ChemWiki - User contributions [en]

User:Ck3112

2015-02-27T11:51:05Z

Ck3112: /* The Cope Rearrangement Tutorial */

==='''The Cope Rearrangement Tutorial'''===

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

'''Optimizing the Reactants and Products'''

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformer being slightly lower in energy, this is what is expected simply judging from sterics.

[[File:Part b syn.jpg| thumb |Figure 1:gauche linkage of 1,5-hexadiene]]

In figure 2 a lower energy gauche conformer can be seen, with an energy of -231.69266122 Hartree.

[[File:React c.png| thumb |Figure 2:Gauche 3]]

Then anti2 conformation was built and optimised giving an energy of -231.69253510 Hartree and a point group Ci - seen figure 3. The value given for the energy of this conformer is -231.69254 Hartree, which is the same as the value calculated from Gaussian (to less decimal places).

[[File:Anti2yoyo.jpg| thumb |Figure 3: Anti 2]]

The anti2 conformer was then reoptimised at the B3LYP/6-31G* level giving an energy of -233.33634309 Hartrees.

[[File:Anti2yoyoDTF.png| thumb |Figure 4: Anti 2 reoptimised at B3LYP/6-31G* level]]

A frequency calculation was then performed on the B3LYP/6-31G* optimised molecule. This confirmed that this is a minimum as all the vibrational frequencies were real and positive.

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

==='''Optimizing the "Chair" and "Boat" Transition Structures'''===

The boat and chair transition structures of the cope rearrangement are made and optimised so they can be compared. To do this firstly a C3H5 allyl fragment is built and optimised to HF/3-21G level of theory. Then two of these optimised fragments were combined to make a rough guess of what the chair transition state should look like, setting the two fragmetns 2.2 Å apart.

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

This guess was then optimised in two ways. The first was optimising it to a transition state by selecting optimization to a TS (Berny) in the calculate menu.This gave bond forming/bond breaking bond lengths 2.02159 Å and 2.02098 Å, and an energy of -231.61932181 Hartree.

<jmolFile text="Chair, optimised to a TS">Chair_b_thu3.mol</jmolFile>

The next method of optimising the chair transition state was to optimise it using the frozen coordinate method. This involves freezing the allyl fragment bonds that will be made to a set length (2.2 Å) then optimising the structure to a minimum. Then unfreezing the bonds and optimising the structure to a transition state. This method gave bond forming/bond breaking bond lengths 2.02071 Å and 2.02074 Å, and an energy of -231.61932233 Hartree.

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

These two method gave very similar results with the frozen coordinate method giving a slight lower energy and short bond lengths.

The QST2 method was used to optimise the boat transition structure. For this two gauche conformers of 1,5-hexadiene were put into GaussView and numbered so they corresponded to the reactant and product of the cope rearrangement. Then the QST2 calculation was run. This gave bond forming/bond breaking bond lengths 2.14181 Å and 2.14046 Å, and energy -231.60280217 Hartree. This is a higher energy and longer bond lengths then the chair transition state, implying that the reaction would prefer to go via the chair transition state. Although, there's not much in it.

<jmolFile text="Optimised boat QST2 method">2nd_QST2_thu.mol</jmolFile>

===The Diels Alder Cycloaddition===

GaussView was used to build cis butadiene and then optimized to the HF/3-21G level. The HOMO and LUMO were plotted and it can be seen that both orbitals are asymmetric with respect to the plane.

[[File:Cisbutadiene.kitts.jpg| thumb |Figure 5: LUMO of cisbutadiene]]

[[File:Cisbutadiene HOMO.jpg| thumb |Figure 6: HOMO of cisbutadiene]]

In order to obtain a transition state geometry of the reaction between ethylene and butadiene, firstly a bicyclo system was built in GaussView and optimised to a minimum. Then the CH2CH2 fragment was deleted and the transition state optimised using the frozen coordinate method, setting the interfragment distance originally as 2.2 Å. The transition state had transition bond lengths of 2.200130 Å, this is higher than the Van der Waal radi of carbon atoms (around 1.75 Å<sup>1) - meaning that the bond has not formed.
[[File:Guess ts bii.jpg| thumb |Figure 7: Guess of transition state of bicyclo system]]

[[File:TS ii.jpg| thumb |Figure 8: Transition state of ethylene and butadiene]]

[[File:Guess ts ii HOMO.jpg| thumb |Figure 9: HOMO of Diels-Alder Transition State]]

[[File:TS ii LUMO.jpg| thumb |Figure 10: LUMO of Diels-Alder Transition State]]

The HOMO of this transition state can be seen to be symmetrical whilst the LUMO is asymmetrical.

The Diels-Alder reaction between cyclohexa-1,3-diene and maleic anhydride can potentially give either an endo or an exo product. To examine which would be favoured we can examine the exo and endo transition states, to see which is lower in energy. First, cyclohexa-1,3-diene and maleic anhydride are built and optimised to the HF/3-21G level. Then these are used to build a rough estimate of the endo and exo transition states. Primarily the endo adduct is given as this is lower in energy (and this reaction is kinetically controlled.

[[File:Maleic anhydride Cyclohexa-1,3-diene.jpg| thumb |Figure 11: Maleic anhydride (left) and cyclohexa-1,3-diene (right)]]

[[File:Endoexoyo.jpg| thumb |Figure 12: Endo and exo guess transition structures]]

===References===

1. R. Scott Rowland, Robin Taylor: Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii. In: J. Phys. Chem. 1996, 100, S. 7384–7391, doi:10.1021/jp953141+.

User:Ck3112

2015-02-27T11:44:19Z

Ck3112: /* The Diels Alder Cycloaddition */

==='''The Cope Rearrangement Tutorial'''===

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

'''Optimizing the Reactants and Products'''

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformer being slightly lower in energy, this is what is expected simply judging from sterics.

[[File:Part b syn.jpg| thumb |Figure 1:gauche linkage of 1,5-hexadiene]]

In figure 2 a lower energy gauche conformer can be seen, with an energy of -231.69266122 Hartree.

[[File:React c.png| thumb |Figure 2:Gauche 3]]

Then anti2 conformation was built and optimised giving an energy of -231.69253510 Hartree and a point group Ci - seen figure 3. The value given for the energy of this conformer is -231.69254 Hartree, which is the same as the value calculated from Gaussian (to less decimal places).

[[File:Anti2yoyo.jpg| thumb |Figure 3: Anti 2]]

The anti2 conformer was then reoptimised at the B3LYP/6-31G* level giving an energy of -233.33634309 Hartrees.

[[File:Anti2yoyoDTF.png| thumb |Figure 4: Anti 2 reoptimised at B3LYP/6-31G* level]]

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

==='''Optimizing the "Chair" and "Boat" Transition Structures'''===

The boat and chair transition structures of the cope rearrangement are made and optimised so they can be compared. To do this firstly a C3H5 allyl fragment is built and optimised to HF/3-21G level of theory. Then two of these optimised fragments were combined to make a rough guess of what the chair transition state should look like, setting the two fragmetns 2.2 Å apart.

