ChemWiki - User contributions [en]

Rep:Mod:hb1013

2017-03-20T00:22:07Z

Hb1013: /* Conclusion */

=Computational Chemistry: Transition States and reactivity=
==Introduction==
By using mathematical method and chemistry theories, reaction of molecules can be simulated by computer. In this module, geometry and reactivity of cycloaddition were investigated. Transition states, molecular orbitals of three different types of cycloaddition were explored by Gaussian and GaussView.

Potential energy surface(PES) describes the energy of a molecule as a function of its geometry. The first derivative of energy is zero, the second derivative energy is negative and the transition state is the highest position in the pathway(saddle point). Two methods can be used to find out the transition state: frequency calculation and Intrinsic Reaction Coordination(IRC).

IRC is a method that can check whether transition state is in the position of the highest energy by exploring energy changing in both directions from the transition state.

Also, in this module optimisation of the molecules is really important to get more accurate geometry and energy of the transition state due to it can determine the geometry with lowest energy.

==Exercise 1: Reaction of Butadiene with Ethylene==
[[File:Hb1013 01.png|thumb|594x594px|Fig. 1 - MO diagram for the DA reaction of Butadiene(LHS) with Ethylene(RHS).|none]]Fragments Orbitals(FOs) with the same symmetry can interact and overlap with each other. In Fig.1, transitions states are formed by overlap of HOMO and LUMO of FOs with the same symmetry.

The Cis-butadiene and ethylene were drawn in GaussView and optimised at PM6 level.
{| class="wikitable"
|Molecule
|Cis-butadiene
|Cis-butadiene
|Ethene
|Ethene
|-
|MO
|HOMO
|LUMO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 4.PNG]]
|[[File:Hb1013 3.PNG]]
|[[File:Hb1013 5.PNG]]
|[[File:Hb1013 6.PNG]]
|-
|Symmetry
|Anti-symmetric
|Symmetric
|Symmetric
|Anti-symmetric
|-
|Energy/a.u.
|<nowiki>-0.35168</nowiki>
|0.01103
|<nowiki>-0.39228</nowiki>
|0.04256
|}
'''Table 1. '''Homo and LUMO of Cis-butadiene and ethene.

Optimised transition state is shown below.
[[File:Hb1013 10.PNG|none|thumb|Figure 2. Optimised transition state]]
To confirm this transition state is correct, frequency calculation and IRC are shown below.
[[File:Hb1013 8.PNG|none|thumb|Figure 3. Frequency calculation for the cycloaddition reaction of butadiene and ethene.]]
[[File:Hb1013 9.PNG|none|thumb|384x384px|Figure 4. IRC of the transition state.]]
As shown in Figure 3 and Figure 4, there is only one negative frequency for the transition state and a saddle point, which means this structure is correct.
[[File:Hb1013 2.PNG|none|thumb|500x500px|Figure 5. Bond lengths of reactants and product.]]
According to Fig. 2 and Fig. 5, Bond lengths of reactants, ts and product can be known.
{| class="wikitable"
|Bond
|Length in reactant
|Length in TS
|Length in product
|-
|C=C in TS of cis-Butadiene
|1.33
|1.38
|1.50
|-
|C-C in TS of cis-Butadiene
|1.47
|1.41
|1.34
|-
|C=C in TS of Ethene
|1.33
|1.38
|1.54
|-
|Partially formed bond in TS
|n/a
|2.11
|1.54
|}
'''Table 2. '''Bond lengths of reactants, ts and product. Units in Å.

Normally, C-C single bond is 1.54 Å and C=C double bond is 1.33 Å.<ref>CRC Handbook of chemistry and physics, 2005, '''86''', pp. 9-19.</ref> But in the transition state C-C and C=C are 1.41 Å and 1.31 Å respectively, which means C-C single bond is shortened and C=C double bond is elongated. The partially formed bond in TS is shortened to 2.11 Å and it is shorter than 2 * Van der Waal's radius of carbon (1.7Å).<ref>Bondi A., ''J. Phys. Chem'', 1964,''' 68''', 441-451.</ref> This indicates overlap of p-orbitals between terminal carbons in cis-Butadiene and ethene.

6-pi electrons in TS and according to Hoffmann rules, the reaction will be thermally allowed when p-orbitals interaction between terminal carbons in cis-Butadiene and ethene includes two types: superfacial and antarfacial.
{| class="wikitable"
|Molecule
|TS cyclohexene
|TS cyclohexene
|-
|MO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 12.PNG]]
|[[File:Hb1013 11.PNG]]
|-
|Symmetry
|Symmetric
|Symmetric
|-
|Energy a.u.
|<nowiki>-0.32533</nowiki>
|0.01732
|}
'''Table 3. '''TS of HOMO and LUMO.

Cis-Butadiene has one AS HOMO and one S LUMO and ethene has one S HOMO and one AS LUMO. Therefore, there are two possible interactions in this reaction. Because the diene is nucloephilic and the dienophile is electrophilic, the interaction between AS HOMO of cis-butadiene and AS LUMO of ethene is more favoured.

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==
{| class="wikitable"
|
|Cyclohexdiene
|1,3-Dioxole
|-
|
|[[File:Hb1013 13.PNG]]
|[[File:Hb1013 14.PNG]]
|-
|
|endo
|exo
|-
|TS
|[[File:Hb1013 15.PNG]]
|[[File:Hb1013 17.PNG]]
|-
|product
|[[File:Hb1013 16.PNG]]
|[[File:Hb1013 18.PNG]]
|}
'''Table 4. '''Structures of optimised reagents, TS and products.
{| class="wikitable"
|Orientation
|endo
|endo
|exo
|exo
|-
|MO
|HOMO
|LUMO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 19.PNG]]
|[[File:Hb1013 20.PNG]]
|[[File:Hb1013 21.PNG]]
|[[File:Hb1013 22.PNG]]
|-
|Symmetry
|As
|As
|As
|As
|}
'''Table 5. '''MOs of TS of endo and exo orientations(secondary orbital overlap in the endo).
[[File:Hb1013 27.PNG|none|thumb|Figure 6. Frequency calculation of endo.]]
[[File:Hb1013 29.PNG|none|thumb|Figure 7. Frequency calculation of exo.]]
Fig.6 and Fig.7 ensure the endo and exo structures are correct.
[[File:Hb1013 23.PNG|none|thumb|413x413px|Figure 6, Reaction Scheme of exercise 2.]]
This reaction is a normal demand DA reaction, the reason is C=C double bond is more electron deficient due to existing of two electron withdrawing oxygens in the dienophile.
[[File:Hb1013 25.PNG|none|thumb|499x499px|'''Table 7'''. Data of Reaction.]]
[[File:Hb1013 24.PNG|none|thumb|Figure 7. Energy Diagram of the reaction.]]
In this reaction, product of endo is thermodynamic product due to lower energy makes it more stable, and secondary orbital interaction in endo can provides an extra interaction in the reactants, it causes lower energy barrier of endo product.Therefore,product of endo is kinetically favoured as well.

