A and the average sp2 C-C bond length is 1.47 A

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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

[[File:reaction2KMF14.jpg|centre]]

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Construct a new MO diagram using these new orbitals, adjusting energy levels as necessary. Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - Energy' under Job Type - will yield an ordered list of MOs that you can use to start you off).

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are

more lovely texticles

== Diels Alder vs Cheotropic Reactions ==

[[File:reaction3KMF14.jpg]]

1) Optimise the TSs for the endo- and exo- Diels-Alder and the Cheletropic reactions at the PM6 level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

Expt6 – starting material diene experiment 2
Expt5 – starting material dieneophile experiment 2
Expt 2 ts4-transition state experiment 2 exo
Esxpt2endots2 – transition state experiment 2 endo