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

This guess was then optimised in two ways. The first was optimising it to a transition state by selecting optimization to a TS (Berny) in the calculate menu.This gave bond forming/bond breaking bond lengths 2.02159 Å and 2.02098 Å, and an energy of -231.61932181 Hartree.

<jmolFile text="Chair, optimised to a TS">Chair_b_thu3.mol</jmolFile>

The next method of optimising the chair transition state was to optimise it using the frozen coordinate method. This involves freezing the allyl fragment bonds that will be made to a set length (2.2 Å) then optimising the structure to a minimum. Then unfreezing the bonds and optimising the structure to a transition state. This method gave bond forming/bond breaking bond lengths 2.02071 Å and 2.02074 Å, and an energy of -231.61932233 Hartree.

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

These two method gave very similar results with the frozen coordinate method giving a slight lower energy and short bond lengths.

The QST2 method was used to optimise the boat transition structure. For this two gauche conformers of 1,5-hexadiene were put into GaussView and numbered so they corresponded to the reactant and product of the cope rearrangement. Then the QST2 calculation was run. This gave bond forming/bond breaking bond lengths 2.14181 Å and 2.14046 Å, and energy -231.60280217 Hartree. This is a higher energy and longer bond lengths then the chair transition state, implying that the reaction would prefer to go via the chair transition state. Although, there's not much in it.

<jmolFile text="Optimised boat QST2 method">2nd_QST2_thu.mol</jmolFile>

===The Diels Alder Cycloaddition===

GaussView was used to build cis butadiene and then optimized to the HF/3-21G level. The HOMO and LUMO were plotted and it can be seen that both orbitals are asymmetric with respect to the plane.

[[File:Cisbutadiene.kitts.jpg| thumb |Figure 5: LUMO of cisbutadiene]]

[[File:Cisbutadiene HOMO.jpg| thumb |Figure 6: HOMO of cisbutadiene]]

In order to obtain a transition state geometry of the reaction between ethylene and butadiene, firstly a bicyclo system was built in GaussView and optimised to a minimum. Then the CH2CH2 fragment was deleted and the transition state optimised using the frozen coordinate method, setting the interfragment distance originally as 2.2 Å. The transition state had transition bond lengths of 2.200130 Å, this is higher than the Van der Waal radi of carbon atoms (around 1.75 Å<sup>1) - meaning that the bond has not formed.
[[File:Guess ts bii.jpg| thumb |Figure 7: Guess of transition state of bicyclo system]]

[[File:TS ii.jpg| thumb |Figure 8: Transition state of ethylene and butadiene]]

[[File:Guess ts ii HOMO.jpg| thumb |Figure 9: HOMO of Diels-Alder Transition State]]

[[File:TS ii LUMO.jpg| thumb |Figure 10: LUMO of Diels-Alder Transition State]]

The HOMO of this transition state can be seen to be symmetrical whilst the LUMO is asymmetrical.

The Diels-Alder reaction between cyclohexa-1,3-diene and maleic anhydride can potentially give either an endo or an exo product. To examine which would be favoured we can examine the exo and endo transition states, to see which is lower in energy. First, cyclohexa-1,3-diene and maleic anhydride are built and optimised to the HF/3-21G level. Then these are used to build a rough estimate of the endo and exo transition states. Primarily the endo adduct is given as this is lower in energy (and this reaction is kinetically controlled.

[[File:Maleic anhydride Cyclohexa-1,3-diene.jpg| thumb |Figure 11: Maleic anhydride (left) and cyclohexa-1,3-diene (right)]]

[[File:Endoexoyo.jpg| thumb |Figure 12: Endo and exo guess transition structures]]

===References===

1. R. Scott Rowland, Robin Taylor: Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii. In: J. Phys. Chem. 1996, 100, S. 7384–7391, doi:10.1021/jp953141+.

File:Endoexoyo.jpg

2015-02-27T11:43:41Z

Ck3112: Endo and exo guess transition structures

Endo and exo guess transition structures

User:Ck3112

2015-02-27T11:24:29Z

Ck3112: /* The Diels Alder Cycloaddition */

==='''The Cope Rearrangement Tutorial'''===

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

'''Optimizing the Reactants and Products'''

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformer being slightly lower in energy, this is what is expected simply judging from sterics.

[[File:Part b syn.jpg| thumb |Figure 1:gauche linkage of 1,5-hexadiene]]

In figure 2 a lower energy gauche conformer can be seen, with an energy of -231.69266122 Hartree.

[[File:React c.png| thumb |Figure 2:Gauche 3]]

Then anti2 conformation was built and optimised giving an energy of -231.69253510 Hartree and a point group Ci - seen figure 3. The value given for the energy of this conformer is -231.69254 Hartree, which is the same as the value calculated from Gaussian (to less decimal places).

[[File:Anti2yoyo.jpg| thumb |Figure 3: Anti 2]]

The anti2 conformer was then reoptimised at the B3LYP/6-31G* level giving an energy of -233.33634309 Hartrees.

[[File:Anti2yoyoDTF.png| thumb |Figure 4: Anti 2 reoptimised at B3LYP/6-31G* level]]

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

==='''Optimizing the "Chair" and "Boat" Transition Structures'''===

The boat and chair transition structures of the cope rearrangement are made and optimised so they can be compared. To do this firstly a C3H5 allyl fragment is built and optimised to HF/3-21G level of theory. Then two of these optimised fragments were combined to make a rough guess of what the chair transition state should look like, setting the two fragmetns 2.2 Å apart.

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

This guess was then optimised in two ways. The first was optimising it to a transition state by selecting optimization to a TS (Berny) in the calculate menu.This gave bond forming/bond breaking bond lengths 2.02159 Å and 2.02098 Å, and an energy of -231.61932181 Hartree.

<jmolFile text="Chair, optimised to a TS">Chair_b_thu3.mol</jmolFile>

The next method of optimising the chair transition state was to optimise it using the frozen coordinate method. This involves freezing the allyl fragment bonds that will be made to a set length (2.2 Å) then optimising the structure to a minimum. Then unfreezing the bonds and optimising the structure to a transition state. This method gave bond forming/bond breaking bond lengths 2.02071 Å and 2.02074 Å, and an energy of -231.61932233 Hartree.

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

These two method gave very similar results with the frozen coordinate method giving a slight lower energy and short bond lengths.

The QST2 method was used to optimise the boat transition structure. For this two gauche conformers of 1,5-hexadiene were put into GaussView and numbered so they corresponded to the reactant and product of the cope rearrangement. Then the QST2 calculation was run. This gave bond forming/bond breaking bond lengths 2.14181 Å and 2.14046 Å, and energy -231.60280217 Hartree. This is a higher energy and longer bond lengths then the chair transition state, implying that the reaction would prefer to go via the chair transition state. Although, there's not much in it.