==Exercise 3: Diels-Alder vs Cheletropic==
{| class="wikitable"
|
|Exo D-A Reaction
|Endo D-A Reaction
|Cheletropic Reaction
|-
|Structure
|[[File:Hb1013 37.PNG]]
|[[File:Hb1013 38.PNG]]
|[[File:Hb1013 39.PNG]]
|-
|IRC
|[[File:Hb1013 32.PNG]]
|[[File:Hb1013 31.PNG]]
|[[File:Hb1013 33.PNG]]
|}
'''Table 8. '''Structures and IRC.
[[File:Hb1013 34.PNG|none|thumb|399x399px|Figure 8. Reaction Scheme of Exercise 3.]]
[[File:Hb1013 36.PNG|none|thumb|548x548px|'''Table 9'''. Energy data of Exercise 3.]]
[[File:Hb1013 35.PNG|none|thumb|334x334px|Figure 9. Energy diagram.]]
[[File:Hb1013 99.png|none|thumb|426x426px|Figure 10. The energy profile of sulfur dioxide and o-Xylylene cycloaddition.]]
This reaction is exothermic so has negative E and because of high free energy of xylyene, so it is very unstable. The formation of endo one is kinetically favoured, cheletropic one is thermodynamically favoured if there is enough energy. Futhermore, six-membered ring product like bezene to acheieve resonance form that can form an electron pi cloud and make the electrons delocalised.

==Conclusion==
The lengths of carbon bonds will change in D-A reactions, and will be shorter than VDW's radius. Same symmetry Orbitals can overlap with each other and have none 0 orbital overlap integrals.

Product of endo is thermodynamic product due to lower energy makes it more stable, and secondary orbital interaction in endo can provides an extra interaction in the reactants so product of endo is also kinetically favoured.

TS has the maximum energy and the the reaction of sulfur dioxide and o-Xylylene cycloaddition is exothermic and because of high free energy of xylyene, so it is very unstable.

== Reference==

File:Hb1013 39.PNG

2017-03-20T00:20:17Z

Hb1013:

File:Hb1013 38.PNG

2017-03-20T00:19:36Z

Hb1013:

File:Hb1013 37.PNG

2017-03-20T00:19:17Z

Hb1013:

Rep:Mod:hb1013

2017-03-19T21:38:19Z

Hb1013: /* Conclusion */

=Computational Chemistry: Transition States and reactivity=
==Introduction==
By using mathematical method and chemistry theories, reaction of molecules can be simulated by computer. In this module, geometry and reactivity of cycloaddition were investigated. Transition states, molecular orbitals of three different types of cycloaddition were explored by Gaussian and GaussView.

Potential energy surface(PES) describes the energy of a molecule as a function of its geometry. The first derivative of energy is zero, the second derivative energy is negative and the transition state is the highest position in the pathway(saddle point). Two methods can be used to find out the transition state: frequency calculation and Intrinsic Reaction Coordination(IRC).

IRC is a method that can check whether transition state is in the position of the highest energy by exploring energy changing in both directions from the transition state.

Also, in this module optimisation of the molecules is really important to get more accurate geometry and energy of the transition state due to it can determine the geometry with lowest energy.

==Exercise 1: Reaction of Butadiene with Ethylene==
[[File:Hb1013 01.png|thumb|594x594px|Fig. 1 - MO diagram for the DA reaction of Butadiene(LHS) with Ethylene(RHS).|none]]Fragments Orbitals(FOs) with the same symmetry can interact and overlap with each other. In Fig.1, transitions states are formed by overlap of HOMO and LUMO of FOs with the same symmetry.

The Cis-butadiene and ethylene were drawn in GaussView and optimised at PM6 level.
{| class="wikitable"
|Molecule
|Cis-butadiene
|Cis-butadiene
|Ethene
|Ethene
|-
|MO
|HOMO
|LUMO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 4.PNG]]
|[[File:Hb1013 3.PNG]]
|[[File:Hb1013 5.PNG]]
|[[File:Hb1013 6.PNG]]
|-
|Symmetry
|Anti-symmetric
|Symmetric
|Symmetric
|Anti-symmetric
|-
|Energy/a.u.
|<nowiki>-0.35168</nowiki>
|0.01103
|<nowiki>-0.39228</nowiki>
|0.04256
|}
'''Table 1. '''Homo and LUMO of Cis-butadiene and ethene.

Optimised transition state is shown below.
[[File:Hb1013 10.PNG|none|thumb|Figure 2. Optimised transition state]]
To confirm this transition state is correct, frequency calculation and IRC are shown below.
[[File:Hb1013 8.PNG|none|thumb|Figure 3. Frequency calculation for the cycloaddition reaction of butadiene and ethene.]]
[[File:Hb1013 9.PNG|none|thumb|384x384px|Figure 4. IRC of the transition state.]]
As shown in Figure 3 and Figure 4, there is only one negative frequency for the transition state and a saddle point, which means this structure is correct.
[[File:Hb1013 2.PNG|none|thumb|500x500px|Figure 5. Bond lengths of reactants and product.]]
According to Fig. 2 and Fig. 5, Bond lengths of reactants, ts and product can be known.
{| class="wikitable"
|Bond
|Length in reactant
|Length in TS
|Length in product
|-
|C=C in TS of cis-Butadiene
|1.33
|1.38
|1.50
|-
|C-C in TS of cis-Butadiene
|1.47
|1.41
|1.34
|-
|C=C in TS of Ethene
|1.33
|1.38
|1.54
|-
|Partially formed bond in TS
|n/a
|2.11
|1.54
|}
'''Table 2. '''Bond lengths of reactants, ts and product. Units in Å.