<jmolFile text="Optimised boat QST2 method">2nd_QST2_thu.mol</jmolFile>

===The Diels Alder Cycloaddition===

GaussView was used to build cis butadiene and then optimized to the HF/3-21G level. The HOMO and LUMO were plotted and it can be seen that both orbitals are asymmetric with respect to the plane.

[[File:Cisbutadiene.kitts.jpg| thumb |Figure 5: LUMO of cisbutadiene]]

[[File:Cisbutadiene HOMO.jpg| thumb |Figure 6: HOMO of cisbutadiene]]

In order to obtain a transition state geometry of the reaction between ethylene and butadiene, firstly a bicyclo system was built in GaussView and optimised to a minimum. Then the CH2CH2 fragment was deleted and the transition state optimised using the frozen coordinate method, setting the interfragment distance originally as 2.2 Å. The transition state had transition bond lengths of __, this is higher than the Van der Waal radi of carbon atoms (around 1.75 Å<sup>1)
[[File:Guess ts bii.jpg| thumb |Figure 7: Guess of transition state of bicyclo system]]

[[File:TS ii.jpg| thumb |Figure 8: Transition state of ethylene and butadiene]]

[[File:Guess ts ii HOMO.jpg| thumb |Figure 9: HOMO of Diels-Alder Transition State]]

[[File:TS ii LUMO.jpg| thumb |Figure 10: LUMO of Diels-Alder Transition State]]

The HOMO of this transition state can be seen to be symmetrical whilst the LUMO is asymmetrical.

The Diels-Alder reaction between cyclohexa-1,3-diene and maleic anhydride can potentially give either an endo or an exo product. To examine which would be favoured we can examine the exo and endo transition states, to see which is lower in energy. First, cyclohexa-1,3-diene and maleic anhydride are built and optimised to the HF/3-21G level. Then these are used to build a rough estimate of the endo and exo transition states.

[[File:Maleic anhydride Cyclohexa-1,3-diene.jpg| thumb |Figure 11: Maleic anhydride (left) and cyclohexa-1,3-diene (right)]]

===References===

1. R. Scott Rowland, Robin Taylor: Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii. In: J. Phys. Chem. 1996, 100, S. 7384–7391, doi:10.1021/jp953141+.

User:Ck3112

2015-02-27T11:23:09Z

Ck3112: /* The Diels Alder Cycloaddition */

==='''The Cope Rearrangement Tutorial'''===

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

'''Optimizing the Reactants and Products'''

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformer being slightly lower in energy, this is what is expected simply judging from sterics.

[[File:Part b syn.jpg| thumb |Figure 1:gauche linkage of 1,5-hexadiene]]

In figure 2 a lower energy gauche conformer can be seen, with an energy of -231.69266122 Hartree.

[[File:React c.png| thumb |Figure 2:Gauche 3]]

Then anti2 conformation was built and optimised giving an energy of -231.69253510 Hartree and a point group Ci - seen figure 3. The value given for the energy of this conformer is -231.69254 Hartree, which is the same as the value calculated from Gaussian (to less decimal places).

[[File:Anti2yoyo.jpg| thumb |Figure 3: Anti 2]]

The anti2 conformer was then reoptimised at the B3LYP/6-31G* level giving an energy of -233.33634309 Hartrees.

[[File:Anti2yoyoDTF.png| thumb |Figure 4: Anti 2 reoptimised at B3LYP/6-31G* level]]

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

==='''Optimizing the "Chair" and "Boat" Transition Structures'''===

The boat and chair transition structures of the cope rearrangement are made and optimised so they can be compared. To do this firstly a C3H5 allyl fragment is built and optimised to HF/3-21G level of theory. Then two of these optimised fragments were combined to make a rough guess of what the chair transition state should look like, setting the two fragmetns 2.2 Å apart.

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

This guess was then optimised in two ways. The first was optimising it to a transition state by selecting optimization to a TS (Berny) in the calculate menu.This gave bond forming/bond breaking bond lengths 2.02159 Å and 2.02098 Å, and an energy of -231.61932181 Hartree.

<jmolFile text="Chair, optimised to a TS">Chair_b_thu3.mol</jmolFile>

The next method of optimising the chair transition state was to optimise it using the frozen coordinate method. This involves freezing the allyl fragment bonds that will be made to a set length (2.2 Å) then optimising the structure to a minimum. Then unfreezing the bonds and optimising the structure to a transition state. This method gave bond forming/bond breaking bond lengths 2.02071 Å and 2.02074 Å, and an energy of -231.61932233 Hartree.

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

These two method gave very similar results with the frozen coordinate method giving a slight lower energy and short bond lengths.

The QST2 method was used to optimise the boat transition structure. For this two gauche conformers of 1,5-hexadiene were put into GaussView and numbered so they corresponded to the reactant and product of the cope rearrangement. Then the QST2 calculation was run. This gave bond forming/bond breaking bond lengths 2.14181 Å and 2.14046 Å, and energy -231.60280217 Hartree. This is a higher energy and longer bond lengths then the chair transition state, implying that the reaction would prefer to go via the chair transition state. Although, there's not much in it.

<jmolFile text="Optimised boat QST2 method">2nd_QST2_thu.mol</jmolFile>

===The Diels Alder Cycloaddition===

GaussView was used to build cis butadiene and then optimized to the HF/3-21G level. The HOMO and LUMO were plotted and it can be seen that both orbitals are asymmetric with respect to the plane.

[[File:Cisbutadiene.kitts.jpg| thumb |Figure 5: LUMO of cisbutadiene]]

[[File:Cisbutadiene HOMO.jpg| thumb |Figure 6: HOMO of cisbutadiene]]

In order to obtain a transition state geometry of the reaction between ethylene and butadiene, firstly a bicyclo system was built in GaussView and optimised to a minimum. Then the CH2CH2 fragment was deleted and the transition state optimised using the frozen coordinate method, setting the interfragment distance originally as 2.2 Å. The transition state had transition bond lengths of __, this is higher than the Van der Waal radi of carbon atoms (around 1.75 Å^1)
[[File:Guess ts bii.jpg| thumb |Figure 7: Guess of transition state of bicyclo system]]

[[File:TS ii.jpg| thumb |Figure 8: Transition state of ethylene and butadiene]]

[[File:Guess ts ii HOMO.jpg| thumb |Figure 9: HOMO of Diels-Alder Transition State]]

[[File:TS ii LUMO.jpg| thumb |Figure 10: LUMO of Diels-Alder Transition State]]

The HOMO of this transition state can be seen to be symmetrical whilst the LUMO is asymmetrical.

The Diels-Alder reaction between cyclohexa-1,3-diene and maleic anhydride can potentially give either an endo or an exo product. To examine which would be favoured we can examine the exo and endo transition states, to see which is lower in energy. First, cyclohexa-1,3-diene and maleic anhydride are built and optimised to the HF/3-21G level. Then these are used to build a rough estimate of the endo and exo transition states.

[[File:Maleic anhydride Cyclohexa-1,3-diene.jpg| thumb |Figure 11: Maleic anhydride (left) and cyclohexa-1,3-diene (right)]]

===References===

1. R. Scott Rowland, Robin Taylor: Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii. In: J. Phys. Chem. 1996, 100, S. 7384–7391, doi:10.1021/jp953141+.

User:Ck3112

2015-02-27T11:21:30Z

Ck3112: /* The Diels Alder Cycloaddition */

==='''The Cope Rearrangement Tutorial'''===

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

'''Optimizing the Reactants and Products'''

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformer being slightly lower in energy, this is what is expected simply judging from sterics.

[[File:Part b syn.jpg| thumb |Figure 1:gauche linkage of 1,5-hexadiene]]

In figure 2 a lower energy gauche conformer can be seen, with an energy of -231.69266122 Hartree.

[[File:React c.png| thumb |Figure 2:Gauche 3]]

Then anti2 conformation was built and optimised giving an energy of -231.69253510 Hartree and a point group Ci - seen figure 3. The value given for the energy of this conformer is -231.69254 Hartree, which is the same as the value calculated from Gaussian (to less decimal places).

[[File:Anti2yoyo.jpg| thumb |Figure 3: Anti 2]]

The anti2 conformer was then reoptimised at the B3LYP/6-31G* level giving an energy of -233.33634309 Hartrees.

[[File:Anti2yoyoDTF.png| thumb |Figure 4: Anti 2 reoptimised at B3LYP/6-31G* level]]

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

==='''Optimizing the "Chair" and "Boat" Transition Structures'''===

The boat and chair transition structures of the cope rearrangement are made and optimised so they can be compared. To do this firstly a C3H5 allyl fragment is built and optimised to HF/3-21G level of theory. Then two of these optimised fragments were combined to make a rough guess of what the chair transition state should look like, setting the two fragmetns 2.2 Å apart.

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

This guess was then optimised in two ways. The first was optimising it to a transition state by selecting optimization to a TS (Berny) in the calculate menu.This gave bond forming/bond breaking bond lengths 2.02159 Å and 2.02098 Å, and an energy of -231.61932181 Hartree.

<jmolFile text="Chair, optimised to a TS">Chair_b_thu3.mol</jmolFile>

The next method of optimising the chair transition state was to optimise it using the frozen coordinate method. This involves freezing the allyl fragment bonds that will be made to a set length (2.2 Å) then optimising the structure to a minimum. Then unfreezing the bonds and optimising the structure to a transition state. This method gave bond forming/bond breaking bond lengths 2.02071 Å and 2.02074 Å, and an energy of -231.61932233 Hartree.

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

These two method gave very similar results with the frozen coordinate method giving a slight lower energy and short bond lengths.

The QST2 method was used to optimise the boat transition structure. For this two gauche conformers of 1,5-hexadiene were put into GaussView and numbered so they corresponded to the reactant and product of the cope rearrangement. Then the QST2 calculation was run. This gave bond forming/bond breaking bond lengths 2.14181 Å and 2.14046 Å, and energy -231.60280217 Hartree. This is a higher energy and longer bond lengths then the chair transition state, implying that the reaction would prefer to go via the chair transition state. Although, there's not much in it.

<jmolFile text="Optimised boat QST2 method">2nd_QST2_thu.mol</jmolFile>

===The Diels Alder Cycloaddition===

GaussView was used to build cis butadiene and then optimized to the HF/3-21G level. The HOMO and LUMO were plotted and it can be seen that both orbitals are asymmetric with respect to the plane.

[[File:Cisbutadiene.kitts.jpg| thumb |Figure 5: LUMO of cisbutadiene]]

[[File:Cisbutadiene HOMO.jpg| thumb |Figure 6: HOMO of cisbutadiene]]

In order to obtain a transition state geometry of the reaction between ethylene and butadiene, firstly a bicyclo system was built in GaussView and optimised to a minimum. Then the CH2CH2 fragment was deleted and the transition state optimised using the frozen coordinate method, setting the interfragment distance originally as 2.2 Å. The transition state had transition bond lengths of __, this is higher than the Van der Waal radi of carbon atoms (around 1.75 Å)
[[File:Guess ts bii.jpg| thumb |Figure 7: Guess of transition state of bicyclo system]]

[[File:TS ii.jpg| thumb |Figure 8: Transition state of ethylene and butadiene]]

[[File:Guess ts ii HOMO.jpg| thumb |Figure 9: HOMO of Diels-Alder Transition State]]

[[File:TS ii LUMO.jpg| thumb |Figure 10: LUMO of Diels-Alder Transition State]]

The HOMO of this transition state can be seen to be symmetrical whilst the LUMO is asymmetrical.

The Diels-Alder reaction between cyclohexa-1,3-diene and maleic anhydride can potentially give either an endo or an exo product. To examine which would be favoured we can examine the exo and endo transition states, to see which is lower in energy. First, cyclohexa-1,3-diene and maleic anhydride are built and optimised to the HF/3-21G level. Then these are used to build a rough estimate of the endo and exo transition states.

[[File:Maleic anhydride Cyclohexa-1,3-diene.jpg| thumb |Figure 11: Maleic anhydride (left) and cyclohexa-1,3-diene (right)]]

User:Ck3112

2015-02-27T11:08:22Z

Ck3112: /* The Diels Alder Cycloaddition */

==='''The Cope Rearrangement Tutorial'''===

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

'''Optimizing the Reactants and Products'''

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformer being slightly lower in energy, this is what is expected simply judging from sterics.

[[File:Part b syn.jpg| thumb |Figure 1:gauche linkage of 1,5-hexadiene]]

In figure 2 a lower energy gauche conformer can be seen, with an energy of -231.69266122 Hartree.

[[File:React c.png| thumb |Figure 2:Gauche 3]]

Then anti2 conformation was built and optimised giving an energy of -231.69253510 Hartree and a point group Ci - seen figure 3. The value given for the energy of this conformer is -231.69254 Hartree, which is the same as the value calculated from Gaussian (to less decimal places).

[[File:Anti2yoyo.jpg| thumb |Figure 3: Anti 2]]

The anti2 conformer was then reoptimised at the B3LYP/6-31G* level giving an energy of -233.33634309 Hartrees.

[[File:Anti2yoyoDTF.png| thumb |Figure 4: Anti 2 reoptimised at B3LYP/6-31G* level]]

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

==='''Optimizing the "Chair" and "Boat" Transition Structures'''===

The boat and chair transition structures of the cope rearrangement are made and optimised so they can be compared. To do this firstly a C3H5 allyl fragment is built and optimised to HF/3-21G level of theory. Then two of these optimised fragments were combined to make a rough guess of what the chair transition state should look like, setting the two fragmetns 2.2 Å apart.