Normally, C-C single bond is 1.54 Å and C=C double bond is 1.33 Å.<ref>CRC Handbook of chemistry and physics, 2005, '''86''', pp. 9-19.</ref> But in the transition state C-C and C=C are 1.41 Å and 1.31 Å respectively, which means C-C single bond is shortened and C=C double bond is elongated. The partially formed bond in TS is shortened to 2.11 Å and it is shorter than 2 * Van der Waal's radius of carbon (1.7Å).<ref>Bondi A., ''J. Phys. Chem'', 1964,''' 68''', 441-451.</ref> This indicates overlap of p-orbitals between terminal carbons in cis-Butadiene and ethene.

6-pi electrons in TS and according to Hoffmann rules, the reaction will be thermally allowed when p-orbitals interaction between terminal carbons in cis-Butadiene and ethene includes two types: superfacial and antarfacial.
{| class="wikitable"
|Molecule
|TS cyclohexene
|TS cyclohexene
|-
|MO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 12.PNG]]
|[[File:Hb1013 11.PNG]]
|-
|Symmetry
|Symmetric
|Symmetric
|-
|Energy a.u.
|<nowiki>-0.32533</nowiki>
|0.01732
|}
'''Table 3. '''TS of HOMO and LUMO.

Cis-Butadiene has one AS HOMO and one S LUMO and ethene has one S HOMO and one AS LUMO. Therefore, there are two possible interactions in this reaction. Because the diene is nucloephilic and the dienophile is electrophilic, the interaction between AS HOMO of cis-butadiene and AS LUMO of ethene is more favoured.

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==
{| class="wikitable"
|
|Cyclohexdiene
|1,3-Dioxole
|-
|
|[[File:Hb1013 13.PNG]]
|[[File:Hb1013 14.PNG]]
|-
|
|endo
|exo
|-
|TS
|[[File:Hb1013 15.PNG]]
|[[File:Hb1013 17.PNG]]
|-
|product
|[[File:Hb1013 16.PNG]]
|[[File:Hb1013 18.PNG]]
|}
'''Table 4. '''Structures of optimised reagents, TS and products.
{| class="wikitable"
|Orientation
|endo
|endo
|exo
|exo
|-
|MO
|HOMO
|LUMO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 19.PNG]]
|[[File:Hb1013 20.PNG]]
|[[File:Hb1013 21.PNG]]
|[[File:Hb1013 22.PNG]]
|-
|Symmetry
|As
|As
|As
|As
|}
'''Table 5. '''MOs of TS of endo and exo orientations(secondary orbital overlap in the endo).
[[File:Hb1013 27.PNG|none|thumb|Figure 6. Frequency calculation of endo.]]
[[File:Hb1013 29.PNG|none|thumb|Figure 7. Frequency calculation of exo.]]
Fig.6 and Fig.7 ensure the endo and exo structures are correct.
[[File:Hb1013 23.PNG|none|thumb|413x413px|Figure 6, Reaction Scheme of exercise 2.]]
This reaction is a normal demand DA reaction, the reason is C=C double bond is more electron deficient due to existing of two electron withdrawing oxygens in the dienophile.
[[File:Hb1013 25.PNG|none|thumb|499x499px|'''Table 7'''. Data of Reaction.]]
[[File:Hb1013 24.PNG|none|thumb|Figure 7. Energy Diagram of the reaction.]]
In this reaction, product of endo is thermodynamic product due to lower energy makes it more stable, and secondary orbital interaction in endo can provides an extra interaction in the reactants. product of exo is kinetic product.

==Exercise 3: Diels-Alder vs Cheletropic==
{| class="wikitable"
|
|Exo D-A Reaction
|Endo D-A Reaction
|Cheletropic Reaction
|-
|Structure
|
|
|
|-
|IRC
|[[File:Hb1013 32.PNG]]
|[[File:Hb1013 31.PNG]]
|[[File:Hb1013 33.PNG]]
|}
'''Table 8. '''Structures and IRC.
[[File:Hb1013 34.PNG|none|thumb|399x399px|Figure 8. Reaction Scheme of Exercise 3.]]
[[File:Hb1013 36.PNG|none|thumb|548x548px|'''Table 9'''. Energy data of Exercise 3.]]
[[File:Hb1013 35.PNG|none|thumb|334x334px|Figure 9. Energy diagram.]]
[[File:Hb1013 99.png|none|thumb|426x426px|Figure 10. The energy profile of sulfur dioxide and o-Xylylene cycloaddition.]]
This reaction is exothermic so has negative E and because of high free energy of xylyene, so it is very unstable. The formation of endo one is kinetically favoured, cheletropic one is thermodynamically favoured if there is enough energy. Futhermore, six-membered ring product like bezene to acheieve resonance form that can form an electron pi cloud and make the electrons delocalised.

==Conclusion==
The lengths of carbon bonds will change in D-A reactions, and will be shorter than VDW's radius. Same symmetry Orbitals can overlap with each other and have none 0 orbital overlap integrals.

Product of endo is thermodynamic product due to lower energy makes it more stable, and secondary orbital interaction in endo can provides an extra interaction in the reactants. product of exo is kinetic product.

TS has the maximum energy and the the reaction of sulfur dioxide and o-Xylylene cycloaddition is exothermic and because of high free energy of xylyene, so it is very unstable.

== Reference==

Rep:Mod:hb1013

2017-03-19T21:21:01Z

Hb1013: /* Exercise 3: Diels-Alder vs Cheletropic */

=Computational Chemistry: Transition States and reactivity=
==Introduction==
By using mathematical method and chemistry theories, reaction of molecules can be simulated by computer. In this module, geometry and reactivity of cycloaddition were investigated. Transition states, molecular orbitals of three different types of cycloaddition were explored by Gaussian and GaussView.