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

This guess was then optimised in two ways. The first was optimising it to a transition state by selecting optimization to a TS (Berny) in the calculate menu.This gave bond forming/bond breaking bond lengths 2.02159 Å and 2.02098 Å, and an energy of -231.61932181 Hartree.

<jmolFile text="Chair, optimised to a TS">Chair_b_thu3.mol</jmolFile>

The next method of optimising the chair transition state was to optimise it using the frozen coordinate method. This involves freezing the allyl fragment bonds that will be made to a set length (2.2 Å) then optimising the structure to a minimum. Then unfreezing the bonds and optimising the structure to a transition state. This method gave bond forming/bond breaking bond lengths 2.02071 Å and 2.02074 Å, and an energy of -231.61932233 Hartree.

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

These two method gave very similar results with the frozen coordinate method giving a slight lower energy and short bond lengths.

The QST2 method was used to optimise the boat transition structure. For this two gauche conformers of 1,5-hexadiene were put into GaussView and numbered so they corresponded to the reactant and product of the cope rearrangement. Then the QST2 calculation was run. This gave bond forming/bond breaking bond lengths 2.14181 Å and 2.14046 Å, and energy -231.60280217 Hartree. This is a higher energy and longer bond lengths then the chair transition state, implying that the reaction would prefer to go via the chair transition state. Although, there's not much in it.

<jmolFile text="Optimised boat QST2 method">2nd_QST2_thu.mol</jmolFile>

===The Diels Alder Cycloaddition===

GaussView was used to build cis butadiene and then optimized to the HF/3-21G level. The HOMO and LUMO were plotted and it can be seen that both orbitals are asymmetric with respect to the plane.

[[File:Cisbutadiene.kitts.jpg| thumb |Figure 5: LUMO of cisbutadiene]]

[[File:Cisbutadiene HOMO.jpg| thumb |Figure 6: HOMO of cisbutadiene]]

In order to obtain a transition state geometry of the reaction between ethylene and butadiene, firstly a bicyclo system was built in GaussView and optimised to a minimum. Then the CH2CH2 fragment was deleted and the transition state optimised using the frozen coordinate method, setting the interfragment distance originally as 2.2 Å.
[[File:Guess ts bii.jpg| thumb |Figure 7: Guess of transition state of bicyclo system]]

[[File:TS ii.jpg| thumb |Figure 8: Transition state of ethylene and butadiene]]

[[File:Guess ts ii HOMO.jpg| thumb |Figure 9: HOMO of Diels-Alder Transition State]]

[[File:TS ii LUMO.jpg| thumb |Figure 10: LUMO of Diels-Alder Transition State]]

The HOMO of this transition state can be seen to be symmetrical whilst the LUMO is asymmetrical.

The Diels-Alder reaction between cyclohexa-1,3-diene and maleic anhydride can potentially give either an endo or an exo product. To examine which would be favoured we can examine the exo and endo transition states, to see which is lower in energy. First, cyclohexa-1,3-diene and maleic anhydride are built and optimised to the HF/3-21G level. Then these are used to build a rough estimate of the endo and exo transition states.

[[File:Maleic anhydride Cyclohexa-1,3-diene.jpg| thumb |Figure 11: Maleic anhydride (left) and cyclohexa-1,3-diene (right)]]

User:Ck3112

2015-02-27T11:06:23Z

Ck3112: /* Optimizing the "Chair" and "Boat" Transition Structures */

==='''The Cope Rearrangement Tutorial'''===

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

'''Optimizing the Reactants and Products'''

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformer being slightly lower in energy, this is what is expected simply judging from sterics.

[[File:Part b syn.jpg| thumb |Figure 1:gauche linkage of 1,5-hexadiene]]

In figure 2 a lower energy gauche conformer can be seen, with an energy of -231.69266122 Hartree.

[[File:React c.png| thumb |Figure 2:Gauche 3]]

Then anti2 conformation was built and optimised giving an energy of -231.69253510 Hartree and a point group Ci - seen figure 3. The value given for the energy of this conformer is -231.69254 Hartree, which is the same as the value calculated from Gaussian (to less decimal places).

[[File:Anti2yoyo.jpg| thumb |Figure 3: Anti 2]]

The anti2 conformer was then reoptimised at the B3LYP/6-31G* level giving an energy of -233.33634309 Hartrees.

[[File:Anti2yoyoDTF.png| thumb |Figure 4: Anti 2 reoptimised at B3LYP/6-31G* level]]

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

==='''Optimizing the "Chair" and "Boat" Transition Structures'''===

The boat and chair transition structures of the cope rearrangement are made and optimised so they can be compared. To do this firstly a C3H5 allyl fragment is built and optimised to HF/3-21G level of theory. Then two of these optimised fragments were combined to make a rough guess of what the chair transition state should look like, setting the two fragmetns 2.2 Å apart.

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

This guess was then optimised in two ways. The first was optimising it to a transition state by selecting optimization to a TS (Berny) in the calculate menu.This gave bond forming/bond breaking bond lengths 2.02159 Å and 2.02098 Å, and an energy of -231.61932181 Hartree.

<jmolFile text="Chair, optimised to a TS">Chair_b_thu3.mol</jmolFile>

The next method of optimising the chair transition state was to optimise it using the frozen coordinate method. This involves freezing the allyl fragment bonds that will be made to a set length (2.2 Å) then optimising the structure to a minimum. Then unfreezing the bonds and optimising the structure to a transition state. This method gave bond forming/bond breaking bond lengths 2.02071 Å and 2.02074 Å, and an energy of -231.61932233 Hartree.

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

These two method gave very similar results with the frozen coordinate method giving a slight lower energy and short bond lengths.

The QST2 method was used to optimise the boat transition structure. For this two gauche conformers of 1,5-hexadiene were put into GaussView and numbered so they corresponded to the reactant and product of the cope rearrangement. Then the QST2 calculation was run. This gave bond forming/bond breaking bond lengths 2.14181 Å and 2.14046 Å, and energy -231.60280217 Hartree. This is a higher energy and longer bond lengths then the chair transition state, implying that the reaction would prefer to go via the chair transition state. Although, there's not much in it.

<jmolFile text="Optimised boat QST2 method">2nd_QST2_thu.mol</jmolFile>

===The Diels Alder Cycloaddition===

GaussView was used to build cis butadiene and then optimized to the HF/3-21G level. The HOMO and LUMO were plotted and it can be seen that both orbitals are asymmetric with respect to the plane.

[[File:Cisbutadiene.kitts.jpg| thumb |LUMO of cisbutadiene]]

[[File:Cisbutadiene HOMO.jpg| thumb |HOMO of cisbutadiene]]

In order to obtain a transition state geometry of the reaction between ethylene and butadiene, firstly a bicyclo system was built in GaussView and optimised to a minimum. Then the CH2CH2 fragment was deleted and the transition state optimised using the frozen coordinate method, setting the interfragment distance originally as 2.2 Å.
[[File:Guess ts bii.jpg| thumb |Guess of transition state of bicyclo system]]

[[File:TS ii.jpg| thumb |Transition state of ethylene and butadiene]]

[[File:Guess ts ii HOMO.jpg| thumb |HOMO of Diels-Alder Transition State]]

[[File:TS ii LUMO.jpg| thumb |LUMO of Diels-Alder Transition State]]

The HOMO of this transition state can be seen to be symmetrical whilst the LUMO is asymmetrical.

The Diels-Alder reaction between cyclohexa-1,3-diene and maleic anhydride can potentially give either an endo or an exo product. To examine which would be favoured we can examine the exo and endo transition states, to see which is lower in energy. First, cyclohexa-1,3-diene and maleic anhydride are built and optimised to the HF/3-21G level. Then these are used to build a rough estimate of the endo and exo transition states.

[[File:Maleic anhydride Cyclohexa-1,3-diene.jpg| thumb |Maleic anhydride (left) and cyclohexa-1,3-diene (right)]]

User:Ck3112

2015-02-27T10:59:07Z

Ck3112: /* Optimizing the "Chair" and "Boat" Transition Structures */

==='''The Cope Rearrangement Tutorial'''===

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

'''Optimizing the Reactants and Products'''

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformer being slightly lower in energy, this is what is expected simply judging from sterics.

[[File:Part b syn.jpg| thumb |Figure 1:gauche linkage of 1,5-hexadiene]]

In figure 2 a lower energy gauche conformer can be seen, with an energy of -231.69266122 Hartree.

[[File:React c.png| thumb |Figure 2:Gauche 3]]

Then anti2 conformation was built and optimised giving an energy of -231.69253510 Hartree and a point group Ci - seen figure 3. The value given for the energy of this conformer is -231.69254 Hartree, which is the same as the value calculated from Gaussian (to less decimal places).

[[File:Anti2yoyo.jpg| thumb |Figure 3: Anti 2]]

The anti2 conformer was then reoptimised at the B3LYP/6-31G* level giving an energy of -233.33634309 Hartrees.

[[File:Anti2yoyoDTF.png| thumb |Figure 4: Anti 2 reoptimised at B3LYP/6-31G* level]]

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

==='''Optimizing the "Chair" and "Boat" Transition Structures'''===

The boat and chair transition structures of the cope rearrangement are made and optimised so they can be compared. To do this firstly a C3H5 allyl fragment is built and optimised to HF/3-21G level of theory. Then two of these optimised fragments were combined to make a rough guess of what the chair transition state should look like, setting the two fragmetns 2.2 Å apart.

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

This guess was then optimised in two ways. The first was optimising it to a transition state by selecting optimization to a TS (Berny) in the calculate menu.This gave bond forming/bond breaking bond lengths 2.02159 Å and 2.02098 Å, and an energy of -231.61932181 Hartree.

<jmolFile text="Chair, optimised to a TS">Chair_b_thu3.mol</jmolFile>

The next method of optimising the chair transition state was to optimise it using the frozen coordinate method. This involves freezing the allyl fragment bonds that will be made to a set length (2.2 Å) then optimising the structure to a minimum. Then unfreezing the bonds and optimising the structure to a transition state. This method gave bond forming/bond breaking bond lengths 2.02071 Å and 2.02074 Å, and an energy of -231.61932233 Hartree.

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

These two method gave very similar results with the frozen coordinate method giving a slight lower energy and short bond lengths.

The QST2 method was used to optimise the boat transition structure. For this two anti2 conformer 1,5-hexadiene
bond forming/bond breaking bond lengths 2.14181 and 2.14046
energy -231.60280217

<jmolFile text="Optimised boat QST2 method">2nd_QST2_thu.mol</jmolFile>

===The Diels Alder Cycloaddition===

GaussView was used to build cis butadiene and then optimized to the HF/3-21G level. The HOMO and LUMO were plotted and it can be seen that both orbitals are asymmetric with respect to the plane.

[[File:Cisbutadiene.kitts.jpg| thumb |LUMO of cisbutadiene]]

[[File:Cisbutadiene HOMO.jpg| thumb |HOMO of cisbutadiene]]

In order to obtain a transition state geometry of the reaction between ethylene and butadiene, firstly a bicyclo system was built in GaussView and optimised to a minimum. Then the CH2CH2 fragment was deleted and the transition state optimised using the frozen coordinate method, setting the interfragment distance originally as 2.2 Å.
[[File:Guess ts bii.jpg| thumb |Guess of transition state of bicyclo system]]

[[File:TS ii.jpg| thumb |Transition state of ethylene and butadiene]]

[[File:Guess ts ii HOMO.jpg| thumb |HOMO of Diels-Alder Transition State]]

[[File:TS ii LUMO.jpg| thumb |LUMO of Diels-Alder Transition State]]

The HOMO of this transition state can be seen to be symmetrical whilst the LUMO is asymmetrical.

The Diels-Alder reaction between cyclohexa-1,3-diene and maleic anhydride can potentially give either an endo or an exo product. To examine which would be favoured we can examine the exo and endo transition states, to see which is lower in energy. First, cyclohexa-1,3-diene and maleic anhydride are built and optimised to the HF/3-21G level. Then these are used to build a rough estimate of the endo and exo transition states.

[[File:Maleic anhydride Cyclohexa-1,3-diene.jpg| thumb |Maleic anhydride (left) and cyclohexa-1,3-diene (right)]]

User:Ck3112

2015-02-27T10:55:28Z

Ck3112: /* Optimizing the "Chair" and "Boat" Transition Structures */

==='''The Cope Rearrangement Tutorial'''===

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

'''Optimizing the Reactants and Products'''

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformer being slightly lower in energy, this is what is expected simply judging from sterics.

[[File:Part b syn.jpg| thumb |Figure 1:gauche linkage of 1,5-hexadiene]]

In figure 2 a lower energy gauche conformer can be seen, with an energy of -231.69266122 Hartree.

[[File:React c.png| thumb |Figure 2:Gauche 3]]

Then anti2 conformation was built and optimised giving an energy of -231.69253510 Hartree and a point group Ci - seen figure 3. The value given for the energy of this conformer is -231.69254 Hartree, which is the same as the value calculated from Gaussian (to less decimal places).

[[File:Anti2yoyo.jpg| thumb |Figure 3: Anti 2]]

The anti2 conformer was then reoptimised at the B3LYP/6-31G* level giving an energy of -233.33634309 Hartrees.