Potential energy surface(PES) describes the energy of a molecule as a function of its geometry. The first derivative of energy is zero, the second derivative energy is negative and the transition state is the highest position in the pathway(saddle point). Two methods can be used to find out the transition state: frequency calculation and Intrinsic Reaction Coordination(IRC).

IRC is a method that can check whether transition state is in the position of the highest energy by exploring energy changing in both directions from the transition state.

Also, in this module optimisation of the molecules is really important to get more accurate geometry and energy of the transition state due to it can determine the geometry with lowest energy.

==Exercise 1: Reaction of Butadiene with Ethylene==
[[File:Hb1013 01.png|thumb|594x594px|Fig. 1 - MO diagram for the DA reaction of Butadiene(LHS) with Ethylene(RHS).|none]]Fragments Orbitals(FOs) with the same symmetry can interact and overlap with each other. In Fig.1, transitions states are formed by overlap of HOMO and LUMO of FOs with the same symmetry.

The Cis-butadiene and ethylene were drawn in GaussView and optimised at PM6 level.
{| class="wikitable"
|Molecule
|Cis-butadiene
|Cis-butadiene
|Ethene
|Ethene
|-
|MO
|HOMO
|LUMO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 4.PNG]]
|[[File:Hb1013 3.PNG]]
|[[File:Hb1013 5.PNG]]
|[[File:Hb1013 6.PNG]]
|-
|Symmetry
|Anti-symmetric
|Symmetric
|Symmetric
|Anti-symmetric
|-
|Energy/a.u.
|<nowiki>-0.35168</nowiki>
|0.01103
|<nowiki>-0.39228</nowiki>
|0.04256
|}
'''Table 1. '''Homo and LUMO of Cis-butadiene and ethene.

Optimised transition state is shown below.
[[File:Hb1013 10.PNG|none|thumb|Figure 2. Optimised transition state]]
To confirm this transition state is correct, frequency calculation and IRC are shown below.
[[File:Hb1013 8.PNG|none|thumb|Figure 3. Frequency calculation for the cycloaddition reaction of butadiene and ethene.]]
[[File:Hb1013 9.PNG|none|thumb|384x384px|Figure 4. IRC of the transition state.]]
As shown in Figure 3 and Figure 4, there is only one negative frequency for the transition state and a saddle point, which means this structure is correct.
[[File:Hb1013 2.PNG|none|thumb|500x500px|Figure 5. Bond lengths of reactants and product.]]
According to Fig. 2 and Fig. 5, Bond lengths of reactants, ts and product can be known.
{| class="wikitable"
|Bond
|Length in reactant
|Length in TS
|Length in product
|-
|C=C in TS of cis-Butadiene
|1.33
|1.38
|1.50
|-
|C-C in TS of cis-Butadiene
|1.47
|1.41
|1.34
|-
|C=C in TS of Ethene
|1.33
|1.38
|1.54
|-
|Partially formed bond in TS
|n/a
|2.11
|1.54
|}
'''Table 2. '''Bond lengths of reactants, ts and product. Units in Å.

Normally, C-C single bond is 1.54 Å and C=C double bond is 1.33 Å.<ref>CRC Handbook of chemistry and physics, 2005, '''86''', pp. 9-19.</ref> But in the transition state C-C and C=C are 1.41 Å and 1.31 Å respectively, which means C-C single bond is shortened and C=C double bond is elongated. The partially formed bond in TS is shortened to 2.11 Å and it is shorter than 2 * Van der Waal's radius of carbon (1.7Å).<ref>Bondi A., ''J. Phys. Chem'', 1964,''' 68''', 441-451.</ref> This indicates overlap of p-orbitals between terminal carbons in cis-Butadiene and ethene.

6-pi electrons in TS and according to Hoffmann rules, the reaction will be thermally allowed when p-orbitals interaction between terminal carbons in cis-Butadiene and ethene includes two types: superfacial and antarfacial.
{| class="wikitable"
|Molecule
|TS cyclohexene
|TS cyclohexene
|-
|MO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 12.PNG]]
|[[File:Hb1013 11.PNG]]
|-
|Symmetry
|Symmetric
|Symmetric
|-
|Energy a.u.
|<nowiki>-0.32533</nowiki>
|0.01732
|}
'''Table 3. '''TS of HOMO and LUMO.

Cis-Butadiene has one AS HOMO and one S LUMO and ethene has one S HOMO and one AS LUMO. Therefore, there are two possible interactions in this reaction. Because the diene is nucloephilic and the dienophile is electrophilic, the interaction between AS HOMO of cis-butadiene and AS LUMO of ethene is more favoured.

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==
{| class="wikitable"
|
|Cyclohexdiene
|1,3-Dioxole
|-
|
|[[File:Hb1013 13.PNG]]
|[[File:Hb1013 14.PNG]]
|-
|
|endo
|exo
|-
|TS
|[[File:Hb1013 15.PNG]]
|[[File:Hb1013 17.PNG]]
|-
|product
|[[File:Hb1013 16.PNG]]
|[[File:Hb1013 18.PNG]]
|}
'''Table 4. '''Structures of optimised reagents, TS and products.
{| class="wikitable"
|Orientation
|endo
|endo
|exo
|exo
|-
|MO
|HOMO
|LUMO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 19.PNG]]
|[[File:Hb1013 20.PNG]]
|[[File:Hb1013 21.PNG]]
|[[File:Hb1013 22.PNG]]
|-
|Symmetry
|As
|As
|As
|As
|}
'''Table 5. '''MOs of TS of endo and exo orientations(secondary orbital overlap in the endo).
[[File:Hb1013 27.PNG|none|thumb|Figure 6. Frequency calculation of endo.]]
[[File:Hb1013 29.PNG|none|thumb|Figure 7. Frequency calculation of exo.]]
Fig.6 and Fig.7 ensure the endo and exo structures are correct.
[[File:Hb1013 23.PNG|none|thumb|413x413px|Figure 6, Reaction Scheme of exercise 2.]]
This reaction is a normal demand DA reaction, the reason is C=C double bond is more electron deficient due to existing of two electron withdrawing oxygens in the dienophile.
[[File:Hb1013 25.PNG|none|thumb|499x499px|'''Table 7'''. Data of Reaction.]]
[[File:Hb1013 24.PNG|none|thumb|Figure 7. Energy Diagram of the reaction.]]
In this reaction, product of endo is thermodynamic product due to lower energy makes it more stable, and secondary orbital interaction in endo can provides an extra interaction in the reactants. product of exo is kinetic product.