[[File:Anti2yoyoDTF.png| thumb |Figure 4: Anti 2 reoptimised at B3LYP/6-31G* level]]

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

==='''Optimizing the "Chair" and "Boat" Transition Structures'''===

The boat and chair transition structures of the cope rearrangement are made and optimised so they can be compared. To do this firstly a C3H5 allyl fragment is built and optimised to HF/3-21G level of theory. Then two of these optimised fragments were combined to make a rough guess of what the chair transition state should look like, setting the two fragmetns 2.2 Å apart.

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

This guess was then optimised in two ways. The first was optimising it to a transition state by selecting optimization to a TS (Berny) in the calculate menu.This gave bond forming/bond breaking bond lengths 2.02159 Å and 2.02098 Å, and an energy of -231.61932181 Hartree.

<jmolFile text="Chair, optimised to a TS">Chair_b_thu3.mol</jmolFile>

The next method of optimising the chair transition state was to optimise it using the frozen coordinate method. This involves freezing the allyl fragment bonds that will be made to a set length (2.2 Å) then optimising the structure to a minimum. Then unfreezing the bonds and optimising the structure to a transition state. This method gave bond forming/bond breaking bond lengths 2.02071 Å and 2.02074 Å, and an energy of -231.61932233 Hartree.

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

These two method gave very similar results with the frozen coordinate method giving a slight lower energy and short bond lengths.

e) Optimised Boat.
bond forming/bond breaking bond lengths 2.14181 and 2.14046
energy -231.60280217

<jmolFile text="Optimised boat QST2 method">2nd_QST2_thu.mol</jmolFile>

===The Diels Alder Cycloaddition===

GaussView was used to build cis butadiene and then optimized to the HF/3-21G level. The HOMO and LUMO were plotted and it can be seen that both orbitals are asymmetric with respect to the plane.

[[File:Cisbutadiene.kitts.jpg| thumb |LUMO of cisbutadiene]]

[[File:Cisbutadiene HOMO.jpg| thumb |HOMO of cisbutadiene]]

In order to obtain a transition state geometry of the reaction between ethylene and butadiene, firstly a bicyclo system was built in GaussView and optimised to a minimum. Then the CH2CH2 fragment was deleted and the transition state optimised using the frozen coordinate method, setting the interfragment distance originally as 2.2 Å.
[[File:Guess ts bii.jpg| thumb |Guess of transition state of bicyclo system]]

[[File:TS ii.jpg| thumb |Transition state of ethylene and butadiene]]

[[File:Guess ts ii HOMO.jpg| thumb |HOMO of Diels-Alder Transition State]]

[[File:TS ii LUMO.jpg| thumb |LUMO of Diels-Alder Transition State]]

The HOMO of this transition state can be seen to be symmetrical whilst the LUMO is asymmetrical.

The Diels-Alder reaction between cyclohexa-1,3-diene and maleic anhydride can potentially give either an endo or an exo product. To examine which would be favoured we can examine the exo and endo transition states, to see which is lower in energy. First, cyclohexa-1,3-diene and maleic anhydride are built and optimised to the HF/3-21G level. Then these are used to build a rough estimate of the endo and exo transition states.

[[File:Maleic anhydride Cyclohexa-1,3-diene.jpg| thumb |Maleic anhydride (left) and cyclohexa-1,3-diene (right)]]

User:Ck3112

2015-02-27T10:38:54Z

Ck3112:

User:Ck3112

2015-02-27T10:36:28Z

Ck3112: /* The Cope Rearrangement Tutorial */

User:Ck3112

2015-02-27T10:24:17Z

Ck3112: /* The Diels Alder Cycloaddition */

User:Ck3112

2015-02-27T10:11:39Z

Ck3112:

File:QST2yo.jpg

2015-02-27T10:09:42Z

Ck3112: QST2

QST2

File:Anti2yoyoDTF.png

2015-02-27T10:08:47Z

Ck3112: anti2 DTF

anti2 DTF

File:Anti2yoyo.jpg

2015-02-27T10:08:27Z

Ck3112: anti2

anti2

User:Ck3112

2015-02-27T10:05:10Z

Ck3112:

File:React c.png

2015-02-27T10:04:07Z

Ck3112: Gauche 3

Gauche 3

User:Ck3112

2015-02-27T10:00:14Z

Ck3112: /* The Diels Alder Cycloaddition */

File:Maleic anhydride Cyclohexa-1,3-diene.jpg

2015-02-27T09:59:31Z

Ck3112: Maleic anhydride (left) and cyclohexa-1,3-diene (right)

Maleic anhydride (left) and cyclohexa-1,3-diene (right)

File:TS ii LUMO.jpg

2015-02-27T09:56:52Z

Ck3112: TS LUMO

TS LUMO

File:Guess ts ii HOMO.jpg

2015-02-27T09:56:33Z

Ck3112: TS HOMO

TS HOMO

File:TS ii.jpg

2015-02-27T09:55:06Z

Ck3112: Transition state of ethylene and butadiene

Transition state of ethylene and butadiene

File:Guess ts bii.jpg

2015-02-27T09:52:54Z

Ck3112: Guess of bicyclo system transition state

Guess of bicyclo system transition state

User:Ck3112

2015-02-27T09:50:23Z

Ck3112:

User:Ck3112

2015-02-27T09:48:20Z

Ck3112: /* The Diels Alder Cycloaddition */

File:Cisbutadiene.kitts.jpg

2015-02-27T09:47:51Z

Ck3112: LUMO of cisbutadiene.

LUMO of cisbutadiene.

User:Ck3112

2015-02-27T09:45:42Z

Ck3112:

User:Ck3112

2015-02-27T09:45:23Z

Ck3112: /* The Diels Alder Cycloaddition */

File:Cisbutadiene HOMO.jpg

2015-02-27T09:42:20Z

Ck3112: Ck3112 uploaded a new version of "File:Cisbutadiene HOMO.jpg"

File:Cisbutadiene.jpg

2015-02-27T09:41:53Z

Ck3112: Ck3112 uploaded a new version of "File:Cisbutadiene.jpg"

User:Ck3112

2015-02-27T09:29:36Z

Ck3112:

User:Ck3112

2015-02-27T09:29:13Z

Ck3112:

File:Part b syn.jpg

2015-02-27T09:27:53Z

Ck3112:

User:Ck3112

2015-02-26T18:17:38Z

Ck3112: /* The Diels Alder Cycloaddition */

'''Basic GaussView Tutorial'''

==='''The Cope Rearrangement Tutorial'''===

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

Optimizing the Reactants and Products

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformor being slightly lower in energy, this is what is expected simply judging from sterics.

c)

60o dihedral angle

energy -231.69266122

C1

d)

gauche3

e)

anti2

energy -231.69253510

Ci/C1

f)

E(RB3LYP) -233.33634309

g)

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

==='''Optimizing the "Chair" and "Boat" Transition Structures'''===

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

b)

bond forming/bond breaking bond lengths 2.02159 and 2.02098
energy -231.61932181

<jmolFile text="Chair, optimised to a TS">Chair_b_thu3.mol</jmolFile>

d) Optimised chair from frozen

bond forming/bond breaking bond lengths 2.02071 and 2.02074
energy -231.61932233

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

e) Optimised Boat.
bond forming/bond breaking bond lengths 2.14181 and 2.14046
energy -231.60280217

<jmolFile text="Optimised boat QST2 method">2nd_QST2_thu.mol</jmolFile>

===The Diels Alder Cycloaddition===

GaussView used to build cis butadiene then and optimized to the HF/3-21G level. The HOMO and LUMO were plotted and it can be seen that both orbitals are asymmetric with respect to the plane.