==Exercise 3: Diels-Alder vs Cheletropic==
{| class="wikitable"
|
|Exo D-A Reaction
|Endo D-A Reaction
|Cheletropic Reaction
|-
|Structure
|
|
|
|-
|IRC
|[[File:Hb1013 32.PNG]]
|[[File:Hb1013 31.PNG]]
|[[File:Hb1013 33.PNG]]
|}
'''Table 8. '''Structures and IRC.
[[File:Hb1013 34.PNG|none|thumb|399x399px|Figure 8. Reaction Scheme of Exercise 3.]]
[[File:Hb1013 36.PNG|none|thumb|548x548px|'''Table 9'''. Energy data of Exercise 3.]]
[[File:Hb1013 35.PNG|none|thumb|334x334px|Figure 9. Energy diagram.]]
[[File:Hb1013 99.png|none|thumb|426x426px|Figure 10. The energy profile of sulfur dioxide and o-Xylylene cycloaddition.]]
This reaction is exothermic so has negative E and because of high free energy of xylyene, so it is very unstable. The formation of endo one is kinetically favoured, cheletropic one is thermodynamically favoured if there is enough energy. Futhermore, six-membered ring product like bezene to acheieve resonance form that can form an electron pi cloud and make the electrons delocalised.

==Conclusion==

==Reference==

Rep:Mod:hb1013

2017-03-19T21:20:09Z

Hb1013: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

=Computational Chemistry: Transition States and reactivity=
==Introduction==
By using mathematical method and chemistry theories, reaction of molecules can be simulated by computer. In this module, geometry and reactivity of cycloaddition were investigated. Transition states, molecular orbitals of three different types of cycloaddition were explored by Gaussian and GaussView.

Potential energy surface(PES) describes the energy of a molecule as a function of its geometry. The first derivative of energy is zero, the second derivative energy is negative and the transition state is the highest position in the pathway(saddle point). Two methods can be used to find out the transition state: frequency calculation and Intrinsic Reaction Coordination(IRC).

IRC is a method that can check whether transition state is in the position of the highest energy by exploring energy changing in both directions from the transition state.

Also, in this module optimisation of the molecules is really important to get more accurate geometry and energy of the transition state due to it can determine the geometry with lowest energy.

==Exercise 1: Reaction of Butadiene with Ethylene==
[[File:Hb1013 01.png|thumb|594x594px|Fig. 1 - MO diagram for the DA reaction of Butadiene(LHS) with Ethylene(RHS).|none]]Fragments Orbitals(FOs) with the same symmetry can interact and overlap with each other. In Fig.1, transitions states are formed by overlap of HOMO and LUMO of FOs with the same symmetry.

The Cis-butadiene and ethylene were drawn in GaussView and optimised at PM6 level.
{| class="wikitable"
|Molecule
|Cis-butadiene
|Cis-butadiene
|Ethene
|Ethene
|-
|MO
|HOMO
|LUMO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 4.PNG]]
|[[File:Hb1013 3.PNG]]
|[[File:Hb1013 5.PNG]]
|[[File:Hb1013 6.PNG]]
|-
|Symmetry
|Anti-symmetric
|Symmetric
|Symmetric
|Anti-symmetric
|-
|Energy/a.u.
|<nowiki>-0.35168</nowiki>
|0.01103
|<nowiki>-0.39228</nowiki>
|0.04256
|}
'''Table 1. '''Homo and LUMO of Cis-butadiene and ethene.

Optimised transition state is shown below.
[[File:Hb1013 10.PNG|none|thumb|Figure 2. Optimised transition state]]
To confirm this transition state is correct, frequency calculation and IRC are shown below.
[[File:Hb1013 8.PNG|none|thumb|Figure 3. Frequency calculation for the cycloaddition reaction of butadiene and ethene.]]
[[File:Hb1013 9.PNG|none|thumb|384x384px|Figure 4. IRC of the transition state.]]
As shown in Figure 3 and Figure 4, there is only one negative frequency for the transition state and a saddle point, which means this structure is correct.
[[File:Hb1013 2.PNG|none|thumb|500x500px|Figure 5. Bond lengths of reactants and product.]]
According to Fig. 2 and Fig. 5, Bond lengths of reactants, ts and product can be known.
{| class="wikitable"
|Bond
|Length in reactant
|Length in TS
|Length in product
|-
|C=C in TS of cis-Butadiene
|1.33
|1.38
|1.50
|-
|C-C in TS of cis-Butadiene
|1.47
|1.41
|1.34
|-
|C=C in TS of Ethene
|1.33
|1.38
|1.54
|-
|Partially formed bond in TS
|n/a
|2.11
|1.54
|}
'''Table 2. '''Bond lengths of reactants, ts and product. Units in Å.

Normally, C-C single bond is 1.54 Å and C=C double bond is 1.33 Å.<ref>CRC Handbook of chemistry and physics, 2005, '''86''', pp. 9-19.</ref> But in the transition state C-C and C=C are 1.41 Å and 1.31 Å respectively, which means C-C single bond is shortened and C=C double bond is elongated. The partially formed bond in TS is shortened to 2.11 Å and it is shorter than 2 * Van der Waal's radius of carbon (1.7Å).<ref>Bondi A., ''J. Phys. Chem'', 1964,''' 68''', 441-451.</ref> This indicates overlap of p-orbitals between terminal carbons in cis-Butadiene and ethene.

6-pi electrons in TS and according to Hoffmann rules, the reaction will be thermally allowed when p-orbitals interaction between terminal carbons in cis-Butadiene and ethene includes two types: superfacial and antarfacial.
{| class="wikitable"
|Molecule
|TS cyclohexene
|TS cyclohexene
|-
|MO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 12.PNG]]
|[[File:Hb1013 11.PNG]]
|-
|Symmetry
|Symmetric
|Symmetric
|-
|Energy a.u.
|<nowiki>-0.32533</nowiki>
|0.01732
|}
'''Table 3. '''TS of HOMO and LUMO.

Cis-Butadiene has one AS HOMO and one S LUMO and ethene has one S HOMO and one AS LUMO. Therefore, there are two possible interactions in this reaction. Because the diene is nucloephilic and the dienophile is electrophilic, the interaction between AS HOMO of cis-butadiene and AS LUMO of ethene is more favoured.

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==
{| class="wikitable"
|
|Cyclohexdiene
|1,3-Dioxole
|-
|
|[[File:Hb1013 13.PNG]]
|[[File:Hb1013 14.PNG]]
|-
|
|endo
|exo
|-
|TS
|[[File:Hb1013 15.PNG]]
|[[File:Hb1013 17.PNG]]
|-
|product
|[[File:Hb1013 16.PNG]]
|[[File:Hb1013 18.PNG]]
|}
'''Table 4. '''Structures of optimised reagents, TS and products.
{| class="wikitable"
|Orientation
|endo
|endo
|exo
|exo
|-
|MO
|HOMO
|LUMO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 19.PNG]]
|[[File:Hb1013 20.PNG]]
|[[File:Hb1013 21.PNG]]
|[[File:Hb1013 22.PNG]]
|-
|Symmetry
|As
|As
|As
|As
|}
'''Table 5. '''MOs of TS of endo and exo orientations(secondary orbital overlap in the endo).
[[File:Hb1013 27.PNG|none|thumb|Figure 6. Frequency calculation of endo.]]
[[File:Hb1013 29.PNG|none|thumb|Figure 7. Frequency calculation of exo.]]
Fig.6 and Fig.7 ensure the endo and exo structures are correct.
[[File:Hb1013 23.PNG|none|thumb|413x413px|Figure 6, Reaction Scheme of exercise 2.]]
This reaction is a normal demand DA reaction, the reason is C=C double bond is more electron deficient due to existing of two electron withdrawing oxygens in the dienophile.
[[File:Hb1013 25.PNG|none|thumb|499x499px|'''Table 7'''. Data of Reaction.]]
[[File:Hb1013 24.PNG|none|thumb|Figure 7. Energy Diagram of the reaction.]]
In this reaction, product of endo is thermodynamic product due to lower energy makes it more stable, and secondary orbital interaction in endo can provides an extra interaction in the reactants. product of exo is kinetic product.

==Exercise 3: Diels-Alder vs Cheletropic==
{| class="wikitable"
|
|Exo D-A Reaction
|Endo D-A Reaction
|Cheletropic Reaction
|-
|Structure
|
|
|
|-
|IRC
|[[File:Hb1013 32.PNG]]
|[[File:Hb1013 31.PNG]]
|[[File:Hb1013 33.PNG]]
|}
'''Table 8. '''Structures and IRC.
[[File:Hb1013 34.PNG|none|thumb|399x399px|Figure 8. Reaction Scheme of Exercise 3.]]
[[File:Hb1013 36.PNG|none|thumb|548x548px|'''Table 9'''. Energy data of Exercise 3.]]
[[File:Hb1013 35.PNG|none|thumb|334x334px|Figure 9. Energy diagram.]]
[[File:Hb1013 99.png|none|thumb|426x426px|Figure 10. The energy profile of sulfur dioxide and o-Xylylene cycloaddition.]]
This reaction is exothermic so has negative E and because of high free energy of xylyene, so it is very unstable. The formation of endo one is kinetically favoured, cheletropic one is thermodynamically favoured if there is enough energy. Futhermore, six-membered ring product like bezene to acheieve resonance form that can form an electron pi cloud and make the electrons delocalised.

==Reference==

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Rep:Mod:hb1013

2017-03-19T01:01:16Z

Hb1013: /* Computational Chemistry: Transition States and reactivity */

=Computational Chemistry: Transition States and reactivity=
==Introduction==
By using mathematical method and chemistry theories, reaction of molecules can be simulated by computer. In this module, geometry and reactivity of cycloaddition were investigated. Transition states, molecular orbitals of three different types of cycloaddition were explored by Gaussian and GaussView.

Potential energy surface(PES) describes the energy of a molecule as a function of its geometry. The first derivative of energy is zero, the second derivative energy is negative and the transition state is the highest position in the pathway(saddle point). Two methods can be used to find out the transition state: frequency calculation and Intrinsic Reaction Coordination(IRC).

IRC is a method that can check whether transition state is in the position of the highest energy by exploring energy changing in both directions from the transition state.

Also, in this module optimisation of the molecules is really important to get more accurate geometry and energy of the transition state due to it can determine the geometry with lowest energy.

==Exercise 1: Reaction of Butadiene with Ethylene==
[[File:Hb1013 01.png|thumb|594x594px|Fig. 1 - MO diagram for the DA reaction of Butadiene(LHS) with Ethylene(RHS).|none]]Fragments Orbitals(FOs) with the same symmetry can interact and overlap with each other. In Fig.1, transitions states are formed by overlap of HOMO and LUMO of FOs with the same symmetry.

The Cis-butadiene and ethylene were drawn in GaussView and optimised at PM6 level.
{| class="wikitable"
|Molecule
|Cis-butadiene
|Cis-butadiene
|Ethene
|Ethene
|-
|MO
|HOMO
|LUMO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 4.PNG]]
|[[File:Hb1013 3.PNG]]
|[[File:Hb1013 5.PNG]]
|[[File:Hb1013 6.PNG]]
|-
|Symmetry
|Anti-symmetric
|Symmetric
|Symmetric
|Anti-symmetric
|-
|Energy/a.u.
|<nowiki>-0.35168</nowiki>
|0.01103
|<nowiki>-0.39228</nowiki>
|0.04256
|}
'''Table 1. '''Homo and LUMO of Cis-butadiene and ethene.