User:Ck3112

2015-02-26T17:49:20Z

Ck3112: /* Optimizing the "Chair" and "Boat" Transition Structures */

User:Ck3112

2015-02-26T17:30:40Z

Ck3112: /* Optimizing the "Chair" and "Boat" Transition Structures */

File:2nd QST2 thu.mol

2015-02-26T17:29:42Z

Ck3112:

User:Ck3112

2015-02-26T16:40:30Z

Ck3112:

User:Ck3112

2015-02-26T15:51:44Z

Ck3112:

'''Basic GaussView Tutorial'''

'''The Cope Rearrangement Tutorial'''

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

Optimizing the Reactants and Products

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformor being slightly lower in energy, this is what is expected simply judging from sterics.

c)

60o dihedral angle

energy -231.69266122

C1

d)

gauche3

e)

anti2

energy -231.69253510

Ci/C1

f)

E(RB3LYP) -233.33634309

g)

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

'''Optimizing the "Chair" and "Boat" Transition Structures'''

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

b)

bond forming/bond breaking bond lengths 2.02159 and 2.02098
energy -231.61932181

<jmolFile text="Chair, optimised to a TS">Chair_b_thu3.mol</jmolFile>

d) Optimised chair from frozen

bond forming/bond breaking bond lengths 2.02071 and 2.02074
energy -231.61932233

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

User:Ck3112

2015-02-26T15:49:30Z

Ck3112:

'''Basic GaussView Tutorial'''

'''The Cope Rearrangement Tutorial'''

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

Optimizing the Reactants and Products

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformor being slightly lower in energy, this is what is expected simply judging from sterics.

c)

60o dihedral angle

energy -231.69266122

C1

d)

gauche3

e)

anti2

energy -231.69253510

Ci/C1

f)

E(RB3LYP) -233.33634309

g)

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

'''Optimizing the "Chair" and "Boat" Transition Structures'''

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

b)

bond forming/bond breaking bond lengths 2.02159 and 2.02098
energy -231.61932181

<jmolFile text="Chair, optimised to a TS">Chair_b_thu3.mol</jmolFile>
Chair_b_thu.gjf ‎
[[File:Chair_b_thu.gjf| thumb | Chair, optimised to a TS]]
d) Optimised chair from frozen

bond forming/bond breaking bond lengths 2.02071 and 2.02074
energy -231.61932233

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

User:Ck3112

2015-02-26T15:47:48Z

Ck3112:

'''Basic GaussView Tutorial'''

'''The Cope Rearrangement Tutorial'''

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

Optimizing the Reactants and Products

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformor being slightly lower in energy, this is what is expected simply judging from sterics.

c)

60o dihedral angle

energy -231.69266122

C1

d)

gauche3

e)

anti2

energy -231.69253510

Ci/C1

f)

E(RB3LYP) -233.33634309

g)

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

'''Optimizing the "Chair" and "Boat" Transition Structures'''

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

b)

bond forming/bond breaking bond lengths 2.02159 and 2.02098
energy -231.61932181

<jmolFile text="Chair, optimised to a TS">Chair_b_thu3.mol</jmolFile>
Chair_b_thu.gjf ‎
<jmolFile text="Chair, optimised to a TS.">Chair_b_thu.gjf</jmolFile>
d) Optimised chair from frozen

bond forming/bond breaking bond lengths 2.02071 and 2.02074
energy -231.61932233

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

File:Chair b thu.gjf

2015-02-26T15:46:45Z

Ck3112:

User:Ck3112

2015-02-26T15:44:33Z

Ck3112:

File:Chair b thu3.mol

2015-02-26T15:43:35Z

Ck3112: Chair, optimised to a TS

Chair, optimised to a TS

User:Ck3112

2015-02-26T15:19:50Z

Ck3112:

'''Basic GaussView Tutorial'''

'''The Cope Rearrangement Tutorial'''

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

Optimizing the Reactants and Products

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformor being slightly lower in energy, this is what is expected simply judging from sterics.

c)

60o dihedral angle

energy -231.69266122

C1

d)

gauche3

e)

anti2

energy -231.69253510

Ci/C1

f)

E(RB3LYP) -233.33634309

g)

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

'''Optimizing the "Chair" and "Boat" Transition Structures'''

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

d) Optimised chair from frozen

bond forming/bond breaking bond lengths 2.02071 and 2.02074
energy -231.61932233

<jmolFile text="Chair, optimised with frozen coordinate method">Chair_opt_d_thu3.mol</jmolFile>

File:Chair opt d thu3.mol

2015-02-26T15:18:47Z

Ck3112: Chair, optimised with frozen coordinate method

Chair, optimised with frozen coordinate method

User:Ck3112

2015-02-26T13:59:00Z

Ck3112:

'''Basic GaussView Tutorial'''

'''The Cope Rearrangement Tutorial'''

The cope rearrangement is a pericyclic reaction, it is a [3,3] sigmatropic rearrangement of 1,5-dienes. In this experiment the cope rearrangement of 1,5-hexadiene is examined.

Optimizing the Reactants and Products

Firstly 1,5-hexadiene was drawn in the antiperiplanar conformation and the structure was optimised; giving an energy of -231.69253528 Hartree and a point group Ci/C1.

Then the gauche linkage of 1,5-hexadiene was drawn and optimised; giving an energy of -231.68302548 Hartree and a point group Cs/C1. Both these energies are very similar with the antiperiplanar conformor being slightly lower in energy, this is what is expected simply judging from sterics.

c)

60o dihedral angle

energy -231.69266122

C1

d)

gauche3

e)

anti2

energy -231.69253510

Ci/C1

f)

E(RB3LYP) -233.33634309

g)

i) Sum of electronic and zero-point Energies= -233.192896
ii)Sum of electronic and thermal Energies= -233.185589
iii) Sum of electronic and thermal Enthalpies= -233.184644
iv) Sum of electronic and thermal Free Energies= -233.224571

<jmolFile text="allyl fragment, energy -115.82304010 Hartree, C2v point group">Allylfragment_thu.mol</jmolFile>

File:Allylfragment thu.mol

2015-02-26T13:56:05Z

Ck3112: allyl fragment, energy -115.82304010 Hartree, C2v point group

allyl fragment, energy -115.82304010 Hartree, C2v point group