Optimised transition state is shown below.
[[File:Hb1013 10.PNG|none|thumb|Figure 2. Optimised transition state]]
To confirm this transition state is correct, frequency calculation and IRC are shown below.
[[File:Hb1013 8.PNG|none|thumb|Figure 3. Frequency calculation for the cycloaddition reaction of butadiene and ethene.]]
[[File:Hb1013 9.PNG|none|thumb|384x384px|Figure 4. IRC of the transition state.]]
As shown in Figure 3 and Figure 4, there is only one negative frequency for the transition state and a saddle point, which means this structure is correct.
[[File:Hb1013 2.PNG|none|thumb|500x500px|Figure 5. Bond lengths of reactants and product.]]
According to Fig. 2 and Fig. 5, Bond lengths of reactants, ts and product can be known.
{| class="wikitable"
|Bond
|Length in reactant
|Length in TS
|Length in product
|-
|C=C in TS of cis-Butadiene
|1.33
|1.38
|1.50
|-
|C-C in TS of cis-Butadiene
|1.47
|1.41
|1.34
|-
|C=C in TS of Ethene
|1.33
|1.38
|1.54
|-
|Partially formed bond in TS
|n/a
|2.11
|1.54
|}
'''Table 2. '''Bond lengths of reactants, ts and product. Units in Å.

Normally, C-C single bond is 1.54 Å and C=C double bond is 1.33 Å.<ref>CRC Handbook of chemistry and physics, 2005, '''86''', pp. 9-19.</ref> But in the transition state C-C and C=C are 1.41 Å and 1.31 Å respectively, which means C-C single bond is shortened and C=C double bond is elongated. The partially formed bond in TS is shortened to 2.11 Å and it is shorter than 2 * Van der Waal's radius of carbon (1.7Å).<ref>Bondi A., ''J. Phys. Chem'', 1964,''' 68''', 441-451.</ref> This indicates overlap of p-orbitals between terminal carbons in cis-Butadiene and ethene.

6-pi electrons in TS and according to Hoffmann rules, the reaction will be thermally allowed when p-orbitals interaction between terminal carbons in cis-Butadiene and ethene includes two types: superfacial and antarfacial.
{| class="wikitable"
|Molecule
|TS cyclohexene
|TS cyclohexene
|-
|MO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 12.PNG]]
|[[File:Hb1013 11.PNG]]
|-
|Symmetry
|Symmetric
|Symmetric
|-
|Energy a.u.
|<nowiki>-0.32533</nowiki>
|0.01732
|}
'''Table 3. '''TS of HOMO and LUMO.

Cis-Butadiene has one AS HOMO and one S LUMO and ethene has one S HOMO and one AS LUMO. Therefore, there are two possible interactions in this reaction. Because the diene is nucloephilic and the dienophile is electrophilic, the interaction between AS HOMO of cis-butadiene and AS LUMO of ethene is more favoured.

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==
{| class="wikitable"
|
|Cyclohexdiene
|1,3-Dioxole
|-
|
|[[File:Hb1013 13.PNG]]
|[[File:Hb1013 14.PNG]]
|-
|
|endo
|exo
|-
|TS
|[[File:Hb1013 15.PNG]]
|[[File:Hb1013 17.PNG]]
|-
|product
|[[File:Hb1013 16.PNG]]
|[[File:Hb1013 18.PNG]]
|}
'''Table 4. '''Structures of optimised reagents, TS and products.
{| class="wikitable"
|Orientation
|endo
|endo
|exo
|exo
|-
|MO
|HOMO
|LUMO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 19.PNG]]
|[[File:Hb1013 20.PNG]]
|[[File:Hb1013 21.PNG]]
|[[File:Hb1013 22.PNG]]
|-
|Symmetry
|As
|As
|As
|As
|}
'''Table 5. '''MOs of TS of endo and exo orientations(secondary orbital overlap in the endo).
[[File:Hb1013 23.PNG|none|thumb|413x413px|Figure 6, Reaction Scheme of exercise 2.]]
This reaction is a normal demand DA reaction, the reason is C=C double bond is more electron deficient due to existing of two electron withdrawing oxygens in the dienophile.
[[File:Hb1013 25.PNG|none|thumb|499x499px|Table]]
[[File:Hb1013 24.PNG|none|thumb|Figure 7. Energy Diagram of the reaction.]]
In this reaction, product of endo has the lowest barrier energy, which means it is the kinetic product. Also, as shown in Table 5, HOMO diagram can support this, because more interaction in endo TS.

==Exercise 3: Diels-Alder vs Cheletropic==

==Reference==

Rep:Mod:hb1013

2017-03-19T01:00:22Z

Hb1013: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

=Computational Chemistry: Transition States and reactivity=
==Introduction==
By using mathematical method and chemistry theories, reaction of molecules can be simulated by computer. In this module, geometry and reactivity of cycloaddition were investigated. Transition states, molecular orbitals of three different types of cycloaddition were explored by Gaussian and GaussView.

Potential energy surface(PES) describes the energy of a molecule as a function of its geometry. The first derivative of energy is zero, the second derivative energy is negative and the transition state is the highest position in the pathway(saddle point). Two methods can be used to find out the transition state: frequency calculation and Intrinsic Reaction Coordination(IRC).

IRC is a method that can check whether transition state is in the position of the highest energy by exploring energy changing in both directions from the transition state.

Also, in this module optimisation of the molecules is really important to get more accurate geometry and energy of the transition state due to it can determine the geometry with lowest energy.

==Exercise 1: Reaction of Butadiene with Ethylene==
[[File:Hb1013 01.png|thumb|594x594px|Fig. 1 - MO diagram for the DA reaction of Butadiene(LHS) with Ethylene(RHS).|none]]Fragments Orbitals(FOs) with the same symmetry can interact and overlap with each other. In Fig.1, transitions states are formed by overlap of HOMO and LUMO of FOs with the same symmetry.

The Cis-butadiene and ethylene were drawn in GaussView and optimised at PM6 level.
{| class="wikitable"
|Molecule
|Cis-butadiene
|Cis-butadiene
|Ethene
|Ethene
|-
|MO
|HOMO
|LUMO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 4.PNG]]
|[[File:Hb1013 3.PNG]]
|[[File:Hb1013 5.PNG]]
|[[File:Hb1013 6.PNG]]
|-
|Symmetry
|Anti-symmetric
|Symmetric
|Symmetric
|Anti-symmetric
|-
|Energy/a.u.
|<nowiki>-0.35168</nowiki>
|0.01103
|<nowiki>-0.39228</nowiki>
|0.04256
|}
'''Table 1. '''Homo and LUMO of Cis-butadiene and ethene.

Optimised transition state is shown below.
[[File:Hb1013 10.PNG|none|thumb|Figure 2. Optimised transition state]]
To confirm this transition state is correct, frequency calculation and IRC are shown below.
[[File:Hb1013 8.PNG|none|thumb|Figure 3. Frequency calculation for the cycloaddition reaction of butadiene and ethene.]]
[[File:Hb1013 9.PNG|none|thumb|384x384px|Figure 4. IRC of the transition state.]]
As shown in Figure 3 and Figure 4, there is only one negative frequency for the transition state and a saddle point, which means this structure is correct.
[[File:Hb1013 2.PNG|none|thumb|500x500px|Figure 5. Bond lengths of reactants and product.]]
According to Fig. 2 and Fig. 5, Bond lengths of reactants, ts and product can be known.
{| class="wikitable"
|Bond
|Length in reactant
|Length in TS
|Length in product
|-
|C=C in TS of cis-Butadiene
|1.33
|1.38
|1.50
|-
|C-C in TS of cis-Butadiene
|1.47
|1.41
|1.34
|-
|C=C in TS of Ethene
|1.33
|1.38
|1.54
|-
|Partially formed bond in TS
|n/a
|2.11
|1.54
|}
'''Table 2. '''Bond lengths of reactants, ts and product. Units in Å.

Normally, C-C single bond is 1.54 Å and C=C double bond is 1.33 Å.<ref>CRC Handbook of chemistry and physics, 2005, '''86''', pp. 9-19.</ref> But in the transition state C-C and C=C are 1.41 Å and 1.31 Å respectively, which means C-C single bond is shortened and C=C double bond is elongated. The partially formed bond in TS is shortened to 2.11 Å and it is shorter than 2 * Van der Waal's radius of carbon (1.7Å).<ref>Bondi A., ''J. Phys. Chem'', 1964,''' 68''', 441-451.</ref> This indicates overlap of p-orbitals between terminal carbons in cis-Butadiene and ethene.

6-pi electrons in TS and according to Hoffmann rules, the reaction will be thermally allowed when p-orbitals interaction between terminal carbons in cis-Butadiene and ethene includes two types: superfacial and antarfacial.
{| class="wikitable"
|Molecule
|TS cyclohexene
|TS cyclohexene
|-
|MO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 12.PNG]]
|[[File:Hb1013 11.PNG]]
|-
|Symmetry
|Symmetric
|Symmetric
|-
|Energy a.u.
|<nowiki>-0.32533</nowiki>
|0.01732
|}
'''Table 3. '''TS of HOMO and LUMO.

Cis-Butadiene has one AS HOMO and one S LUMO and ethene has one S HOMO and one AS LUMO. Therefore, there are two possible interactions in this reaction. Because the diene is nucloephilic and the dienophile is electrophilic, the interaction between AS HOMO of cis-butadiene and AS LUMO of ethene is more favoured.

==Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole==
{| class="wikitable"
|
|Cyclohexdiene
|1,3-Dioxole
|-
|
|[[File:Hb1013 13.PNG]]
|[[File:Hb1013 14.PNG]]
|-
|
|endo
|exo
|-
|TS
|[[File:Hb1013 15.PNG]]
|[[File:Hb1013 17.PNG]]
|-
|product
|[[File:Hb1013 16.PNG]]
|[[File:Hb1013 18.PNG]]
|}
'''Table 4. '''Structures of optimised reagents, TS and products.
{| class="wikitable"
|Orientation
|endo
|endo
|exo
|exo
|-
|MO
|HOMO
|LUMO
|HOMO
|LUMO
|-
|
|[[File:Hb1013 19.PNG]]
|[[File:Hb1013 20.PNG]]
|[[File:Hb1013 21.PNG]]
|[[File:Hb1013 22.PNG]]
|-
|Symmetry
|As
|As
|As
|As
|}
'''Table 5. '''MOs of TS of endo and exo orientations(secondary orbital overlap in the endo).
[[File:Hb1013 23.PNG|none|thumb|413x413px|Figure 6, Reaction Scheme of exercise 2.]]
This reaction is a normal demand DA reaction, the reason is C=C double bond is more electron deficient due to existing of two electron withdrawing oxygens in the dienophile.
[[File:Hb1013 25.PNG|none|thumb|499x499px|Table]]
[[File:Hb1013 24.PNG|none|thumb|Figure 7. Energy Diagram of the reaction.]]
In this reaction, product of endo has the lowest barrier energy, which means it is the kinetic product. Also, as shown in Table 5, HOMO diagram can support this, because more interaction in endo TS.

==Exercise 3: Diels-Alder vs Cheletropic==

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Hb1013:

Rep:Mod:hb1013

2017-03-18T18:27:43Z

Hb1013: /* Exercise 1: Reaction of Butadiene with Ethylene */

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Hb1013:

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Hb1013:

Rep:Mod:hb1013

2017-03-18T15:52:17Z

Hb1013: /* Exercise 1: Reaction of Butadiene with Ethylene */

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Hb1013:

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Hb1013: /* Exercise 1: Reaction of Butadiene with Ethylene */

Rep:Mod:hb1013

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Hb1013: /* Exercise 1: Reaction of Butadiene with Ethylene */

Rep:Mod:hb1013

2017-03-18T02:42:51Z

Hb1013: /* Exercise 1: Reaction of Butadiene with Ethylene */

Rep:Mod:hb1013

2017-03-18T02:17:02Z

Hb1013: /* Exercise 1: Reaction of Butadiene with Ethylene */